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2990 {mso-style-update:auto;
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2991 mso-style-noshow:yes;
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3048 mso-fareast-language:EN-US;}
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3050 {mso-style-noshow:yes;
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3051 mso-style-parent:"";
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3065 {mso-style-parent:"Body Text";
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3066 mso-style-link:"List Char";
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3081 mso-fareast-language:EN-US;}
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3083 {mso-style-parent:List;
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3087 margin-left:18.0pt;
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3099 mso-fareast-language:EN-US;}
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3101 {mso-style-parent:List;
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3119 {mso-style-parent:List;
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3135 p.MsoList3, li.MsoList3, div.MsoList3
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3141 text-align:justify;
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3152 p.MsoList4, li.MsoList4, div.MsoList4
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3168 mso-fareast-language:EN-US;}
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3203 mso-fareast-language:EN-US;}
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3270 mso-fareast-language:EN-US;}
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3288 mso-fareast-language:EN-US;}
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3289 p.MsoListNumber3, li.MsoListNumber3, div.MsoListNumber3
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3290 {mso-style-parent:"List Number";
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3293 margin-bottom:12.0pt;
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3302 mso-fareast-font-family:"Times New Roman";
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3306 mso-fareast-language:EN-US;}
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3311 margin-bottom:12.0pt;
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3325 p.MsoListNumber5, li.MsoListNumber5, div.MsoListNumber5
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3342 mso-fareast-language:EN-US;}
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3382 mso-fareast-language:EN-US;}
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3383 p.MsoBodyTextIndent, li.MsoBodyTextIndent, div.MsoBodyTextIndent
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3399 mso-fareast-language:EN-US;}
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3400 p.MsoListContinue, li.MsoListContinue, div.MsoListContinue
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3401 {mso-style-parent:List;
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3432 p.MsoListContinue3, li.MsoListContinue3, div.MsoListContinue3
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3433 {mso-style-parent:"List Continue";
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3448 p.MsoListContinue4, li.MsoListContinue4, div.MsoListContinue4
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3459 mso-fareast-font-family:"Times New Roman";
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3460 mso-bidi-font-family:"Times New Roman";
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3461 letter-spacing:-.25pt;
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3462 mso-ansi-language:EN-US;
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3463 mso-fareast-language:EN-US;}
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3464 p.MsoListContinue5, li.MsoListContinue5, div.MsoListContinue5
\r
3465 {mso-style-parent:"List Continue";
\r
3468 margin-bottom:8.0pt;
\r
3469 margin-left:108.0pt;
\r
3470 text-align:justify;
\r
3471 mso-pagination:widow-orphan;
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3473 mso-bidi-font-size:10.0pt;
\r
3474 font-family:Garamond;
\r
3475 mso-fareast-font-family:"Times New Roman";
\r
3476 mso-bidi-font-family:"Times New Roman";
\r
3477 letter-spacing:-.25pt;
\r
3478 mso-ansi-language:EN-US;
\r
3479 mso-fareast-language:EN-US;}
\r
3480 p.MsoSubtitle, li.MsoSubtitle, div.MsoSubtitle
\r
3481 {mso-style-parent:Title;
\r
3482 mso-style-next:"Body Text";
\r
3483 margin-top:97.0pt;
\r
3485 margin-bottom:0mm;
\r
3487 margin-bottom:.0001pt;
\r
3488 text-align:center;
\r
3489 line-height:10.0pt;
\r
3490 mso-pagination:widow-orphan;
\r
3491 page-break-after:avoid;
\r
3493 mso-border-bottom-alt:solid gray .75pt;
\r
3495 mso-padding-alt:0mm 0mm 14.0pt 0mm;
\r
3497 mso-bidi-font-size:10.0pt;
\r
3498 font-family:Garamond;
\r
3499 mso-fareast-font-family:"Times New Roman";
\r
3500 mso-bidi-font-family:"Times New Roman";
\r
3502 text-transform:uppercase;
\r
3503 letter-spacing:1.5pt;
\r
3504 mso-font-kerning:14.0pt;
\r
3505 mso-ansi-language:EN-US;
\r
3506 mso-fareast-language:EN-US;
\r
3507 mso-bidi-font-weight:bold;}
\r
3508 p.MsoDate, li.MsoDate, div.MsoDate
\r
3509 {mso-style-parent:"Body Text";
\r
3510 margin-top:24.0pt;
\r
3512 margin-bottom:8.0pt;
\r
3514 text-align:center;
\r
3515 mso-pagination:widow-orphan;
\r
3517 font-family:"Times New Roman";
\r
3518 mso-fareast-font-family:"Times New Roman";
\r
3519 mso-ansi-language:EN-US;
\r
3520 mso-fareast-language:EN-US;
\r
3522 mso-bidi-font-weight:normal;}
\r
3523 a:link, span.MsoHyperlink
\r
3525 text-decoration:underline;
\r
3526 text-underline:single;}
\r
3527 a:visited, span.MsoHyperlinkFollowed
\r
3529 text-decoration:underline;
\r
3530 text-underline:single;}
\r
3532 {mso-style-parent:"";
\r
3533 mso-ansi-font-size:9.0pt;
\r
3534 font-family:"Arial Black";
\r
3535 mso-ascii-font-family:"Arial Black";
\r
3536 mso-hansi-font-family:"Arial Black";
\r
3537 font-style:normal;}
\r
3538 p.MsoPlainText, li.MsoPlainText, div.MsoPlainText
\r
3540 margin-bottom:.0001pt;
\r
3541 mso-pagination:widow-orphan;
\r
3543 font-family:"Courier New";
\r
3544 mso-fareast-font-family:"Times New Roman";
\r
3545 mso-fareast-language:FR;}
\r
3547 {font-family:"Courier New";
\r
3548 mso-ascii-font-family:"Courier New";
\r
3549 mso-fareast-font-family:"MS Mincho";
\r
3550 mso-hansi-font-family:"Courier New";
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3551 mso-bidi-font-family:"Courier New";}
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3553 {mso-style-name:"Heading 1 Char";
\r
3554 mso-style-locked:yes;
\r
3555 mso-style-link:"Heading 1";
\r
3556 mso-ansi-font-size:16.0pt;
\r
3557 font-family:"Arial Black";
\r
3558 mso-ascii-font-family:"Arial Black";
\r
3559 mso-hansi-font-family:"Arial Black";
\r
3561 letter-spacing:-1.25pt;
\r
3562 mso-font-kerning:14.0pt;
\r
3563 mso-ansi-language:EN-US;
\r
3564 mso-fareast-language:EN-US;
\r
3565 mso-bidi-language:AR-SA;}
\r
3566 p.MyNormal, li.MyNormal, div.MyNormal
\r
3567 {mso-style-name:MyNormal;
\r
3568 mso-style-update:auto;
\r
3569 mso-style-link:"MyNormal Char";
\r
3572 margin-bottom:6.0pt;
\r
3573 margin-left:42.55pt;
\r
3574 text-align:justify;
\r
3575 mso-pagination:none;
\r
3576 mso-hyphenate:none;
\r
3577 mso-layout-grid-align:none;
\r
3578 punctuation-wrap:simple;
\r
3579 text-autospace:none;
\r
3581 font-family:"Times New Roman";
\r
3582 mso-fareast-font-family:"Times New Roman";
\r
3583 mso-bidi-font-family:"Courier New";
\r
3584 mso-ansi-language:AF;
\r
3585 mso-fareast-language:EN-US;}
\r
3587 {mso-style-name:"MyNormal Char";
\r
3588 mso-style-locked:yes;
\r
3589 mso-style-parent:"example Char";
\r
3590 mso-style-link:MyNormal;
\r
3591 mso-ansi-font-size:11.0pt;
\r
3592 mso-bidi-font-size:11.0pt;
\r
3593 font-family:"Courier New";
\r
3594 mso-bidi-font-family:"Courier New";
\r
3595 mso-ansi-language:AF;
\r
3596 mso-fareast-language:EN-US;
\r
3597 mso-bidi-language:AR-SA;}
\r
3599 {mso-style-name:"example Char";
\r
3600 mso-style-locked:yes;
\r
3601 mso-style-link:example;
\r
3602 mso-ansi-font-size:8.0pt;
\r
3603 font-family:"Courier New";
\r
3604 mso-ascii-font-family:"Courier New";
\r
3605 mso-hansi-font-family:"Courier New";
\r
3606 mso-bidi-font-family:"Courier New";
\r
3607 mso-ansi-language:EN-US;
\r
3608 mso-fareast-language:EN-US;
\r
3609 mso-bidi-language:AR-SA;}
\r
3610 p.example, li.example, div.example
\r
3611 {mso-style-name:example;
\r
3612 mso-style-update:auto;
\r
3613 mso-style-link:"example Char";
\r
3616 margin-bottom:6.0pt;
\r
3618 text-indent:36.0pt;
\r
3619 mso-pagination:none;
\r
3620 mso-hyphenate:none;
\r
3621 mso-layout-grid-align:none;
\r
3622 punctuation-wrap:simple;
\r
3623 text-autospace:none;
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3625 mso-bidi-font-size:10.0pt;
\r
3626 font-family:"Courier New";
\r
3627 mso-fareast-font-family:"Times New Roman";
\r
3628 mso-ansi-language:EN-US;
\r
3629 mso-fareast-language:EN-US;}
\r
3630 p.FAQ, li.FAQ, div.FAQ
\r
3631 {mso-style-name:FAQ;
\r
3632 mso-style-update:auto;
\r
3633 mso-style-parent:"Heading 3";
\r
3634 margin-top:12.0pt;
\r
3636 margin-bottom:6.0pt;
\r
3637 margin-left:10.0mm;
\r
3638 text-align:justify;
\r
3639 mso-pagination:none;
\r
3640 page-break-after:avoid;
\r
3641 mso-outline-level:3;
\r
3642 mso-hyphenate:none;
\r
3643 mso-layout-grid-align:none;
\r
3644 punctuation-wrap:simple;
\r
3645 text-autospace:none;
\r
3647 font-family:"Comic Sans MS";
\r
3648 mso-fareast-font-family:"Times New Roman";
\r
3649 mso-bidi-font-family:"Times New Roman";
\r
3650 mso-ansi-language:EN-GB;
\r
3651 mso-fareast-language:EN-US;
\r
3653 mso-bidi-font-weight:normal;}
\r
3655 {mso-style-name:"List Char";
\r
3656 mso-style-locked:yes;
\r
3657 mso-style-parent:"Text body Char";
\r
3658 mso-style-link:List;
\r
3659 mso-ansi-font-size:12.0pt;
\r
3660 font-family:Garamond;
\r
3661 mso-ascii-font-family:Garamond;
\r
3662 mso-hansi-font-family:Garamond;
\r
3663 letter-spacing:-.25pt;
\r
3664 mso-ansi-language:EN-US;
\r
3665 mso-fareast-language:EN-US;
\r
3666 mso-bidi-language:AR-SA;}
\r
3668 {mso-style-name:"Text body Char";
\r
3669 mso-style-locked:yes;
\r
3670 mso-style-link:"Text body";
\r
3671 mso-ansi-font-size:12.0pt;
\r
3672 mso-ansi-language:EN-US;
\r
3673 mso-fareast-language:EN-US;
\r
3674 mso-bidi-language:AR-SA;}
\r
3675 p.Textbody, li.Textbody, div.Textbody
\r
3676 {mso-style-name:"Text body";
\r
3677 mso-style-link:"Text body Char";
\r
3679 margin-bottom:.0001pt;
\r
3680 text-align:justify;
\r
3681 mso-pagination:none;
\r
3682 mso-hyphenate:none;
\r
3683 mso-layout-grid-align:none;
\r
3684 punctuation-wrap:simple;
\r
3685 text-autospace:none;
\r
3687 mso-bidi-font-size:10.0pt;
\r
3688 font-family:"Times New Roman";
\r
3689 mso-fareast-font-family:"Times New Roman";
\r
3690 mso-ansi-language:EN-US;
\r
3691 mso-fareast-language:EN-US;}
\r
3692 p.HeadingBase, li.HeadingBase, div.HeadingBase
\r
3693 {mso-style-name:"Heading Base";
\r
3694 mso-style-next:"Body Text";
\r
3695 margin-top:12.0pt;
\r
3697 margin-bottom:6.0pt;
\r
3699 mso-pagination:widow-orphan;
\r
3700 page-break-after:avoid;
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3702 mso-bidi-font-size:10.0pt;
\r
3703 font-family:Arial;
\r
3704 mso-fareast-font-family:"Times New Roman";
\r
3705 mso-bidi-font-family:"Times New Roman";
\r
3706 mso-font-kerning:14.0pt;
\r
3707 mso-ansi-language:EN-US;
\r
3708 mso-fareast-language:EN-US;
\r
3710 mso-bidi-font-weight:normal;}
\r
3711 p.BlockQuotation, li.BlockQuotation, div.BlockQuotation
\r
3712 {mso-style-name:"Block Quotation";
\r
3713 mso-style-next:"Body Text";
\r
3715 margin-right:30.0pt;
\r
3716 margin-bottom:12.0pt;
\r
3717 margin-left:30.0pt;
\r
3718 text-align:justify;
\r
3719 mso-pagination:widow-orphan;
\r
3720 background:#F9F9F9;
\r
3721 mso-shading:windowtext;
\r
3722 mso-pattern:gray-10 gray;
\r
3724 mso-border-alt:solid white .75pt;
\r
3726 mso-padding-alt:12.0pt 12.0pt 12.0pt 12.0pt;
\r
3728 mso-bidi-font-size:10.0pt;
\r
3729 font-family:Garamond;
\r
3730 mso-fareast-font-family:"Times New Roman";
\r
3731 mso-bidi-font-family:"Times New Roman";
\r
3732 letter-spacing:-.25pt;
\r
3733 mso-ansi-language:EN-US;
\r
3734 mso-fareast-language:EN-US;}
\r
3735 p.BlockQuotationFirst, li.BlockQuotationFirst, div.BlockQuotationFirst
\r
3736 {mso-style-name:"Block Quotation First";
\r
3737 mso-style-next:"Block Quotation";
\r
3739 margin-right:24.0pt;
\r
3740 margin-bottom:0mm;
\r
3741 margin-left:24.0pt;
\r
3742 margin-bottom:.0001pt;
\r
3743 text-indent:3.0pt;
\r
3744 mso-pagination:widow-orphan lines-together;
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3745 background:#E5E5E5;
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3746 mso-shading:windowtext;
\r
3747 mso-pattern:gray-10 auto;
\r
3749 mso-border-top-alt:solid white .75pt;
\r
3750 mso-border-left-alt:solid white .75pt;
\r
3751 mso-border-right-alt:solid white .75pt;
\r
3753 mso-padding-alt:6.0pt 6.0pt 0mm 6.0pt;
\r
3755 mso-bidi-font-size:10.0pt;
\r
3756 font-family:"Arial Black";
\r
3757 mso-fareast-font-family:"Times New Roman";
\r
3758 mso-bidi-font-family:"Times New Roman";
\r
3759 letter-spacing:-.5pt;
\r
3760 mso-ansi-language:EN-US;
\r
3761 mso-fareast-language:EN-US;}
\r
3762 p.BlockQuotationLast, li.BlockQuotationLast, div.BlockQuotationLast
\r
3763 {mso-style-name:"Block Quotation Last";
\r
3764 mso-style-parent:"Block Quotation";
\r
3765 mso-style-next:"Body Text";
\r
3767 margin-right:36.0pt;
\r
3768 margin-bottom:12.0pt;
\r
3769 margin-left:36.0pt;
\r
3770 mso-pagination:widow-orphan lines-together;
\r
3772 font-family:"Times New Roman";
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3773 mso-fareast-font-family:"Times New Roman";
\r
3774 mso-ansi-language:EN-US;
\r
3775 mso-fareast-language:EN-US;
\r
3776 font-style:italic;
\r
3777 mso-bidi-font-style:normal;}
\r
3778 p.BodyTextKeep, li.BodyTextKeep, div.BodyTextKeep
\r
3779 {mso-style-name:"Body Text Keep";
\r
3780 mso-style-parent:"Body Text";
\r
3781 mso-style-next:"Body Text";
\r
3784 margin-bottom:12.0pt;
\r
3786 text-align:justify;
\r
3787 mso-pagination:widow-orphan;
\r
3788 page-break-after:avoid;
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3790 mso-bidi-font-size:10.0pt;
\r
3791 font-family:Garamond;
\r
3792 mso-fareast-font-family:"Times New Roman";
\r
3793 mso-bidi-font-family:"Times New Roman";
\r
3794 letter-spacing:-.25pt;
\r
3795 mso-ansi-language:EN-US;
\r
3796 mso-fareast-language:EN-US;}
\r
3797 p.ChapterLabel, li.ChapterLabel, div.ChapterLabel
\r
3798 {mso-style-name:"Chapter Label";
\r
3799 mso-style-next:"Body Text";
\r
3802 margin-bottom:12.0pt;
\r
3804 mso-pagination:widow-orphan;
\r
3805 page-break-after:avoid;
\r
3807 mso-border-bottom-alt:solid windowtext .75pt;
\r
3809 mso-padding-alt:0mm 0mm 3.0pt 0mm;
\r
3811 mso-bidi-font-size:10.0pt;
\r
3812 font-family:"Arial Black";
\r
3813 mso-fareast-font-family:"Times New Roman";
\r
3814 mso-bidi-font-family:"Times New Roman";
\r
3815 text-transform:uppercase;
\r
3816 letter-spacing:3.5pt;
\r
3817 mso-font-kerning:14.0pt;
\r
3818 mso-ansi-language:EN-US;
\r
3819 mso-fareast-language:EN-US;}
\r
3820 p.ChapterSubtitle, li.ChapterSubtitle, div.ChapterSubtitle
\r
3821 {mso-style-name:"Chapter Subtitle";
\r
3822 mso-style-next:"Body Text";
\r
3824 margin-right:90.0pt;
\r
3825 margin-bottom:18.0pt;
\r
3827 mso-line-height-alt:12.0pt;
\r
3828 mso-pagination:widow-orphan lines-together;
\r
3829 page-break-after:avoid;
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3831 mso-bidi-font-size:10.0pt;
\r
3832 font-family:Garamond;
\r
3833 mso-fareast-font-family:"Times New Roman";
\r
3834 mso-bidi-font-family:"Times New Roman";
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3835 letter-spacing:-1.0pt;
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3836 mso-font-kerning:14.0pt;
\r
3837 mso-ansi-language:EN-US;
\r
3838 mso-fareast-language:EN-US;
\r
3839 font-style:italic;
\r
3840 mso-bidi-font-style:normal;}
\r
3841 p.ChapterTitle, li.ChapterTitle, div.ChapterTitle
\r
3842 {mso-style-name:"Chapter Title";
\r
3843 mso-style-update:auto;
\r
3844 mso-style-link:"Chapter Title Char";
\r
3845 mso-style-next:"Chapter Subtitle";
\r
3846 margin-top:30.0pt;
\r
3847 margin-right:4.25pt;
\r
3848 margin-bottom:102.0pt;
\r
3850 text-align:center;
\r
3851 mso-line-height-alt:22.0pt;
\r
3852 page-break-before:always;
\r
3853 mso-pagination:widow-orphan lines-together;
\r
3854 page-break-after:avoid;
\r
3855 background:#CCCCCC;
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3857 mso-border-alt:solid windowtext 3.0pt;
\r
3859 mso-padding-alt:1.0pt 4.0pt 1.0pt 4.0pt;
\r
3861 mso-bidi-font-size:48.0pt;
\r
3862 font-family:"Arial Black";
\r
3863 mso-fareast-font-family:"Times New Roman";
\r
3864 mso-bidi-font-family:"Times New Roman";
\r
3866 letter-spacing:-1.75pt;
\r
3867 mso-font-kerning:14.0pt;
\r
3868 mso-ansi-language:EN-US;
\r
3869 mso-fareast-language:EN-US;}
\r
3870 span.ChapterTitleChar
\r
3871 {mso-style-name:"Chapter Title Char";
\r
3872 mso-style-locked:yes;
\r
3873 mso-style-link:"Chapter Title";
\r
3874 mso-ansi-font-size:36.0pt;
\r
3875 mso-bidi-font-size:48.0pt;
\r
3876 font-family:"Arial Black";
\r
3877 mso-ascii-font-family:"Arial Black";
\r
3878 mso-hansi-font-family:"Arial Black";
\r
3880 letter-spacing:-1.75pt;
\r
3881 mso-font-kerning:14.0pt;
\r
3882 mso-ansi-language:EN-US;
\r
3883 mso-fareast-language:EN-US;
\r
3884 mso-bidi-language:AR-SA;}
\r
3885 p.CompanyName, li.CompanyName, div.CompanyName
\r
3886 {mso-style-name:"Company Name";
\r
3887 mso-style-next:Normal;
\r
3888 margin-top:21.0pt;
\r
3890 margin-bottom:3.0pt;
\r
3892 line-height:16.0pt;
\r
3893 mso-line-height-rule:exactly;
\r
3894 mso-pagination:widow-orphan;
\r
3896 mso-bidi-font-size:10.0pt;
\r
3897 font-family:Garamond;
\r
3898 mso-fareast-font-family:"Times New Roman";
\r
3899 mso-bidi-font-family:"Times New Roman";
\r
3900 text-transform:uppercase;
\r
3901 mso-font-kerning:18.0pt;
\r
3902 mso-ansi-language:EN-US;
\r
3903 mso-fareast-language:EN-US;}
\r
3904 p.DocumentLabel, li.DocumentLabel, div.DocumentLabel
\r
3905 {mso-style-name:"Document Label";
\r
3906 margin-top:12.0pt;
\r
3908 margin-bottom:18.0pt;
\r
3910 mso-pagination:widow-orphan;
\r
3911 page-break-after:avoid;
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3913 mso-bidi-font-size:10.0pt;
\r
3914 font-family:Garamond;
\r
3915 mso-fareast-font-family:"Times New Roman";
\r
3916 mso-bidi-font-family:"Times New Roman";
\r
3917 mso-font-kerning:14.0pt;
\r
3918 mso-ansi-language:EN-US;
\r
3919 mso-fareast-language:EN-US;
\r
3921 mso-bidi-font-weight:normal;}
\r
3922 p.FooterEven, li.FooterEven, div.FooterEven
\r
3923 {mso-style-name:"Footer Even";
\r
3924 mso-style-parent:Footer;
\r
3926 margin-bottom:.0001pt;
\r
3927 text-align:center;
\r
3928 mso-pagination:widow-orphan lines-together;
\r
3929 tab-stops:center 216.0pt right 432.0pt;
\r
3931 mso-border-top-alt:solid windowtext .75pt;
\r
3933 mso-padding-alt:3.0pt 0mm 0mm 0mm;
\r
3935 mso-bidi-font-size:10.0pt;
\r
3936 font-family:"Arial Black";
\r
3937 mso-fareast-font-family:"Times New Roman";
\r
3938 mso-bidi-font-family:"Times New Roman";
\r
3939 mso-ansi-language:EN-US;
\r
3940 mso-fareast-language:EN-US;}
\r
3941 p.FooterFirst, li.FooterFirst, div.FooterFirst
\r
3942 {mso-style-name:"Footer First";
\r
3943 mso-style-parent:Footer;
\r
3945 margin-bottom:.0001pt;
\r
3946 text-align:center;
\r
3947 mso-pagination:widow-orphan lines-together;
\r
3948 tab-stops:center 216.0pt;
\r
3950 mso-bidi-font-size:10.0pt;
\r
3951 font-family:"Arial Black";
\r
3952 mso-fareast-font-family:"Times New Roman";
\r
3953 mso-bidi-font-family:"Times New Roman";
\r
3954 letter-spacing:-.5pt;
\r
3955 mso-ansi-language:EN-US;
\r
3956 mso-fareast-language:EN-US;}
\r
3957 p.FooterOdd, li.FooterOdd, div.FooterOdd
\r
3958 {mso-style-name:"Footer Odd";
\r
3959 mso-style-parent:Footer;
\r
3961 margin-bottom:.0001pt;
\r
3962 text-align:center;
\r
3963 mso-pagination:widow-orphan lines-together;
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3964 tab-stops:right 0mm center 216.0pt right 432.0pt;
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4480 mso-style-parent:WW-Absatz-Standardschriftart1;
\r
4481 mso-ansi-font-size:12.0pt;
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4482 vertical-align:super;}
\r
4483 span.WW-Absatz-Standardschriftart11
\r
4484 {mso-style-name:WW-Absatz-Standardschriftart11;
\r
4485 mso-style-parent:"";
\r
4486 mso-ansi-font-size:12.0pt;}
\r
4487 span.WW-FootnoteSymbol1
\r
4488 {mso-style-name:"WW-Footnote Symbol1";
\r
4489 mso-style-parent:WW-Absatz-Standardschriftart11;
\r
4490 mso-ansi-font-size:12.0pt;
\r
4491 vertical-align:super;}
\r
4492 span.WW-Absatz-Standardschriftart111
\r
4493 {mso-style-name:WW-Absatz-Standardschriftart111;
\r
4494 mso-style-parent:"";
\r
4495 mso-ansi-font-size:12.0pt;}
\r
4496 span.WW-FootnoteSymbol11
\r
4497 {mso-style-name:"WW-Footnote Symbol11";
\r
4498 mso-style-parent:WW-Absatz-Standardschriftart111;
\r
4499 mso-ansi-font-size:12.0pt;
\r
4500 vertical-align:super;}
\r
4501 span.WW-Absatz-Standardschriftart1111
\r
4502 {mso-style-name:WW-Absatz-Standardschriftart1111;
\r
4503 mso-style-parent:"";
\r
4504 mso-ansi-font-size:12.0pt;}
\r
4505 span.WW-FootnoteSymbol111
\r
4506 {mso-style-name:"WW-Footnote Symbol111";
\r
4507 mso-style-parent:WW-Absatz-Standardschriftart1111;
\r
4508 mso-ansi-font-size:12.0pt;
\r
4509 vertical-align:super;}
\r
4510 span.WW-Absatz-Standardschriftart11111
\r
4511 {mso-style-name:WW-Absatz-Standardschriftart11111;
\r
4512 mso-style-parent:"";
\r
4513 mso-ansi-font-size:12.0pt;}
\r
4514 span.WW-FootnoteSymbol1111
\r
4515 {mso-style-name:"WW-Footnote Symbol1111";
\r
4516 mso-style-parent:WW-Absatz-Standardschriftart11111;
\r
4517 mso-ansi-font-size:12.0pt;
\r
4518 vertical-align:super;}
\r
4519 span.WW-Absatz-Standardschriftart111111
\r
4520 {mso-style-name:WW-Absatz-Standardschriftart111111;
\r
4521 mso-style-parent:"";
\r
4522 mso-ansi-font-size:12.0pt;}
\r
4523 span.WW-FootnoteSymbol11111
\r
4524 {mso-style-name:"WW-Footnote Symbol11111";
\r
4525 mso-style-parent:WW-Absatz-Standardschriftart111111;
\r
4526 mso-ansi-font-size:12.0pt;
\r
4527 vertical-align:super;}
\r
4528 span.WW-Absatz-Standardschriftart1111111
\r
4529 {mso-style-name:WW-Absatz-Standardschriftart1111111;
\r
4530 mso-style-parent:"";
\r
4531 mso-ansi-font-size:12.0pt;}
\r
4532 span.WW-FootnoteSymbol111111
\r
4533 {mso-style-name:"WW-Footnote Symbol111111";
\r
4534 mso-style-parent:WW-Absatz-Standardschriftart1111111;
\r
4535 mso-ansi-font-size:12.0pt;
\r
4536 vertical-align:super;}
\r
4537 span.WW-Absatz-Standardschriftart11111111
\r
4538 {mso-style-name:WW-Absatz-Standardschriftart11111111;
\r
4539 mso-style-parent:"";
\r
4540 mso-ansi-font-size:12.0pt;}
\r
4541 span.WW-FootnoteSymbol1111111
\r
4542 {mso-style-name:"WW-Footnote Symbol1111111";
\r
4543 mso-style-parent:WW-Absatz-Standardschriftart11111111;
\r
4544 mso-ansi-font-size:12.0pt;
\r
4545 vertical-align:super;}
\r
4546 span.WW-Absatz-Standardschriftart111111111
\r
4547 {mso-style-name:WW-Absatz-Standardschriftart111111111;
\r
4548 mso-style-parent:"";
\r
4549 mso-ansi-font-size:12.0pt;}
\r
4550 span.WW-FootnoteSymbol11111111
\r
4551 {mso-style-name:"WW-Footnote Symbol11111111";
\r
4552 mso-style-parent:WW-Absatz-Standardschriftart111111111;
\r
4553 mso-ansi-font-size:12.0pt;
\r
4554 vertical-align:super;}
\r
4555 span.EndnoteSymbol
\r
4556 {mso-style-name:"Endnote Symbol";
\r
4557 mso-style-parent:"";
\r
4558 mso-ansi-font-size:12.0pt;}
\r
4559 span.WW-EndnoteSymbol
\r
4560 {mso-style-name:"WW-Endnote Symbol";
\r
4561 mso-style-parent:"";
\r
4562 mso-ansi-font-size:12.0pt;}
\r
4563 span.WW-EndnoteSymbol1
\r
4564 {mso-style-name:"WW-Endnote Symbol1";
\r
4565 mso-style-parent:"";
\r
4566 mso-ansi-font-size:12.0pt;}
\r
4567 span.WW-EndnoteSymbol11
\r
4568 {mso-style-name:"WW-Endnote Symbol11";
\r
4569 mso-style-parent:"";
\r
4570 mso-ansi-font-size:12.0pt;}
\r
4571 span.WW-EndnoteSymbol111
\r
4572 {mso-style-name:"WW-Endnote Symbol111";
\r
4573 mso-style-parent:"";
\r
4574 mso-ansi-font-size:12.0pt;}
\r
4575 span.WW-EndnoteSymbol1111
\r
4576 {mso-style-name:"WW-Endnote Symbol1111";
\r
4577 mso-style-parent:"";
\r
4578 mso-ansi-font-size:12.0pt;}
\r
4579 span.WW-EndnoteSymbol11111
\r
4580 {mso-style-name:"WW-Endnote Symbol11111";
\r
4581 mso-style-parent:"";
\r
4582 mso-ansi-font-size:12.0pt;}
\r
4583 span.WW-EndnoteSymbol111111
\r
4584 {mso-style-name:"WW-Endnote Symbol111111";
\r
4585 mso-style-parent:"";
\r
4586 mso-ansi-font-size:12.0pt;}
\r
4587 span.WW-EndnoteSymbol1111111
\r
4588 {mso-style-name:"WW-Endnote Symbol1111111";
\r
4589 mso-style-parent:"";
\r
4590 mso-ansi-font-size:12.0pt;}
\r
4592 {mso-style-name:"Internet link";
\r
4593 mso-style-parent:"";
\r
4594 mso-ansi-font-size:12.0pt;
\r
4596 text-decoration:underline;
\r
4597 text-underline:single;}
\r
4598 span.WW-Internetlink
\r
4599 {mso-style-name:"WW-Internet link";
\r
4600 mso-style-parent:"";
\r
4601 mso-ansi-font-size:12.0pt;
\r
4603 text-decoration:underline;
\r
4604 text-underline:single;}
\r
4605 span.WW-Internetlink1
\r
4606 {mso-style-name:"WW-Internet link1";
\r
4607 mso-style-parent:"";
\r
4608 mso-ansi-font-size:12.0pt;
\r
4610 text-decoration:underline;
\r
4611 text-underline:single;}
\r
4612 span.WW-Internetlink11
\r
4613 {mso-style-name:"WW-Internet link11";
\r
4614 mso-style-parent:"";
\r
4615 mso-ansi-font-size:12.0pt;
\r
4617 text-decoration:underline;
\r
4618 text-underline:single;}
\r
4619 span.WW-Internetlink111
\r
4620 {mso-style-name:"WW-Internet link111";
\r
4621 mso-style-parent:"";
\r
4622 mso-ansi-font-size:12.0pt;
\r
4624 text-decoration:underline;
\r
4625 text-underline:single;}
\r
4626 span.WW-Internetlink1111
\r
4627 {mso-style-name:"WW-Internet link1111";
\r
4628 mso-style-parent:"";
\r
4629 mso-ansi-font-size:12.0pt;
\r
4631 text-decoration:underline;
\r
4632 text-underline:single;}
\r
4633 span.WW-Internetlink11111
\r
4634 {mso-style-name:"WW-Internet link11111";
\r
4635 mso-style-parent:"";
\r
4636 mso-ansi-font-size:12.0pt;
\r
4638 text-decoration:underline;
\r
4639 text-underline:single;}
\r
4640 span.WW-Internetlink111111
\r
4641 {mso-style-name:"WW-Internet link111111";
\r
4642 mso-style-parent:"";
\r
4643 mso-ansi-font-size:12.0pt;
\r
4645 text-decoration:underline;
\r
4646 text-underline:single;}
\r
4647 span.WW-Internetlink1111111
\r
4648 {mso-style-name:"WW-Internet link1111111";
\r
4649 mso-style-parent:"";
\r
4650 mso-ansi-font-size:12.0pt;
\r
4652 text-decoration:underline;
\r
4653 text-underline:single;}
\r
4654 span.VisitedInternetLink
\r
4655 {mso-style-name:"Visited Internet Link";
\r
4656 mso-style-parent:"";
\r
4657 mso-ansi-font-size:12.0pt;
\r
4659 text-decoration:underline;
\r
4660 text-underline:single;}
\r
4661 span.WW-VisitedInternetLink
\r
4662 {mso-style-name:"WW-Visited Internet Link";
\r
4663 mso-style-parent:"";
\r
4664 mso-ansi-font-size:12.0pt;
\r
4666 text-decoration:underline;
\r
4667 text-underline:single;}
\r
4668 span.WW-VisitedInternetLink1
\r
4669 {mso-style-name:"WW-Visited Internet Link1";
\r
4670 mso-style-parent:"";
\r
4671 mso-ansi-font-size:12.0pt;
\r
4673 text-decoration:underline;
\r
4674 text-underline:single;}
\r
4675 span.WW-VisitedInternetLink11
\r
4676 {mso-style-name:"WW-Visited Internet Link11";
\r
4677 mso-style-parent:"";
\r
4678 mso-ansi-font-size:12.0pt;
\r
4680 text-decoration:underline;
\r
4681 text-underline:single;}
\r
4682 span.WW-VisitedInternetLink111
\r
4683 {mso-style-name:"WW-Visited Internet Link111";
\r
4684 mso-style-parent:"";
\r
4685 mso-ansi-font-size:12.0pt;
\r
4687 text-decoration:underline;
\r
4688 text-underline:single;}
\r
4689 span.WW-VisitedInternetLink1111
\r
4690 {mso-style-name:"WW-Visited Internet Link1111";
\r
4691 mso-style-parent:"";
\r
4692 mso-ansi-font-size:12.0pt;
\r
4694 text-decoration:underline;
\r
4695 text-underline:single;}
\r
4696 span.WW-VisitedInternetLink11111
\r
4697 {mso-style-name:"WW-Visited Internet Link11111";
\r
4698 mso-style-parent:"";
\r
4699 mso-ansi-font-size:12.0pt;
\r
4701 text-decoration:underline;
\r
4702 text-underline:single;}
\r
4703 span.WW-VisitedInternetLink111111
\r
4704 {mso-style-name:"WW-Visited Internet Link111111";
\r
4705 mso-style-parent:"";
\r
4706 mso-ansi-font-size:12.0pt;
\r
4708 text-decoration:underline;
\r
4709 text-underline:single;}
\r
4710 span.WW-VisitedInternetLink1111111
\r
4711 {mso-style-name:"WW-Visited Internet Link1111111";
\r
4712 mso-style-parent:"";
\r
4713 mso-ansi-font-size:12.0pt;
\r
4715 text-decoration:underline;
\r
4716 text-underline:single;}
\r
4717 span.NumberingSymbols
\r
4718 {mso-style-name:"Numbering Symbols";
\r
4719 mso-style-parent:"";
\r
4720 mso-ansi-font-size:12.0pt;}
\r
4721 span.WW-NumberingSymbols
\r
4722 {mso-style-name:"WW-Numbering Symbols";
\r
4723 mso-style-parent:"";
\r
4724 mso-ansi-font-size:12.0pt;}
\r
4725 span.WW-NumberingSymbols1
\r
4726 {mso-style-name:"WW-Numbering Symbols1";
\r
4727 mso-style-parent:"";
\r
4728 mso-ansi-font-size:12.0pt;}
\r
4729 span.WW-NumberingSymbols11
\r
4730 {mso-style-name:"WW-Numbering Symbols11";
\r
4731 mso-style-parent:"";
\r
4732 mso-ansi-font-size:12.0pt;}
\r
4733 span.WW-NumberingSymbols111
\r
4734 {mso-style-name:"WW-Numbering Symbols111";
\r
4735 mso-style-parent:"";
\r
4736 mso-ansi-font-size:12.0pt;}
\r
4737 span.WW-NumberingSymbols1111
\r
4738 {mso-style-name:"WW-Numbering Symbols1111";
\r
4739 mso-style-parent:"";
\r
4740 mso-ansi-font-size:12.0pt;}
\r
4741 span.WW-NumberingSymbols11111
\r
4742 {mso-style-name:"WW-Numbering Symbols11111";
\r
4743 mso-style-parent:"";
\r
4744 mso-ansi-font-size:12.0pt;}
\r
4745 span.BulletSymbols
\r
4746 {mso-style-name:"Bullet Symbols";
\r
4747 mso-style-parent:"";
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4748 mso-ansi-font-size:9.0pt;
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4749 font-family:starbats;
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4750 mso-ascii-font-family:starbats;
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4751 mso-hansi-font-family:starbats;}
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4752 span.WW-BulletSymbols
\r
4753 {mso-style-name:"WW-Bullet Symbols";
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4755 mso-ansi-font-size:9.0pt;
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4756 font-family:starbats;
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4757 mso-ascii-font-family:starbats;
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4758 mso-hansi-font-family:starbats;}
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4759 span.WW-BulletSymbols1
\r
4760 {mso-style-name:"WW-Bullet Symbols1";
\r
4761 mso-style-parent:"";
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4762 mso-ansi-font-size:9.0pt;
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4763 font-family:starbats;
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4764 mso-ascii-font-family:starbats;
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4765 mso-hansi-font-family:starbats;}
\r
4766 span.WW-BulletSymbols11
\r
4767 {mso-style-name:"WW-Bullet Symbols11";
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4768 mso-style-parent:"";
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4769 mso-ansi-font-size:9.0pt;
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4770 font-family:starbats;
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4771 mso-ascii-font-family:starbats;
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4772 mso-hansi-font-family:starbats;}
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4773 p.Index, li.Index, div.Index
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4774 {mso-style-name:Index;
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4776 margin-bottom:.0001pt;
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4777 mso-pagination:none;
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4778 mso-hyphenate:none;
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4779 mso-layout-grid-align:none;
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4780 punctuation-wrap:simple;
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4781 text-autospace:none;
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4783 mso-bidi-font-size:10.0pt;
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4784 font-family:"Times New Roman";
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4785 mso-fareast-font-family:"Times New Roman";
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4786 mso-ansi-language:EN-US;
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4787 mso-fareast-language:EN-US;}
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4788 p.ContentsHeading, li.ContentsHeading, div.ContentsHeading
\r
4789 {mso-style-name:"Contents Heading";
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4790 margin-top:12.0pt;
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4792 margin-bottom:6.0pt;
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4794 mso-pagination:none;
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4795 page-break-after:avoid;
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4796 mso-hyphenate:none;
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4805 mso-ansi-language:EN-US;
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4806 mso-fareast-language:EN-US;
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4808 mso-bidi-font-weight:normal;}
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4809 p.Tableofcontents6, li.Tableofcontents6, div.Tableofcontents6
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4810 {mso-style-name:"Table of contents 6";
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4811 mso-style-parent:Index;
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4814 margin-bottom:0mm;
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4824 mso-bidi-font-size:10.0pt;
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4825 font-family:"Times New Roman";
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4826 mso-fareast-font-family:"Times New Roman";
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4827 mso-ansi-language:EN-US;
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4828 mso-fareast-language:EN-US;}
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4829 p.Tableofcontents7, li.Tableofcontents7, div.Tableofcontents7
\r
4830 {mso-style-name:"Table of contents 7";
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4845 font-family:"Times New Roman";
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4846 mso-fareast-font-family:"Times New Roman";
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4847 mso-ansi-language:EN-US;
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4848 mso-fareast-language:EN-US;}
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4849 p.Tableofcontents8, li.Tableofcontents8, div.Tableofcontents8
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4851 mso-style-parent:Index;
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4865 font-family:"Times New Roman";
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4866 mso-fareast-font-family:"Times New Roman";
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4867 mso-ansi-language:EN-US;
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4868 mso-fareast-language:EN-US;}
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4869 p.Tableofcontents9, li.Tableofcontents9, div.Tableofcontents9
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4870 {mso-style-name:"Table of contents 9";
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4871 mso-style-parent:Index;
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4874 margin-bottom:0mm;
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4875 margin-left:113.2pt;
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4876 margin-bottom:.0001pt;
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4877 mso-pagination:none;
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4878 mso-hyphenate:none;
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4879 tab-stops:right dotted 432.0pt;
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4880 mso-layout-grid-align:none;
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4884 mso-bidi-font-size:10.0pt;
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4885 font-family:"Times New Roman";
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4886 mso-fareast-font-family:"Times New Roman";
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4887 mso-ansi-language:EN-US;
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4888 mso-fareast-language:EN-US;}
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4889 p.Tableofcontents10, li.Tableofcontents10, div.Tableofcontents10
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4890 {mso-style-name:"Table of contents 10";
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4891 mso-style-parent:Index;
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4894 margin-bottom:0mm;
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4895 margin-left:127.35pt;
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4902 text-autospace:none;
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4904 mso-bidi-font-size:10.0pt;
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4906 mso-fareast-font-family:"Times New Roman";
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4907 mso-ansi-language:EN-US;
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4908 mso-fareast-language:EN-US;}
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4909 p.Textbodyindent, li.Textbodyindent, div.Textbodyindent
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4910 {mso-style-name:"Text body indent";
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4911 mso-style-parent:"Text body";
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4914 margin-bottom:0mm;
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4915 margin-left:14.15pt;
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4916 margin-bottom:.0001pt;
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4917 text-align:justify;
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4918 mso-pagination:none;
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4919 mso-hyphenate:none;
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4920 mso-layout-grid-align:none;
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4921 punctuation-wrap:simple;
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4924 mso-bidi-font-size:10.0pt;
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4925 font-family:"Times New Roman";
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4926 mso-fareast-font-family:"Times New Roman";
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4927 mso-ansi-language:EN-US;
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4928 mso-fareast-language:EN-US;}
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4929 p.ListContents, li.ListContents, div.ListContents
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4930 {mso-style-name:"List Contents";
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4933 margin-bottom:0mm;
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4934 margin-left:28.3pt;
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4935 margin-bottom:.0001pt;
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4936 mso-pagination:none;
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4937 mso-hyphenate:none;
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4938 mso-layout-grid-align:none;
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4942 mso-bidi-font-size:10.0pt;
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4943 font-family:"Times New Roman";
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4944 mso-fareast-font-family:"Times New Roman";
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4945 mso-ansi-language:EN-US;
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4946 mso-fareast-language:EN-US;}
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4949 mso-style-parent:example;
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4988 mso-fareast-language:EN-US;
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4990 mso-bidi-font-weight:normal;}
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5011 mso-fareast-language:EN-US;
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5035 mso-bidi-font-weight:normal;}
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5053 mso-fareast-language:EN-US;}
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5054 p.Hangingindent, li.Hangingindent, div.Hangingindent
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5055 {mso-style-name:"Hanging indent";
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5056 mso-style-parent:"Text body";
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5059 margin-bottom:0mm;
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5073 mso-fareast-font-family:"Times New Roman";
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5074 mso-ansi-language:EN-US;
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5075 mso-fareast-language:EN-US;}
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5076 p.Numbering3, li.Numbering3, div.Numbering3
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5077 {mso-style-name:"Numbering 3";
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5078 mso-style-parent:List;
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5081 margin-bottom:6.0pt;
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5082 margin-left:42.45pt;
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5095 mso-fareast-language:EN-US;}
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5097 {mso-style-name:"Table Contents";
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5098 mso-style-parent:"Text body";
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5101 text-align:justify;
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5112 mso-fareast-language:EN-US;}
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5114 {mso-style-name:"Table Heading";
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5115 mso-style-parent:"Table Contents";
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5119 mso-pagination:none;
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5151 mso-bidi-font-weight:normal;}
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5177 font-style:italic;
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5178 mso-bidi-font-style:normal;}
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5180 {mso-style-name:"Notebox\.title";
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5182 margin-bottom:.0001pt;
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5183 text-align:center;
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5184 mso-pagination:none;
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5193 mso-ansi-language:EN-US;
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5194 mso-fareast-language:EN-US;
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5195 font-weight:bold;}
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5197 {mso-style-name:"notebox\.example";
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5210 mso-ansi-language:EN-US;
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5211 mso-fareast-language:EN-US;
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5212 font-weight:bold;}
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5213 p.noteboxbody, li.noteboxbody, div.noteboxbody
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5214 {mso-style-name:"notebox\.body";
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5216 margin-bottom:.0001pt;
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5217 mso-pagination:none;
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5218 mso-hyphenate:none;
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5219 mso-layout-grid-align:none;
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5225 mso-fareast-font-family:"Times New Roman";
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5226 mso-ansi-language:EN-US;
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5227 mso-fareast-language:EN-US;
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5228 font-style:italic;}
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5229 p.Note, li.Note, div.Note
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5230 {mso-style-name:Note;
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5231 mso-style-update:auto;
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5232 mso-style-link:"Note Char";
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5236 margin-left:42.55pt;
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5259 mso-bidi-language:AR-SA;
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5261 mso-bidi-font-weight:normal;}
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5263 {mso-style-name:Table;
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5264 mso-style-parent:Index;
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5266 margin-bottom:.0001pt;
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5277 mso-fareast-language:EN-US;}
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5280 mso-style-parent:"Heading 4";
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5360 mso-ansi-language:EN-US;
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5365 mso-style-link:"flag description";
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5370 {mso-style-name:"flag Note";
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5387 p.flagdescriptionid1, li.flagdescriptionid1, div.flagdescriptionid1
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5399 punctuation-wrap:simple;
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5400 text-autospace:none;
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5425 mso-ansi-language:EN-US;
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5426 mso-fareast-language:EN-US;}
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5427 p.instruction, li.instruction, div.instruction
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5428 {mso-style-name:instruction;
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5429 mso-style-update:auto;
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5430 mso-style-parent:example;
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5433 margin-bottom:0mm;
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5445 mso-ansi-language:EN-US;
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5446 mso-fareast-language:EN-US;
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5448 mso-bidi-font-weight:normal;}
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5449 p.Format, li.Format, div.Format
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5450 {mso-style-name:Format;
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5451 mso-style-parent:example;
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5452 margin-top:12.0pt;
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5462 text-autospace:none;
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5464 font-family:"Courier New";
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5465 mso-fareast-font-family:"Times New Roman";
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5466 mso-ansi-language:EN-GB;
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5467 mso-fareast-language:EN-US;
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5469 mso-bidi-font-weight:normal;}
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5485 text-autospace:none;
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5488 mso-fareast-font-family:"Times New Roman";
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5489 mso-ansi-language:EN-GB;
\r
5490 mso-fareast-language:EN-US;
\r
5492 mso-bidi-font-weight:normal;}
\r
5493 p.FormatCxSpMiddle, li.FormatCxSpMiddle, div.FormatCxSpMiddle
\r
5494 {mso-style-name:FormatCxSpMiddle;
\r
5495 mso-style-parent:example;
\r
5496 mso-style-type:export-only;
\r
5499 margin-bottom:0mm;
\r
5500 margin-left:10.0mm;
\r
5501 margin-bottom:.0001pt;
\r
5502 mso-add-space:auto;
\r
5504 mso-pagination:widow-orphan lines-together;
\r
5505 page-break-after:avoid;
\r
5506 mso-layout-grid-align:none;
\r
5507 punctuation-wrap:simple;
\r
5508 text-autospace:none;
\r
5510 font-family:"Courier New";
\r
5511 mso-fareast-font-family:"Times New Roman";
\r
5512 mso-ansi-language:EN-GB;
\r
5513 mso-fareast-language:EN-US;
\r
5515 mso-bidi-font-weight:normal;}
\r
5516 p.FormatCxSpLast, li.FormatCxSpLast, div.FormatCxSpLast
\r
5517 {mso-style-name:FormatCxSpLast;
\r
5518 mso-style-parent:example;
\r
5519 mso-style-type:export-only;
\r
5522 margin-bottom:12.0pt;
\r
5523 margin-left:10.0mm;
\r
5524 mso-add-space:auto;
\r
5526 mso-pagination:widow-orphan lines-together;
\r
5527 page-break-after:avoid;
\r
5528 mso-layout-grid-align:none;
\r
5529 punctuation-wrap:simple;
\r
5530 text-autospace:none;
\r
5532 font-family:"Courier New";
\r
5533 mso-fareast-font-family:"Times New Roman";
\r
5534 mso-ansi-language:EN-GB;
\r
5535 mso-fareast-language:EN-US;
\r
5537 mso-bidi-font-weight:normal;}
\r
5538 p.ListinFlag, li.ListinFlag, div.ListinFlag
\r
5539 {mso-style-name:"List in Flag";
\r
5540 mso-style-parent:List;
\r
5542 margin-bottom:.0001pt;
\r
5543 text-align:justify;
\r
5544 mso-pagination:none;
\r
5545 mso-hyphenate:none;
\r
5546 mso-layout-grid-align:none;
\r
5547 punctuation-wrap:simple;
\r
5548 text-autospace:none;
\r
5550 mso-bidi-font-size:10.0pt;
\r
5551 font-family:"Times New Roman";
\r
5552 mso-fareast-font-family:"Times New Roman";
\r
5553 mso-ansi-language:EN-US;
\r
5554 mso-fareast-language:EN-US;}
\r
5555 p.example2, li.example2, div.example2
\r
5556 {mso-style-name:example2;
\r
5557 mso-style-parent:example;
\r
5558 margin-top:12.0pt;
\r
5560 margin-bottom:12.0pt;
\r
5561 margin-left:20.0mm;
\r
5562 mso-add-space:auto;
\r
5564 mso-pagination:widow-orphan lines-together;
\r
5565 page-break-after:avoid;
\r
5566 mso-layout-grid-align:none;
\r
5567 punctuation-wrap:simple;
\r
5568 text-autospace:none;
\r
5570 font-family:"Courier New";
\r
5571 mso-fareast-font-family:"Times New Roman";
\r
5572 mso-ansi-language:EN-US;
\r
5573 mso-fareast-language:EN-US;
\r
5575 mso-bidi-font-weight:normal;}
\r
5576 p.example2CxSpFirst, li.example2CxSpFirst, div.example2CxSpFirst
\r
5577 {mso-style-name:example2CxSpFirst;
\r
5578 mso-style-parent:example;
\r
5579 mso-style-type:export-only;
\r
5580 margin-top:12.0pt;
\r
5582 margin-bottom:0mm;
\r
5583 margin-left:20.0mm;
\r
5584 margin-bottom:.0001pt;
\r
5585 mso-add-space:auto;
\r
5587 mso-pagination:widow-orphan lines-together;
\r
5588 page-break-after:avoid;
\r
5589 mso-layout-grid-align:none;
\r
5590 punctuation-wrap:simple;
\r
5591 text-autospace:none;
\r
5593 font-family:"Courier New";
\r
5594 mso-fareast-font-family:"Times New Roman";
\r
5595 mso-ansi-language:EN-US;
\r
5596 mso-fareast-language:EN-US;
\r
5598 mso-bidi-font-weight:normal;}
\r
5599 p.example2CxSpMiddle, li.example2CxSpMiddle, div.example2CxSpMiddle
\r
5600 {mso-style-name:example2CxSpMiddle;
\r
5601 mso-style-parent:example;
\r
5602 mso-style-type:export-only;
\r
5605 margin-bottom:0mm;
\r
5606 margin-left:20.0mm;
\r
5607 margin-bottom:.0001pt;
\r
5608 mso-add-space:auto;
\r
5610 mso-pagination:widow-orphan lines-together;
\r
5611 page-break-after:avoid;
\r
5612 mso-layout-grid-align:none;
\r
5613 punctuation-wrap:simple;
\r
5614 text-autospace:none;
\r
5616 font-family:"Courier New";
\r
5617 mso-fareast-font-family:"Times New Roman";
\r
5618 mso-ansi-language:EN-US;
\r
5619 mso-fareast-language:EN-US;
\r
5621 mso-bidi-font-weight:normal;}
\r
5622 p.example2CxSpLast, li.example2CxSpLast, div.example2CxSpLast
\r
5623 {mso-style-name:example2CxSpLast;
\r
5624 mso-style-parent:example;
\r
5625 mso-style-type:export-only;
\r
5628 margin-bottom:12.0pt;
\r
5629 margin-left:20.0mm;
\r
5630 mso-add-space:auto;
\r
5632 mso-pagination:widow-orphan lines-together;
\r
5633 page-break-after:avoid;
\r
5634 mso-layout-grid-align:none;
\r
5635 punctuation-wrap:simple;
\r
5636 text-autospace:none;
\r
5638 font-family:"Courier New";
\r
5639 mso-fareast-font-family:"Times New Roman";
\r
5640 mso-ansi-language:EN-US;
\r
5641 mso-fareast-language:EN-US;
\r
5643 mso-bidi-font-weight:normal;}
\r
5644 p.StyleNote, li.StyleNote, div.StyleNote
\r
5645 {mso-style-name:"Style Note";
\r
5646 mso-style-parent:Note;
\r
5649 margin-bottom:12.0pt;
\r
5650 margin-left:-35.45pt;
\r
5651 text-align:justify;
\r
5652 mso-pagination:none;
\r
5653 mso-hyphenate:none;
\r
5655 mso-layout-grid-align:none;
\r
5656 punctuation-wrap:simple;
\r
5657 text-autospace:none;
\r
5659 mso-bidi-font-size:8.0pt;
\r
5660 font-family:"Times New Roman";
\r
5661 mso-fareast-font-family:"Times New Roman";
\r
5662 mso-ansi-language:EN-GB;
\r
5663 mso-fareast-language:EN-US;
\r
5664 font-weight:bold;}
\r
5665 p.examplefile, li.examplefile, div.examplefile
\r
5666 {mso-style-name:example_file;
\r
5667 mso-style-update:auto;
\r
5670 margin-bottom:6.0pt;
\r
5672 mso-add-space:auto;
\r
5673 text-align:justify;
\r
5674 mso-pagination:none;
\r
5675 mso-hyphenate:none;
\r
5676 background:#E6E6E6;
\r
5677 mso-layout-grid-align:none;
\r
5678 punctuation-wrap:simple;
\r
5679 text-autospace:none;
\r
5681 mso-border-alt:solid windowtext .5pt;
\r
5683 mso-padding-alt:1.0pt 4.0pt 1.0pt 4.0pt;
\r
5685 font-family:"Courier New";
\r
5686 mso-fareast-font-family:"Times New Roman";
\r
5687 mso-ansi-language:EN-US;
\r
5688 mso-fareast-language:EN-US;}
\r
5689 p.examplefileCxSpFirst, li.examplefileCxSpFirst, div.examplefileCxSpFirst
\r
5690 {mso-style-name:example_fileCxSpFirst;
\r
5691 mso-style-update:auto;
\r
5692 mso-style-type:export-only;
\r
5695 margin-bottom:0mm;
\r
5697 margin-bottom:.0001pt;
\r
5698 mso-add-space:auto;
\r
5699 text-align:justify;
\r
5700 mso-pagination:none;
\r
5701 mso-hyphenate:none;
\r
5702 background:#E6E6E6;
\r
5703 mso-layout-grid-align:none;
\r
5704 punctuation-wrap:simple;
\r
5705 text-autospace:none;
\r
5707 mso-border-alt:solid windowtext .5pt;
\r
5709 mso-padding-alt:1.0pt 4.0pt 1.0pt 4.0pt;
\r
5711 font-family:"Courier New";
\r
5712 mso-fareast-font-family:"Times New Roman";
\r
5713 mso-ansi-language:EN-US;
\r
5714 mso-fareast-language:EN-US;}
\r
5715 p.examplefileCxSpMiddle, li.examplefileCxSpMiddle, div.examplefileCxSpMiddle
\r
5716 {mso-style-name:example_fileCxSpMiddle;
\r
5717 mso-style-update:auto;
\r
5718 mso-style-type:export-only;
\r
5720 margin-bottom:.0001pt;
\r
5721 mso-add-space:auto;
\r
5722 text-align:justify;
\r
5723 mso-pagination:none;
\r
5724 mso-hyphenate:none;
\r
5725 background:#E6E6E6;
\r
5726 mso-layout-grid-align:none;
\r
5727 punctuation-wrap:simple;
\r
5728 text-autospace:none;
\r
5730 mso-border-alt:solid windowtext .5pt;
\r
5732 mso-padding-alt:1.0pt 4.0pt 1.0pt 4.0pt;
\r
5734 font-family:"Courier New";
\r
5735 mso-fareast-font-family:"Times New Roman";
\r
5736 mso-ansi-language:EN-US;
\r
5737 mso-fareast-language:EN-US;}
\r
5738 p.examplefileCxSpLast, li.examplefileCxSpLast, div.examplefileCxSpLast
\r
5739 {mso-style-name:example_fileCxSpLast;
\r
5740 mso-style-update:auto;
\r
5741 mso-style-type:export-only;
\r
5744 margin-bottom:6.0pt;
\r
5746 mso-add-space:auto;
\r
5747 text-align:justify;
\r
5748 mso-pagination:none;
\r
5749 mso-hyphenate:none;
\r
5750 background:#E6E6E6;
\r
5751 mso-layout-grid-align:none;
\r
5752 punctuation-wrap:simple;
\r
5753 text-autospace:none;
\r
5755 mso-border-alt:solid windowtext .5pt;
\r
5757 mso-padding-alt:1.0pt 4.0pt 1.0pt 4.0pt;
\r
5759 font-family:"Courier New";
\r
5760 mso-fareast-font-family:"Times New Roman";
\r
5761 mso-ansi-language:EN-US;
\r
5762 mso-fareast-language:EN-US;}
\r
5763 p.Warning, li.Warning, div.Warning
\r
5764 {mso-style-name:Warning;
\r
5765 mso-style-update:auto;
\r
5766 mso-style-link:"Warning Char";
\r
5767 mso-margin-top-alt:auto;
\r
5769 mso-margin-bottom-alt:auto;
\r
5771 mso-pagination:widow-orphan;
\r
5772 background:#F7CBB7;
\r
5774 mso-border-alt:solid windowtext 1.5pt;
\r
5776 mso-padding-alt:0mm 0mm 0mm 0mm;
\r
5778 font-family:Garamond;
\r
5779 mso-fareast-font-family:"Times New Roman";
\r
5780 mso-bidi-font-family:"Times New Roman";
\r
5781 mso-ansi-language:EN-US;
\r
5782 mso-fareast-language:EN-US;
\r
5784 mso-bidi-font-weight:normal;}
\r
5786 {mso-style-name:"Warning Char";
\r
5787 mso-style-locked:yes;
\r
5788 mso-style-parent:"Note Char";
\r
5789 mso-style-link:Warning;
\r
5790 mso-bidi-font-size:8.0pt;
\r
5791 font-family:Garamond;
\r
5792 mso-ascii-font-family:Garamond;
\r
5793 mso-hansi-font-family:Garamond;
\r
5794 mso-ansi-language:EN-US;
\r
5795 mso-fareast-language:EN-US;
\r
5796 mso-bidi-language:AR-SA;
\r
5798 mso-bidi-font-weight:normal;}
\r
5799 p.Heaing3, li.Heaing3, div.Heaing3
\r
5800 {mso-style-name:"Heaing 3";
\r
5801 mso-style-parent:Note;
\r
5804 margin-bottom:12.0pt;
\r
5805 margin-left:42.55pt;
\r
5806 text-align:justify;
\r
5807 mso-pagination:none;
\r
5808 mso-hyphenate:none;
\r
5810 mso-layout-grid-align:none;
\r
5811 punctuation-wrap:simple;
\r
5812 text-autospace:none;
\r
5814 mso-bidi-font-size:8.0pt;
\r
5815 font-family:"Times New Roman";
\r
5816 mso-fareast-font-family:"Times New Roman";
\r
5817 mso-ansi-language:EN-GB;
\r
5818 mso-fareast-language:EN-US;
\r
5820 mso-bidi-font-weight:normal;}
\r
5821 p.NormalJustified, li.NormalJustified, div.NormalJustified
\r
5822 {mso-style-name:"Normal + Justified";
\r
5823 mso-style-link:"Normal + Justified Char";
\r
5825 margin-bottom:.0001pt;
\r
5826 text-align:justify;
\r
5827 mso-pagination:none;
\r
5828 mso-hyphenate:none;
\r
5829 mso-layout-grid-align:none;
\r
5830 punctuation-wrap:simple;
\r
5831 text-autospace:none;
\r
5833 mso-bidi-font-size:10.0pt;
\r
5834 font-family:"Times New Roman";
\r
5835 mso-fareast-font-family:"Times New Roman";
\r
5836 mso-ansi-language:EN-GB;
\r
5837 mso-fareast-language:EN-US;}
\r
5838 span.NormalJustifiedChar
\r
5839 {mso-style-name:"Normal + Justified Char";
\r
5840 mso-style-locked:yes;
\r
5841 mso-style-link:"Normal + Justified";
\r
5842 mso-ansi-font-size:12.0pt;
\r
5843 mso-ansi-language:EN-GB;
\r
5844 mso-fareast-language:EN-US;
\r
5845 mso-bidi-language:AR-SA;}
\r
5846 p.MyNormalID, li.MyNormalID, div.MyNormalID
\r
5847 {mso-style-name:MyNormalID;
\r
5848 mso-style-update:auto;
\r
5849 mso-style-parent:"List Bullet";
\r
5852 margin-bottom:0mm;
\r
5853 margin-left:31.2pt;
\r
5854 margin-bottom:.0001pt;
\r
5856 mso-pagination:none;
\r
5857 mso-list:l8 level1 lfo7;
\r
5858 mso-hyphenate:none;
\r
5859 tab-stops:list 18.0pt;
\r
5860 mso-layout-grid-align:none;
\r
5861 punctuation-wrap:simple;
\r
5862 text-autospace:none;
\r
5864 mso-bidi-font-size:10.0pt;
\r
5865 font-family:"Times New Roman";
\r
5866 mso-fareast-font-family:"Times New Roman";
\r
5867 mso-ansi-language:EN-US;
\r
5868 mso-fareast-language:EN-US;}
\r
5869 p.MyExample, li.MyExample, div.MyExample
\r
5870 {mso-style-name:MyExample;
\r
5871 mso-style-update:auto;
\r
5872 mso-margin-top-alt:auto;
\r
5874 mso-margin-bottom-alt:auto;
\r
5875 margin-left:20.0mm;
\r
5876 mso-pagination:none;
\r
5877 mso-hyphenate:none;
\r
5878 background:#FFFFCC;
\r
5879 mso-layout-grid-align:none;
\r
5880 punctuation-wrap:simple;
\r
5881 text-autospace:none;
\r
5883 mso-border-top-alt:solid black .25pt;
\r
5884 mso-border-bottom-alt:solid black .25pt;
\r
5886 mso-padding-alt:10.0pt 0mm 10.0pt 0mm;
\r
5888 font-family:"Courier New";
\r
5889 mso-fareast-font-family:"Times New Roman";
\r
5890 mso-bidi-font-family:"Times New Roman";
\r
5891 mso-ansi-language:EN-US;
\r
5892 mso-fareast-language:EN-US;
\r
5894 mso-bidi-font-weight:normal;}
\r
5895 p.Style1, li.Style1, div.Style1
\r
5896 {mso-style-name:Style1;
\r
5897 mso-style-update:auto;
\r
5899 margin-bottom:.0001pt;
\r
5900 mso-pagination:widow-orphan;
\r
5902 mso-bidi-font-size:10.0pt;
\r
5903 font-family:Garamond;
\r
5904 mso-fareast-font-family:"Times New Roman";
\r
5905 mso-bidi-font-family:"Times New Roman";
\r
5906 mso-ansi-language:EN-GB;
\r
5907 mso-fareast-language:EN-US;
\r
5909 mso-bidi-font-weight:normal;}
\r
5910 p.StyleHeading6Bold, li.StyleHeading6Bold, div.StyleHeading6Bold
\r
5911 {mso-style-name:"Style Heading 6 + Bold";
\r
5912 mso-style-update:auto;
\r
5913 mso-style-link:"Style Heading 6 + Bold Char";
\r
5915 margin-bottom:.0001pt;
\r
5916 mso-pagination:widow-orphan;
\r
5918 mso-bidi-font-size:10.0pt;
\r
5919 font-family:Garamond;
\r
5920 mso-fareast-font-family:"Times New Roman";
\r
5921 mso-bidi-font-family:"Times New Roman";
\r
5922 mso-ansi-language:EN-US;
\r
5923 mso-fareast-language:EN-US;
\r
5924 font-weight:bold;}
\r
5925 span.StyleHeading6BoldChar
\r
5926 {mso-style-name:"Style Heading 6 + Bold Char";
\r
5927 mso-style-locked:yes;
\r
5928 mso-style-link:"Style Heading 6 + Bold";
\r
5929 mso-ansi-font-size:8.0pt;
\r
5930 font-family:Garamond;
\r
5931 mso-ascii-font-family:Garamond;
\r
5932 mso-hansi-font-family:Garamond;
\r
5933 mso-ansi-language:EN-US;
\r
5934 mso-fareast-language:EN-US;
\r
5935 mso-bidi-language:AR-SA;
\r
5936 font-weight:bold;}
\r
5937 p.MyNormaBoldl, li.MyNormaBoldl, div.MyNormaBoldl
\r
5938 {mso-style-name:MyNormaBoldl;
\r
5939 mso-style-parent:MyNormal;
\r
5940 mso-style-link:"MyNormaBoldl Char";
\r
5943 margin-bottom:6.0pt;
\r
5944 margin-left:42.55pt;
\r
5945 text-align:justify;
\r
5946 mso-pagination:none;
\r
5947 mso-hyphenate:none;
\r
5948 mso-layout-grid-align:none;
\r
5949 punctuation-wrap:simple;
\r
5950 text-autospace:none;
\r
5952 font-family:"Times New Roman";
\r
5953 mso-fareast-font-family:"Times New Roman";
\r
5954 mso-bidi-font-family:"Courier New";
\r
5955 mso-ansi-language:AF;
\r
5956 mso-fareast-language:EN-US;}
\r
5957 p.Mylist, li.Mylist, div.Mylist
\r
5958 {mso-style-name:Mylist;
\r
5959 mso-style-parent:MyNormal;
\r
5962 margin-bottom:6.0pt;
\r
5963 margin-left:128.7pt;
\r
5964 text-align:justify;
\r
5965 text-indent:-72.0pt;
\r
5966 mso-pagination:none;
\r
5967 mso-hyphenate:none;
\r
5968 mso-layout-grid-align:none;
\r
5969 punctuation-wrap:simple;
\r
5970 text-autospace:none;
\r
5972 font-family:"Times New Roman";
\r
5973 mso-fareast-font-family:"Times New Roman";
\r
5974 mso-bidi-font-family:"Courier New";
\r
5975 mso-ansi-language:AF;
\r
5976 mso-fareast-language:EN-US;
\r
5977 font-style:italic;
\r
5978 mso-bidi-font-style:normal;}
\r
5979 p.MyNormalBold, li.MyNormalBold, div.MyNormalBold
\r
5980 {mso-style-name:MyNormalBold;
\r
5981 mso-style-parent:MyNormalID;
\r
5984 margin-bottom:12.0pt;
\r
5985 margin-left:31.2pt;
\r
5987 mso-pagination:lines-together;
\r
5988 mso-list:l8 level1 lfo7;
\r
5989 tab-stops:list 18.0pt;
\r
5990 mso-layout-grid-align:none;
\r
5991 punctuation-wrap:simple;
\r
5992 text-autospace:none;
\r
5994 mso-bidi-font-size:10.0pt;
\r
5995 font-family:"Times New Roman";
\r
5996 mso-fareast-font-family:"Times New Roman";
\r
5997 mso-ansi-language:EN-US;
\r
5998 mso-fareast-language:EN-US;}
\r
5999 p.StyleflagdescriptionBoldItalic, li.StyleflagdescriptionBoldItalic, div.StyleflagdescriptionBoldItalic
\r
6000 {mso-style-name:"Style flag description + Bold Italic";
\r
6001 mso-style-update:auto;
\r
6002 mso-style-parent:"flag description";
\r
6003 mso-style-link:"Style flag description + Bold Italic Char";
\r
6006 margin-bottom:3.0pt;
\r
6007 margin-left:42.55pt;
\r
6008 text-align:justify;
\r
6009 mso-pagination:none;
\r
6010 mso-hyphenate:none;
\r
6011 mso-layout-grid-align:none;
\r
6012 punctuation-wrap:simple;
\r
6013 text-autospace:none;
\r
6015 font-family:"Times New Roman";
\r
6016 mso-fareast-font-family:"Times New Roman";
\r
6017 mso-ansi-language:EN-US;
\r
6018 mso-fareast-language:EN-US;
\r
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6078 mso-style-type:export-only;
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6080 margin-right:10.0mm;
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6101 mso-fareast-language:EN-US;}
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6103 {mso-style-name:example_file_smallCxSpMiddle;
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6307 mso-fareast-language:EN-US;
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6310 span.MyNormaBoldlChar
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7062 <![if !supportTextWrap]><br clear=ALL>
\r
7065 <p class=CompanyName><span lang=EN-US style='font-size:14.0pt'>Centre National
\r
7066 De LA Recherche scientifique (France)<br>
\r
7067 CeNTRO De REGULACIO GENOMICA (<st1:place w:st="on"><st1:country-region w:st="on">SPAIN</st1:country-region></st1:place>)<o:p></o:p></span></p>
\r
7069 <div style='mso-element:para-border-div;border:none;border-top:solid windowtext 1.0pt;
\r
7070 mso-border-top-alt:solid windowtext .75pt;padding:1.0pt 0mm 0mm 0mm'>
\r
7072 <p class=SubtitleCover><span lang=EN-US>Cédric Notredame<br>
\r
7073 www.tcoffee.org</span></p>
\r
7077 <div style='mso-element:para-border-div;border:solid white 1.0pt;mso-border-alt:
\r
7078 solid white .75pt;padding:31.0pt 31.0pt 31.0pt 31.0pt;background:#E5E5E5;
\r
7079 mso-shading:windowtext;mso-pattern:gray-10 auto'>
\r
7081 <p class=TitleCover style='margin:0mm;margin-bottom:.0001pt;background:#E5E5E5;
\r
7082 mso-shading:windowtext;mso-pattern:gray-10 auto'><span lang=EN-US>T-Coffee:<br>
\r
7083 Technical Documentation</span></p>
\r
7087 <div style='mso-element:para-border-div;border:none;border-top:solid windowtext 1.0pt;
\r
7088 mso-border-top-alt:solid windowtext .75pt;padding:1.0pt 0mm 0mm 0mm'>
\r
7090 <p class=SubtitleCover><span lang=EN-US><o:p> </o:p></span></p>
\r
7096 <span lang=EN-US style='font-size:72.0pt;mso-bidi-font-size:10.0pt;font-family:
\r
7097 Garamond;mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:"Times New Roman";
\r
7098 letter-spacing:-3.5pt;mso-font-kerning:14.0pt;mso-ansi-language:EN-US;
\r
7099 mso-fareast-language:EN-US;mso-bidi-language:AR-SA'><br clear=all
\r
7100 style='page-break-before:always;mso-break-type:section-break'>
\r
7103 <div class=Section2>
\r
7105 <div style='mso-element:para-border-div;border:none;border-bottom:solid gray 1.0pt;
\r
7106 mso-border-bottom-alt:solid gray .75pt;padding:0mm 0mm 14.0pt 0mm'>
\r
7108 <p class=MsoTitle><span lang=EN-US>T-Coffee Technical Documentation<br>
\r
7109 (Version 8.01, July 2009)<br>
\r
7110 www.tcoffee.org<br>
\r
7112 T-Coffee, seq_reformat<br>
\r
7113 <span style='mso-spacerun:yes'> </span>PSI-Coffee, 3D-Coffee, M-Coffee, R-Coffee,
\r
7114 APDB, iRMSD, T-RMSD</span></p>
\r
7118 <p class=ReturnAddress><span lang=EN-US style='font-family:Symbol;mso-ascii-font-family:
\r
7119 Garamond;mso-hansi-font-family:Garamond;mso-char-type:symbol;mso-symbol-font-family:
\r
7120 Symbol'><span style='mso-char-type:symbol;mso-symbol-font-family:Symbol'>ã</span></span><span
\r
7121 lang=EN-US> Cédric Notredame, Centro de Regulacio Genomica, Centre National de
\r
7122 la Recherche <st1:place w:st="on"><st1:City w:st="on">Scientifique</st1:City>, <st1:country-region
\r
7123 w:st="on">France</st1:country-region></st1:place></span><span lang=EN-US
\r
7124 style='letter-spacing:0pt'><o:p></o:p></span></p>
\r
7128 <span lang=EN-US style='font-size:8.0pt;mso-bidi-font-size:10.0pt;font-family:
\r
7129 Garamond;mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:"Times New Roman";
\r
7130 mso-ansi-language:EN-US;mso-fareast-language:EN-US;mso-bidi-language:AR-SA'><br
\r
7131 clear=all style='page-break-before:always;mso-break-type:section-break'>
\r
7134 <div class=Section3>
\r
7136 <p class=MsoToc1 style='tab-stops:right dotted 474.85pt'><!--[if supportFields]><i
\r
7137 style='mso-bidi-font-style:normal'><span lang=EN-US style='font-size:11.0pt;
\r
7138 font-family:"Times New Roman"'><span style='mso-element:field-begin'></span><span
\r
7139 style='mso-spacerun:yes'> </span>TOC \h \z \t "Heading 1;2;Heading
\r
7140 2;3;Heading 3;4;Chapter Title;1;flag;4;FAQ;4" <span style='mso-element:
\r
7141 field-separator'></span></span></i><![endif]--><span class=MsoHyperlink><span
\r
7142 lang=EN-US style='mso-no-proof:yes'><a href="#_Toc235958452">License and Terms
\r
7143 of Use<span style='color:black;display:none;mso-hide:screen;text-decoration:
\r
7144 none;text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
7145 style='color:black;display:none;mso-hide:screen;text-decoration:none;
\r
7146 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
7147 style='color:black;display:none;mso-hide:screen;text-decoration:none;
\r
7148 text-underline:none'> PAGEREF _Toc235958452 \h </span><span style='color:black;
\r
7149 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7150 style='mso-element:field-separator'></span></span><![endif]--><span
\r
7151 style='color:black;display:none;mso-hide:screen;text-decoration:none;
\r
7152 text-underline:none'>6</span><span style='color:black;display:none;mso-hide:
\r
7153 screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
7154 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400350032000000</w:data>
\r
7155 </xml><![endif]--></span><!--[if supportFields]><span style='color:black;
\r
7156 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7157 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
7158 style='font-size:12.0pt;font-family:"Times New Roman";mso-fareast-font-family:
\r
7159 "MS Mincho";color:windowtext;mso-ansi-language:FR;mso-fareast-language:JA;
\r
7160 font-weight:normal;mso-bidi-font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
7162 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
\r
7163 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
7164 href="#_Toc235958453">T-Coffee is distributed under the Gnu Public License<span
\r
7165 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7166 text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
7167 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7168 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
7169 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7170 text-underline:none'> PAGEREF _Toc235958453 \h </span><span style='color:windowtext;
\r
7171 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7172 style='mso-element:field-separator'></span></span><![endif]--><span
\r
7173 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7174 text-underline:none'>6</span><span style='color:windowtext;display:none;
\r
7175 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
7176 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400350033000000</w:data>
\r
7177 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
7178 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7179 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
7180 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
7181 FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
7183 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
\r
7184 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
7185 href="#_Toc235958454">T-Coffee code can be re-used freely<span
\r
7186 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7187 text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
7188 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7189 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
7190 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7191 text-underline:none'> PAGEREF _Toc235958454 \h </span><span style='color:windowtext;
\r
7192 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7193 style='mso-element:field-separator'></span></span><![endif]--><span
\r
7194 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7195 text-underline:none'>6</span><span style='color:windowtext;display:none;
\r
7196 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
7197 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400350034000000</w:data>
\r
7198 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
7199 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7200 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
7201 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
7202 FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
7204 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
\r
7205 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
7206 href="#_Toc235958455">T-Coffee can be incorporated in most pipelines:
\r
7207 Plug-in/Plug-out
\85<span style='color:windowtext;display:none;mso-hide:screen;
\r
7208 text-decoration:none;text-underline:none'><span style='mso-tab-count:1 dotted'>... </span></span><!--[if supportFields]><span
\r
7209 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7210 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
7211 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7212 text-underline:none'> PAGEREF _Toc235958455 \h </span><span style='color:windowtext;
\r
7213 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7214 style='mso-element:field-separator'></span></span><![endif]--><span
\r
7215 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7216 text-underline:none'>6</span><span style='color:windowtext;display:none;
\r
7217 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
7218 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400350035000000</w:data>
\r
7219 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
7220 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7221 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
7222 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
7223 FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
7225 <p class=MsoToc1 style='tab-stops:right dotted 474.85pt'><span
\r
7226 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
7227 href="#_Toc235958456">Addresses and Contacts<span style='color:black;
\r
7228 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7229 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
7230 style='color:black;display:none;mso-hide:screen;text-decoration:none;
\r
7231 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
7232 style='color:black;display:none;mso-hide:screen;text-decoration:none;
\r
7233 text-underline:none'> PAGEREF _Toc235958456 \h </span><span style='color:black;
\r
7234 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7235 style='mso-element:field-separator'></span></span><![endif]--><span
\r
7236 style='color:black;display:none;mso-hide:screen;text-decoration:none;
\r
7237 text-underline:none'>7</span><span style='color:black;display:none;mso-hide:
\r
7238 screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
7239 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400350036000000</w:data>
\r
7240 </xml><![endif]--></span><!--[if supportFields]><span style='color:black;
\r
7241 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7242 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
7243 style='font-size:12.0pt;font-family:"Times New Roman";mso-fareast-font-family:
\r
7244 "MS Mincho";color:windowtext;mso-ansi-language:FR;mso-fareast-language:JA;
\r
7245 font-weight:normal;mso-bidi-font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
7247 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
\r
7248 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
7249 href="#_Toc235958457">Contributors<span style='color:windowtext;display:none;
\r
7250 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7251 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
7252 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7253 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
7254 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7255 text-underline:none'> PAGEREF _Toc235958457 \h </span><span style='color:windowtext;
\r
7256 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7257 style='mso-element:field-separator'></span></span><![endif]--><span
\r
7258 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7259 text-underline:none'>7</span><span style='color:windowtext;display:none;
\r
7260 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
7261 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400350037000000</w:data>
\r
7262 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
7263 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7264 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
7265 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
7266 FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
7268 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
\r
7269 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
7270 href="#_Toc235958458">Addresses<span style='color:windowtext;display:none;
\r
7271 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7272 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
7273 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7274 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
7275 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7276 text-underline:none'> PAGEREF _Toc235958458 \h </span><span style='color:windowtext;
\r
7277 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7278 style='mso-element:field-separator'></span></span><![endif]--><span
\r
7279 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7280 text-underline:none'>7</span><span style='color:windowtext;display:none;
\r
7281 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
7282 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400350038000000</w:data>
\r
7283 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
7284 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7285 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
7286 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
7287 FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
7289 <p class=MsoToc1 style='tab-stops:right dotted 474.85pt'><span
\r
7290 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
7291 href="#_Toc235958459">Citations<span style='color:black;display:none;
\r
7292 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7293 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
7294 style='color:black;display:none;mso-hide:screen;text-decoration:none;
\r
7295 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
7296 style='color:black;display:none;mso-hide:screen;text-decoration:none;
\r
7297 text-underline:none'> PAGEREF _Toc235958459 \h </span><span style='color:black;
\r
7298 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7299 style='mso-element:field-separator'></span></span><![endif]--><span
\r
7300 style='color:black;display:none;mso-hide:screen;text-decoration:none;
\r
7301 text-underline:none'>8</span><span style='color:black;display:none;mso-hide:
\r
7302 screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
7303 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400350039000000</w:data>
\r
7304 </xml><![endif]--></span><!--[if supportFields]><span style='color:black;
\r
7305 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7306 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
7307 style='font-size:12.0pt;font-family:"Times New Roman";mso-fareast-font-family:
\r
7308 "MS Mincho";color:windowtext;mso-ansi-language:FR;mso-fareast-language:JA;
\r
7309 font-weight:normal;mso-bidi-font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
7311 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
\r
7312 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
7313 href="#_Toc235958460">T-Coffee<span style='color:windowtext;display:none;
\r
7314 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7315 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
7316 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7317 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
7318 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7319 text-underline:none'> PAGEREF _Toc235958460 \h </span><span style='color:windowtext;
\r
7320 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7321 style='mso-element:field-separator'></span></span><![endif]--><span
\r
7322 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7323 text-underline:none'>8</span><span style='color:windowtext;display:none;
\r
7324 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
7325 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400360030000000</w:data>
\r
7326 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
7327 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7328 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
7329 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
7330 FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
7332 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
\r
7333 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
7334 href="#_Toc235958461">Mocca<span style='color:windowtext;display:none;
\r
7335 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7336 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
7337 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7338 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
7339 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7340 text-underline:none'> PAGEREF _Toc235958461 \h </span><span style='color:windowtext;
\r
7341 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7342 style='mso-element:field-separator'></span></span><![endif]--><span
\r
7343 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7344 text-underline:none'>9</span><span style='color:windowtext;display:none;
\r
7345 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
7346 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400360031000000</w:data>
\r
7347 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
7348 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7349 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
7350 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
7351 FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
7353 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
\r
7354 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
7355 href="#_Toc235958462">CORE<span style='color:windowtext;display:none;
\r
7356 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7357 style='mso-tab-count:1 dotted'>.. </span></span><!--[if supportFields]><span
\r
7358 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7359 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
7360 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7361 text-underline:none'> PAGEREF _Toc235958462 \h </span><span style='color:windowtext;
\r
7362 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7363 style='mso-element:field-separator'></span></span><![endif]--><span
\r
7364 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7365 text-underline:none'>10</span><span style='color:windowtext;display:none;
\r
7366 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
7367 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400360032000000</w:data>
\r
7368 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
7369 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7370 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
7371 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
7372 FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
7374 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
\r
7375 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
7376 href="#_Toc235958463">Other Contributions<span style='color:windowtext;
\r
7377 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7378 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
7379 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7380 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
7381 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7382 text-underline:none'> PAGEREF _Toc235958463 \h </span><span style='color:windowtext;
\r
7383 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7384 style='mso-element:field-separator'></span></span><![endif]--><span
\r
7385 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7386 text-underline:none'>10</span><span style='color:windowtext;display:none;
\r
7387 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
7388 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400360033000000</w:data>
\r
7389 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
7390 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7391 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
7392 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
7393 FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
7395 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
\r
7396 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
7397 href="#_Toc235958464">Bug Reports and Feedback<span style='color:windowtext;
\r
7398 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7399 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
7400 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7401 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
7402 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7403 text-underline:none'> PAGEREF _Toc235958464 \h </span><span style='color:windowtext;
\r
7404 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7405 style='mso-element:field-separator'></span></span><![endif]--><span
\r
7406 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7407 text-underline:none'>10</span><span style='color:windowtext;display:none;
\r
7408 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
7409 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400360034000000</w:data>
\r
7410 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
7411 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7412 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
7413 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
7414 FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
7416 <p class=MsoToc1 style='tab-stops:right dotted 474.85pt'><span
\r
7417 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
7418 href="#_Toc235958465">Installation of The T-Coffee Packages<span
\r
7419 style='color:black;display:none;mso-hide:screen;text-decoration:none;
\r
7420 text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
7421 style='color:black;display:none;mso-hide:screen;text-decoration:none;
\r
7422 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
7423 style='color:black;display:none;mso-hide:screen;text-decoration:none;
\r
7424 text-underline:none'> PAGEREF _Toc235958465 \h </span><span style='color:black;
\r
7425 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7426 style='mso-element:field-separator'></span></span><![endif]--><span
\r
7427 style='color:black;display:none;mso-hide:screen;text-decoration:none;
\r
7428 text-underline:none'>11</span><span style='color:black;display:none;mso-hide:
\r
7429 screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
7430 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400360035000000</w:data>
\r
7431 </xml><![endif]--></span><!--[if supportFields]><span style='color:black;
\r
7432 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7433 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
7434 style='font-size:12.0pt;font-family:"Times New Roman";mso-fareast-font-family:
\r
7435 "MS Mincho";color:windowtext;mso-ansi-language:FR;mso-fareast-language:JA;
\r
7436 font-weight:normal;mso-bidi-font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
7438 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
\r
7439 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
7440 href="#_Toc235958466">Third Party Packages and On Demand Installations<span
\r
7441 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7442 text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
7443 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7444 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
7445 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7446 text-underline:none'> PAGEREF _Toc235958466 \h </span><span style='color:windowtext;
\r
7447 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7448 style='mso-element:field-separator'></span></span><![endif]--><span
\r
7449 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7450 text-underline:none'>11</span><span style='color:windowtext;display:none;
\r
7451 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
7452 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400360036000000</w:data>
\r
7453 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
7454 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7455 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
7456 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
7457 FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
7459 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
\r
7460 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
7461 href="#_Toc235958467">Standard Installation of T-Coffee<span style='color:windowtext;
\r
7462 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7463 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
7464 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7465 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
7466 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7467 text-underline:none'> PAGEREF _Toc235958467 \h </span><span style='color:windowtext;
\r
7468 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7469 style='mso-element:field-separator'></span></span><![endif]--><span
\r
7470 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7471 text-underline:none'>11</span><span style='color:windowtext;display:none;
\r
7472 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
7473 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400360037000000</w:data>
\r
7474 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
7475 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7476 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
7477 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
7478 FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
7480 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
7481 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
7482 href="#_Toc235958468">Unix<span style='color:windowtext;display:none;
\r
7483 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7484 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
7485 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7486 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
7487 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7488 text-underline:none'> PAGEREF _Toc235958468 \h </span><span style='color:windowtext;
\r
7489 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7490 style='mso-element:field-separator'></span></span><![endif]--><span
\r
7491 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7492 text-underline:none'>11</span><span style='color:windowtext;display:none;
\r
7493 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
7494 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400360038000000</w:data>
\r
7495 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
7496 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7497 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
7498 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
7499 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
7501 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
7502 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
7503 href="#_Toc235958469">Microsoft Windows/Cygwin<span style='color:windowtext;
\r
7504 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7505 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
7506 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7507 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
7508 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7509 text-underline:none'> PAGEREF _Toc235958469 \h </span><span style='color:windowtext;
\r
7510 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7511 style='mso-element:field-separator'></span></span><![endif]--><span
\r
7512 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7513 text-underline:none'>13</span><span style='color:windowtext;display:none;
\r
7514 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
7515 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400360039000000</w:data>
\r
7516 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
7517 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7518 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
7519 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
7520 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
7522 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
7523 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
7524 href="#_Toc235958470">MAC osX, Linux<span style='color:windowtext;display:none;
\r
7525 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7526 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
7527 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7528 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
7529 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7530 text-underline:none'> PAGEREF _Toc235958470 \h </span><span style='color:windowtext;
\r
7531 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7532 style='mso-element:field-separator'></span></span><![endif]--><span
\r
7533 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7534 text-underline:none'>13</span><span style='color:windowtext;display:none;
\r
7535 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
7536 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400370030000000</w:data>
\r
7537 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
7538 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7539 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
7540 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
7541 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
7543 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
7544 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
7545 href="#_Toc235958471">CLUSTER Installation<span style='color:windowtext;
\r
7546 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7547 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
7548 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7549 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
7550 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7551 text-underline:none'> PAGEREF _Toc235958471 \h </span><span style='color:windowtext;
\r
7552 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7553 style='mso-element:field-separator'></span></span><![endif]--><span
\r
7554 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7555 text-underline:none'>13</span><span style='color:windowtext;display:none;
\r
7556 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
7557 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400370031000000</w:data>
\r
7558 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
7559 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7560 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
7561 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
7562 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
7564 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
7565 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
7566 href="#_Toc235958472">If you have PDB installed:<span style='color:windowtext;
\r
7567 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7568 style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span
\r
7569 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7570 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
7571 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7572 text-underline:none'> PAGEREF _Toc235958472 \h </span><span style='color:windowtext;
\r
7573 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7574 style='mso-element:field-separator'></span></span><![endif]--><span
\r
7575 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7576 text-underline:none'>13</span><span style='color:windowtext;display:none;
\r
7577 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
7578 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400370032000000</w:data>
\r
7579 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
7580 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7581 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
7582 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
7583 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
7585 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
\r
7586 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
7587 href="#_Toc235958473">Installing BLAST for T-Coffee<span style='color:windowtext;
\r
7588 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7589 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
7590 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7591 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
7592 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7593 text-underline:none'> PAGEREF _Toc235958473 \h </span><span style='color:windowtext;
\r
7594 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7595 style='mso-element:field-separator'></span></span><![endif]--><span
\r
7596 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7597 text-underline:none'>14</span><span style='color:windowtext;display:none;
\r
7598 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
7599 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400370033000000</w:data>
\r
7600 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
7601 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7602 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
7603 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
7604 FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
7606 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
7607 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
7608 href="#_Toc235958474">Why Do I need BLAST with T-Coffee?<span style='color:
\r
7609 windowtext;display:none;mso-hide:screen;text-decoration:none;text-underline:
\r
7610 none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
7611 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7612 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
7613 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7614 text-underline:none'> PAGEREF _Toc235958474 \h </span><span style='color:windowtext;
\r
7615 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7616 style='mso-element:field-separator'></span></span><![endif]--><span
\r
7617 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7618 text-underline:none'>14</span><span style='color:windowtext;display:none;
\r
7619 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
7620 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400370034000000</w:data>
\r
7621 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
7622 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7623 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
7624 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
7625 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
7627 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
7628 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
7629 href="#_Toc235958475">Using the EBI BLAST Client<span style='color:windowtext;
\r
7630 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7631 style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span
\r
7632 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7633 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
7634 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7635 text-underline:none'> PAGEREF _Toc235958475 \h </span><span style='color:windowtext;
\r
7636 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7637 style='mso-element:field-separator'></span></span><![endif]--><span
\r
7638 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7639 text-underline:none'>14</span><span style='color:windowtext;display:none;
\r
7640 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
7641 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400370035000000</w:data>
\r
7642 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
7643 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7644 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
7645 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
7646 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
7648 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
7649 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
7650 href="#_Toc235958476">Using the NCBI BLAST Client<span style='color:windowtext;
\r
7651 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7652 style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span
\r
7653 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7654 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
7655 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7656 text-underline:none'> PAGEREF _Toc235958476 \h </span><span style='color:windowtext;
\r
7657 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7658 style='mso-element:field-separator'></span></span><![endif]--><span
\r
7659 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7660 text-underline:none'>15</span><span style='color:windowtext;display:none;
\r
7661 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
7662 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400370036000000</w:data>
\r
7663 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
7664 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7665 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
7666 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
7667 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
7669 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
7670 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
7671 href="#_Toc235958477">Using another Client<span style='color:windowtext;
\r
7672 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7673 style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span
\r
7674 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7675 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
7676 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7677 text-underline:none'> PAGEREF _Toc235958477 \h </span><span style='color:windowtext;
\r
7678 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7679 style='mso-element:field-separator'></span></span><![endif]--><span
\r
7680 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7681 text-underline:none'>15</span><span style='color:windowtext;display:none;
\r
7682 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
7683 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400370037000000</w:data>
\r
7684 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
7685 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7686 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
7687 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
7688 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
7690 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
7691 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
7692 href="#_Toc235958478">Using a BLAST local version on UNIX<span
\r
7693 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7694 text-underline:none'><span style='mso-tab-count:1 dotted'>.. </span></span><!--[if supportFields]><span
\r
7695 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7696 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
7697 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7698 text-underline:none'> PAGEREF _Toc235958478 \h </span><span style='color:windowtext;
\r
7699 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7700 style='mso-element:field-separator'></span></span><![endif]--><span
\r
7701 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7702 text-underline:none'>16</span><span style='color:windowtext;display:none;
\r
7703 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
7704 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400370038000000</w:data>
\r
7705 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
7706 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7707 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
7708 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
7709 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
7711 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
7712 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
7713 href="#_Toc235958479">Using a BLAST local version on Windows/cygwin<span
\r
7714 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7715 text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
7716 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7717 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
7718 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7719 text-underline:none'> PAGEREF _Toc235958479 \h </span><span style='color:windowtext;
\r
7720 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7721 style='mso-element:field-separator'></span></span><![endif]--><span
\r
7722 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7723 text-underline:none'>16</span><span style='color:windowtext;display:none;
\r
7724 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
7725 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400370039000000</w:data>
\r
7726 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
7727 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7728 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
7729 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
7730 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
7732 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
\r
7733 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
7734 href="#_Toc235958480">Installing Other Companion Packages<span
\r
7735 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7736 text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
7737 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7738 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
7739 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7740 text-underline:none'> PAGEREF _Toc235958480 \h </span><span style='color:windowtext;
\r
7741 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7742 style='mso-element:field-separator'></span></span><![endif]--><span
\r
7743 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7744 text-underline:none'>17</span><span style='color:windowtext;display:none;
\r
7745 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
7746 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400380030000000</w:data>
\r
7747 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
7748 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7749 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
7750 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
7751 FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
7753 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
\r
7754 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
7755 href="#_Toc235958481">Installation of PSI-Coffee and Expresso<span
\r
7756 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7757 text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
7758 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7759 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
7760 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7761 text-underline:none'> PAGEREF _Toc235958481 \h </span><span style='color:windowtext;
\r
7762 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7763 style='mso-element:field-separator'></span></span><![endif]--><span
\r
7764 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7765 text-underline:none'>18</span><span style='color:windowtext;display:none;
\r
7766 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
7767 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400380031000000</w:data>
\r
7768 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
7769 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7770 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
7771 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
7772 FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
7774 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
\r
7775 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
7776 href="#_Toc235958482">Installation of M-Coffee<span style='color:windowtext;
\r
7777 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7778 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
7779 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7780 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
7781 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7782 text-underline:none'> PAGEREF _Toc235958482 \h </span><span style='color:windowtext;
\r
7783 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7784 style='mso-element:field-separator'></span></span><![endif]--><span
\r
7785 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7786 text-underline:none'>19</span><span style='color:windowtext;display:none;
\r
7787 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
7788 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400380032000000</w:data>
\r
7789 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
7790 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7791 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
7792 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
7793 FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
7795 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
7796 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
7797 href="#_Toc235958483">Automated Installation<span style='color:windowtext;
\r
7798 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7799 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
7800 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7801 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
7802 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7803 text-underline:none'> PAGEREF _Toc235958483 \h </span><span style='color:windowtext;
\r
7804 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7805 style='mso-element:field-separator'></span></span><![endif]--><span
\r
7806 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7807 text-underline:none'>19</span><span style='color:windowtext;display:none;
\r
7808 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
7809 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400380033000000</w:data>
\r
7810 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
7811 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7812 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
7813 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
7814 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
7816 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
7817 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
7818 href="#_Toc235958484">Manual Installation<span style='color:windowtext;
\r
7819 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7820 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
7821 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7822 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
7823 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7824 text-underline:none'> PAGEREF _Toc235958484 \h </span><span style='color:windowtext;
\r
7825 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7826 style='mso-element:field-separator'></span></span><![endif]--><span
\r
7827 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7828 text-underline:none'>20</span><span style='color:windowtext;display:none;
\r
7829 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
7830 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400380034000000</w:data>
\r
7831 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
7832 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7833 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
7834 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
7835 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
7837 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
\r
7838 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
7839 href="#_Toc235958485">Installation of APDB and iRMSD<span style='color:windowtext;
\r
7840 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7841 style='mso-tab-count:1 dotted'>.. </span></span><!--[if supportFields]><span
\r
7842 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7843 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
7844 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7845 text-underline:none'> PAGEREF _Toc235958485 \h </span><span style='color:windowtext;
\r
7846 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7847 style='mso-element:field-separator'></span></span><![endif]--><span
\r
7848 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7849 text-underline:none'>21</span><span style='color:windowtext;display:none;
\r
7850 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
7851 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400380035000000</w:data>
\r
7852 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
7853 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7854 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
7855 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
7856 FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
7858 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
\r
7859 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
7860 href="#_Toc235958486">Installation of tRMSD<span style='color:windowtext;
\r
7861 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7862 style='mso-tab-count:1 dotted'>.. </span></span><!--[if supportFields]><span
\r
7863 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7864 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
7865 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7866 text-underline:none'> PAGEREF _Toc235958486 \h </span><span style='color:windowtext;
\r
7867 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7868 style='mso-element:field-separator'></span></span><![endif]--><span
\r
7869 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7870 text-underline:none'>21</span><span style='color:windowtext;display:none;
\r
7871 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
7872 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400380036000000</w:data>
\r
7873 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
7874 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7875 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
7876 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
7877 FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
7879 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
\r
7880 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
7881 href="#_Toc235958487">Installation of seq_reformat<span style='color:windowtext;
\r
7882 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7883 style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span
\r
7884 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7885 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
7886 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7887 text-underline:none'> PAGEREF _Toc235958487 \h </span><span style='color:windowtext;
\r
7888 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7889 style='mso-element:field-separator'></span></span><![endif]--><span
\r
7890 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7891 text-underline:none'>22</span><span style='color:windowtext;display:none;
\r
7892 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
7893 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400380037000000</w:data>
\r
7894 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
7895 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7896 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
7897 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
7898 FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
7900 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
\r
7901 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
7902 href="#_Toc235958488">Installation of extract_from_pdb<span style='color:windowtext;
\r
7903 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7904 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
7905 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7906 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
7907 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7908 text-underline:none'> PAGEREF _Toc235958488 \h </span><span style='color:windowtext;
\r
7909 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7910 style='mso-element:field-separator'></span></span><![endif]--><span
\r
7911 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7912 text-underline:none'>22</span><span style='color:windowtext;display:none;
\r
7913 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
7914 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400380038000000</w:data>
\r
7915 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
7916 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7917 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
7918 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
7919 FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
7921 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
\r
7922 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
7923 href="#_Toc235958489">Installation of 3D-Coffee/Expresso<span style='color:
\r
7924 windowtext;display:none;mso-hide:screen;text-decoration:none;text-underline:
\r
7925 none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
7926 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7927 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
7928 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7929 text-underline:none'> PAGEREF _Toc235958489 \h </span><span style='color:windowtext;
\r
7930 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7931 style='mso-element:field-separator'></span></span><![endif]--><span
\r
7932 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7933 text-underline:none'>22</span><span style='color:windowtext;display:none;
\r
7934 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
7935 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400380039000000</w:data>
\r
7936 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
7937 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7938 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
7939 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
7940 FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
7942 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
7943 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
7944 href="#_Toc235958490">Automated Installation<span style='color:windowtext;
\r
7945 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7946 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
7947 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7948 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
7949 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7950 text-underline:none'> PAGEREF _Toc235958490 \h </span><span style='color:windowtext;
\r
7951 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7952 style='mso-element:field-separator'></span></span><![endif]--><span
\r
7953 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7954 text-underline:none'>22</span><span style='color:windowtext;display:none;
\r
7955 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
7956 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400390030000000</w:data>
\r
7957 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
7958 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7959 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
7960 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
7961 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
7963 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
7964 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
7965 href="#_Toc235958491">Manual Installation<span style='color:windowtext;
\r
7966 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7967 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
7968 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7969 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
7970 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7971 text-underline:none'> PAGEREF _Toc235958491 \h </span><span style='color:windowtext;
\r
7972 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7973 style='mso-element:field-separator'></span></span><![endif]--><span
\r
7974 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7975 text-underline:none'>23</span><span style='color:windowtext;display:none;
\r
7976 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
7977 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400390031000000</w:data>
\r
7978 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
7979 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7980 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
7981 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
7982 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
7984 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
7985 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
7986 href="#_Toc235958492">Installing Fugue for T-Coffee<span style='color:windowtext;
\r
7987 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7988 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
7989 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7990 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
7991 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7992 text-underline:none'> PAGEREF _Toc235958492 \h </span><span style='color:windowtext;
\r
7993 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
7994 style='mso-element:field-separator'></span></span><![endif]--><span
\r
7995 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
7996 text-underline:none'>23</span><span style='color:windowtext;display:none;
\r
7997 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
7998 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400390032000000</w:data>
\r
7999 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
8000 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8001 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
8002 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
8003 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
8005 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
\r
8006 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
8007 href="#_Toc235958493">Installation of R-Coffee<span style='color:windowtext;
\r
8008 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8009 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
8010 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8011 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
8012 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8013 text-underline:none'> PAGEREF _Toc235958493 \h </span><span style='color:windowtext;
\r
8014 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8015 style='mso-element:field-separator'></span></span><![endif]--><span
\r
8016 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8017 text-underline:none'>23</span><span style='color:windowtext;display:none;
\r
8018 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
8019 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400390033000000</w:data>
\r
8020 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
8021 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8022 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
8023 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
8024 FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
8026 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
8027 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
8028 href="#_Toc235958494">Automated Installation<span style='color:windowtext;
\r
8029 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8030 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
8031 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8032 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
8033 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8034 text-underline:none'> PAGEREF _Toc235958494 \h </span><span style='color:windowtext;
\r
8035 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8036 style='mso-element:field-separator'></span></span><![endif]--><span
\r
8037 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8038 text-underline:none'>24</span><span style='color:windowtext;display:none;
\r
8039 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
8040 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400390034000000</w:data>
\r
8041 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
8042 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8043 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
8044 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
8045 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
8047 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
8048 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
8049 href="#_Toc235958495">Manual Installation<span style='color:windowtext;
\r
8050 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8051 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
8052 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8053 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
8054 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8055 text-underline:none'> PAGEREF _Toc235958495 \h </span><span style='color:windowtext;
\r
8056 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8057 style='mso-element:field-separator'></span></span><![endif]--><span
\r
8058 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8059 text-underline:none'>24</span><span style='color:windowtext;display:none;
\r
8060 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
8061 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400390035000000</w:data>
\r
8062 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
8063 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8064 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
8065 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
8066 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
8068 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
8069 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
8070 href="#_Toc235958496">Installing ProbbonsRNA for R-Coffee<span
\r
8071 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8072 text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
8073 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8074 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
8075 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8076 text-underline:none'> PAGEREF _Toc235958496 \h </span><span style='color:windowtext;
\r
8077 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8078 style='mso-element:field-separator'></span></span><![endif]--><span
\r
8079 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8080 text-underline:none'>24</span><span style='color:windowtext;display:none;
\r
8081 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
8082 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400390036000000</w:data>
\r
8083 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
8084 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8085 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
8086 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
8087 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
8089 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
8090 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
8091 href="#_Toc235958497">Installing Consan for R-Coffee<span style='color:windowtext;
\r
8092 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8093 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
8094 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8095 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
8096 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8097 text-underline:none'> PAGEREF _Toc235958497 \h </span><span style='color:windowtext;
\r
8098 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8099 style='mso-element:field-separator'></span></span><![endif]--><span
\r
8100 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8101 text-underline:none'>24</span><span style='color:windowtext;display:none;
\r
8102 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
8103 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400390037000000</w:data>
\r
8104 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
8105 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8106 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
8107 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
8108 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
8110 <p class=MsoToc1 style='tab-stops:right dotted 474.85pt'><span
\r
8111 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
8112 href="#_Toc235958498">Quick Start<span style='color:black;display:none;
\r
8113 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8114 style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span
\r
8115 style='color:black;display:none;mso-hide:screen;text-decoration:none;
\r
8116 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
8117 style='color:black;display:none;mso-hide:screen;text-decoration:none;
\r
8118 text-underline:none'> PAGEREF _Toc235958498 \h </span><span style='color:black;
\r
8119 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8120 style='mso-element:field-separator'></span></span><![endif]--><span
\r
8121 style='color:black;display:none;mso-hide:screen;text-decoration:none;
\r
8122 text-underline:none'>25</span><span style='color:black;display:none;mso-hide:
\r
8123 screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
8124 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400390038000000</w:data>
\r
8125 </xml><![endif]--></span><!--[if supportFields]><span style='color:black;
\r
8126 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8127 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
8128 style='font-size:12.0pt;font-family:"Times New Roman";mso-fareast-font-family:
\r
8129 "MS Mincho";color:windowtext;mso-ansi-language:FR;mso-fareast-language:JA;
\r
8130 font-weight:normal;mso-bidi-font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
8132 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
\r
8133 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
8134 href="#_Toc235958499">T-COFFEE<span style='color:windowtext;display:none;
\r
8135 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8136 style='mso-tab-count:1 dotted'>.. </span></span><!--[if supportFields]><span
\r
8137 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8138 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
8139 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8140 text-underline:none'> PAGEREF _Toc235958499 \h </span><span style='color:windowtext;
\r
8141 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8142 style='mso-element:field-separator'></span></span><![endif]--><span
\r
8143 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8144 text-underline:none'>25</span><span style='color:windowtext;display:none;
\r
8145 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
8146 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003400390039000000</w:data>
\r
8147 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
8148 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8149 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
8150 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
8151 FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
8153 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
\r
8154 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
8155 href="#_Toc235958500">M-Coffee<span style='color:windowtext;display:none;
\r
8156 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8157 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
8158 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8159 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
8160 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8161 text-underline:none'> PAGEREF _Toc235958500 \h </span><span style='color:windowtext;
\r
8162 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8163 style='mso-element:field-separator'></span></span><![endif]--><span
\r
8164 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8165 text-underline:none'>25</span><span style='color:windowtext;display:none;
\r
8166 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
8167 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500300030000000</w:data>
\r
8168 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
8169 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8170 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
8171 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
8172 FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
8174 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
\r
8175 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
8176 href="#_Toc235958501">Expresso<span style='color:windowtext;display:none;
\r
8177 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8178 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
8179 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8180 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
8181 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8182 text-underline:none'> PAGEREF _Toc235958501 \h </span><span style='color:windowtext;
\r
8183 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8184 style='mso-element:field-separator'></span></span><![endif]--><span
\r
8185 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8186 text-underline:none'>26</span><span style='color:windowtext;display:none;
\r
8187 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
8188 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500300031000000</w:data>
\r
8189 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
8190 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8191 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
8192 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
8193 FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
8195 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
\r
8196 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
8197 href="#_Toc235958502">R-Coffee<span style='color:windowtext;display:none;
\r
8198 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8199 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
8200 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8201 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
8202 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8203 text-underline:none'> PAGEREF _Toc235958502 \h </span><span style='color:windowtext;
\r
8204 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8205 style='mso-element:field-separator'></span></span><![endif]--><span
\r
8206 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8207 text-underline:none'>26</span><span style='color:windowtext;display:none;
\r
8208 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
8209 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500300032000000</w:data>
\r
8210 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
8211 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8212 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
8213 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
8214 FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
8216 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
\r
8217 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
8218 href="#_Toc235958503">iRMSD and APDB<span style='color:windowtext;display:none;
\r
8219 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8220 style='mso-tab-count:1 dotted'>.. </span></span><!--[if supportFields]><span
\r
8221 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8222 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
8223 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8224 text-underline:none'> PAGEREF _Toc235958503 \h </span><span style='color:windowtext;
\r
8225 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8226 style='mso-element:field-separator'></span></span><![endif]--><span
\r
8227 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8228 text-underline:none'>27</span><span style='color:windowtext;display:none;
\r
8229 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
8230 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500300033000000</w:data>
\r
8231 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
8232 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8233 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
8234 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
8235 FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
8237 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
\r
8238 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
8239 href="#_Toc235958504">tRMSD<span style='color:windowtext;display:none;
\r
8240 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8241 style='mso-tab-count:1 dotted'>.. </span></span><!--[if supportFields]><span
\r
8242 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8243 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
8244 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8245 text-underline:none'> PAGEREF _Toc235958504 \h </span><span style='color:windowtext;
\r
8246 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8247 style='mso-element:field-separator'></span></span><![endif]--><span
\r
8248 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8249 text-underline:none'>27</span><span style='color:windowtext;display:none;
\r
8250 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
8251 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500300034000000</w:data>
\r
8252 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
8253 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8254 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
8255 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
8256 FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
8258 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
\r
8259 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
8260 href="#_Toc235958505">MOCCA<span style='color:windowtext;display:none;
\r
8261 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8262 style='mso-tab-count:1 dotted'>.. </span></span><!--[if supportFields]><span
\r
8263 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8264 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
8265 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8266 text-underline:none'> PAGEREF _Toc235958505 \h </span><span style='color:windowtext;
\r
8267 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8268 style='mso-element:field-separator'></span></span><![endif]--><span
\r
8269 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8270 text-underline:none'>28</span><span style='color:windowtext;display:none;
\r
8271 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
8272 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500300035000000</w:data>
\r
8273 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
8274 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8275 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
8276 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
8277 FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
8279 <p class=MsoToc1 style='tab-stops:right dotted 474.85pt'><span
\r
8280 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
8281 href="#_Toc235958506">Recent Modifications<span style='color:black;display:
\r
8282 none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8283 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
8284 style='color:black;display:none;mso-hide:screen;text-decoration:none;
\r
8285 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
8286 style='color:black;display:none;mso-hide:screen;text-decoration:none;
\r
8287 text-underline:none'> PAGEREF _Toc235958506 \h </span><span style='color:black;
\r
8288 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8289 style='mso-element:field-separator'></span></span><![endif]--><span
\r
8290 style='color:black;display:none;mso-hide:screen;text-decoration:none;
\r
8291 text-underline:none'>29</span><span style='color:black;display:none;mso-hide:
\r
8292 screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
8293 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500300036000000</w:data>
\r
8294 </xml><![endif]--></span><!--[if supportFields]><span style='color:black;
\r
8295 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8296 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
8297 style='font-size:12.0pt;font-family:"Times New Roman";mso-fareast-font-family:
\r
8298 "MS Mincho";color:windowtext;mso-ansi-language:FR;mso-fareast-language:JA;
\r
8299 font-weight:normal;mso-bidi-font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
8301 <p class=MsoToc1 style='tab-stops:right dotted 474.85pt'><span
\r
8302 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
8303 href="#_Toc235958507">Reference Manual<span style='color:black;display:none;
\r
8304 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8305 style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span
\r
8306 style='color:black;display:none;mso-hide:screen;text-decoration:none;
\r
8307 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
8308 style='color:black;display:none;mso-hide:screen;text-decoration:none;
\r
8309 text-underline:none'> PAGEREF _Toc235958507 \h </span><span style='color:black;
\r
8310 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8311 style='mso-element:field-separator'></span></span><![endif]--><span
\r
8312 style='color:black;display:none;mso-hide:screen;text-decoration:none;
\r
8313 text-underline:none'>30</span><span style='color:black;display:none;mso-hide:
\r
8314 screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
8315 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500300037000000</w:data>
\r
8316 </xml><![endif]--></span><!--[if supportFields]><span style='color:black;
\r
8317 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8318 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
8319 style='font-size:12.0pt;font-family:"Times New Roman";mso-fareast-font-family:
\r
8320 "MS Mincho";color:windowtext;mso-ansi-language:FR;mso-fareast-language:JA;
\r
8321 font-weight:normal;mso-bidi-font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
8323 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
\r
8324 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
8325 href="#_Toc235958508">Environment Variables<span style='color:windowtext;
\r
8326 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8327 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
8328 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8329 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
8330 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8331 text-underline:none'> PAGEREF _Toc235958508 \h </span><span style='color:windowtext;
\r
8332 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8333 style='mso-element:field-separator'></span></span><![endif]--><span
\r
8334 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8335 text-underline:none'>30</span><span style='color:windowtext;display:none;
\r
8336 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
8337 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500300038000000</w:data>
\r
8338 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
8339 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8340 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
8341 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
8342 FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
8344 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
8345 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
8346 href="#_Toc235958509">http_proxy_4_TCOFFEE<span style='color:windowtext;
\r
8347 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8348 style='mso-tab-count:1 dotted'>.. </span></span><!--[if supportFields]><span
\r
8349 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8350 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
8351 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8352 text-underline:none'> PAGEREF _Toc235958509 \h </span><span style='color:windowtext;
\r
8353 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8354 style='mso-element:field-separator'></span></span><![endif]--><span
\r
8355 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8356 text-underline:none'>30</span><span style='color:windowtext;display:none;
\r
8357 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
8358 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500300039000000</w:data>
\r
8359 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
8360 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8361 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
8362 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
8363 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
8365 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
8366 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
8367 href="#_Toc235958510">email_4_TCOFFEE<span style='color:windowtext;display:
\r
8368 none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8369 style='mso-tab-count:1 dotted'>.. </span></span><!--[if supportFields]><span
\r
8370 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8371 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
8372 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8373 text-underline:none'> PAGEREF _Toc235958510 \h </span><span style='color:windowtext;
\r
8374 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8375 style='mso-element:field-separator'></span></span><![endif]--><span
\r
8376 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8377 text-underline:none'>31</span><span style='color:windowtext;display:none;
\r
8378 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
8379 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500310030000000</w:data>
\r
8380 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
8381 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8382 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
8383 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
8384 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
8386 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
8387 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
8388 href="#_Toc235958511">DIR_4_TCOFFEE<span style='color:windowtext;display:none;
\r
8389 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8390 style='mso-tab-count:1 dotted'>.. </span></span><!--[if supportFields]><span
\r
8391 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8392 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
8393 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8394 text-underline:none'> PAGEREF _Toc235958511 \h </span><span style='color:windowtext;
\r
8395 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8396 style='mso-element:field-separator'></span></span><![endif]--><span
\r
8397 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8398 text-underline:none'>31</span><span style='color:windowtext;display:none;
\r
8399 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
8400 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500310031000000</w:data>
\r
8401 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
8402 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8403 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
8404 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
8405 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
8407 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
8408 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
8409 href="#_Toc235958512">TMP_4_TCOFFEE<span style='color:windowtext;display:none;
\r
8410 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8411 style='mso-tab-count:1 dotted'>.. </span></span><!--[if supportFields]><span
\r
8412 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8413 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
8414 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8415 text-underline:none'> PAGEREF _Toc235958512 \h </span><span style='color:windowtext;
\r
8416 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8417 style='mso-element:field-separator'></span></span><![endif]--><span
\r
8418 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8419 text-underline:none'>31</span><span style='color:windowtext;display:none;
\r
8420 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
8421 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500310032000000</w:data>
\r
8422 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
8423 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8424 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
8425 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
8426 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
8428 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
8429 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
8430 href="#_Toc235958513">CACHE_4_TCOFFEE<span style='color:windowtext;display:
\r
8431 none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8432 style='mso-tab-count:1 dotted'>.. </span></span><!--[if supportFields]><span
\r
8433 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8434 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
8435 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8436 text-underline:none'> PAGEREF _Toc235958513 \h </span><span style='color:windowtext;
\r
8437 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8438 style='mso-element:field-separator'></span></span><![endif]--><span
\r
8439 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8440 text-underline:none'>31</span><span style='color:windowtext;display:none;
\r
8441 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
8442 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500310033000000</w:data>
\r
8443 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
8444 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8445 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
8446 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
8447 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
8449 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
8450 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
8451 href="#_Toc235958514">NO_ERROR_REPORT_4_TCOFFEE<span style='color:windowtext;
\r
8452 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8453 style='mso-tab-count:1 dotted'>.. </span></span><!--[if supportFields]><span
\r
8454 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8455 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
8456 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8457 text-underline:none'> PAGEREF _Toc235958514 \h </span><span style='color:windowtext;
\r
8458 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8459 style='mso-element:field-separator'></span></span><![endif]--><span
\r
8460 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8461 text-underline:none'>31</span><span style='color:windowtext;display:none;
\r
8462 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
8463 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500310034000000</w:data>
\r
8464 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
8465 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8466 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
8467 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
8468 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
8470 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
8471 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
8472 href="#_Toc235958515">PDB_DIR<span style='color:windowtext;display:none;
\r
8473 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8474 style='mso-tab-count:1 dotted'>.. </span></span><!--[if supportFields]><span
\r
8475 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8476 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
8477 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8478 text-underline:none'> PAGEREF _Toc235958515 \h </span><span style='color:windowtext;
\r
8479 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8480 style='mso-element:field-separator'></span></span><![endif]--><span
\r
8481 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8482 text-underline:none'>31</span><span style='color:windowtext;display:none;
\r
8483 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
8484 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500310035000000</w:data>
\r
8485 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
8486 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8487 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
8488 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
8489 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
8491 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
8492 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
8493 href="#_Toc235958516">NO_WARNING_4_TCOFFEE<span style='color:windowtext;
\r
8494 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8495 style='mso-tab-count:1 dotted'>.. </span></span><!--[if supportFields]><span
\r
8496 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8497 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
8498 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8499 text-underline:none'> PAGEREF _Toc235958516 \h </span><span style='color:windowtext;
\r
8500 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8501 style='mso-element:field-separator'></span></span><![endif]--><span
\r
8502 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8503 text-underline:none'>31</span><span style='color:windowtext;display:none;
\r
8504 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
8505 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500310036000000</w:data>
\r
8506 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
8507 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8508 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
8509 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
8510 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
8512 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
\r
8513 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
8514 href="#_Toc235958517">Setting up the T-Coffee environment variables<span
\r
8515 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8516 text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
8517 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8518 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
8519 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8520 text-underline:none'> PAGEREF _Toc235958517 \h </span><span style='color:windowtext;
\r
8521 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8522 style='mso-element:field-separator'></span></span><![endif]--><span
\r
8523 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8524 text-underline:none'>31</span><span style='color:windowtext;display:none;
\r
8525 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
8526 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500310037000000</w:data>
\r
8527 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
8528 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8529 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
8530 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
8531 FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
8533 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
\r
8534 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
8535 href="#_Toc235958518">Well Behaved Parameters<span style='color:windowtext;
\r
8536 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8537 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
8538 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8539 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
8540 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8541 text-underline:none'> PAGEREF _Toc235958518 \h </span><span style='color:windowtext;
\r
8542 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8543 style='mso-element:field-separator'></span></span><![endif]--><span
\r
8544 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8545 text-underline:none'>32</span><span style='color:windowtext;display:none;
\r
8546 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
8547 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500310038000000</w:data>
\r
8548 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
8549 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8550 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
8551 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
8552 FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
8554 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
8555 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
8556 href="#_Toc235958519">Separation<span style='color:windowtext;display:none;
\r
8557 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8558 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
8559 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8560 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
8561 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8562 text-underline:none'> PAGEREF _Toc235958519 \h </span><span style='color:windowtext;
\r
8563 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8564 style='mso-element:field-separator'></span></span><![endif]--><span
\r
8565 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8566 text-underline:none'>32</span><span style='color:windowtext;display:none;
\r
8567 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
8568 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500310039000000</w:data>
\r
8569 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
8570 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8571 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
8572 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
8573 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
8575 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
8576 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
8577 href="#_Toc235958520">Posix<span style='color:windowtext;display:none;
\r
8578 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8579 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
8580 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8581 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
8582 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8583 text-underline:none'> PAGEREF _Toc235958520 \h </span><span style='color:windowtext;
\r
8584 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8585 style='mso-element:field-separator'></span></span><![endif]--><span
\r
8586 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8587 text-underline:none'>32</span><span style='color:windowtext;display:none;
\r
8588 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
8589 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500320030000000</w:data>
\r
8590 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
8591 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8592 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
8593 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
8594 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
8596 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
8597 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
8598 href="#_Toc235958521">Entering the right parameters<span style='color:windowtext;
\r
8599 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8600 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
8601 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8602 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
8603 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8604 text-underline:none'> PAGEREF _Toc235958521 \h </span><span style='color:windowtext;
\r
8605 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8606 style='mso-element:field-separator'></span></span><![endif]--><span
\r
8607 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8608 text-underline:none'>32</span><span style='color:windowtext;display:none;
\r
8609 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
8610 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500320031000000</w:data>
\r
8611 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
8612 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8613 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
8614 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
8615 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
8617 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
\r
8618 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
8619 href="#_Toc235958522">Parameters Syntax<span style='color:windowtext;
\r
8620 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8621 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
8622 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8623 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
8624 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8625 text-underline:none'> PAGEREF _Toc235958522 \h </span><span style='color:windowtext;
\r
8626 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8627 style='mso-element:field-separator'></span></span><![endif]--><span
\r
8628 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8629 text-underline:none'>32</span><span style='color:windowtext;display:none;
\r
8630 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
8631 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500320032000000</w:data>
\r
8632 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
8633 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8634 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
8635 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
8636 FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
8638 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
8639 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
8640 href="#_Toc235958523">No Flag<span style='color:windowtext;display:none;
\r
8641 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8642 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
8643 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8644 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
8645 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8646 text-underline:none'> PAGEREF _Toc235958523 \h </span><span style='color:windowtext;
\r
8647 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8648 style='mso-element:field-separator'></span></span><![endif]--><span
\r
8649 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8650 text-underline:none'>32</span><span style='color:windowtext;display:none;
\r
8651 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
8652 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500320033000000</w:data>
\r
8653 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
8654 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8655 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
8656 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
8657 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
8659 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
8660 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
8661 href="#_Toc235958524">-parameters<span style='color:windowtext;display:none;
\r
8662 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8663 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
8664 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8665 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
8666 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8667 text-underline:none'> PAGEREF _Toc235958524 \h </span><span style='color:windowtext;
\r
8668 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8669 style='mso-element:field-separator'></span></span><![endif]--><span
\r
8670 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8671 text-underline:none'>33</span><span style='color:windowtext;display:none;
\r
8672 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
8673 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500320034000000</w:data>
\r
8674 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
8675 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8676 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
8677 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
8678 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
8680 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
8681 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
8682 href="#_Toc235958525">-t_coffee_defaults<span style='color:windowtext;
\r
8683 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8684 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
8685 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8686 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
8687 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8688 text-underline:none'> PAGEREF _Toc235958525 \h </span><span style='color:windowtext;
\r
8689 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8690 style='mso-element:field-separator'></span></span><![endif]--><span
\r
8691 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8692 text-underline:none'>33</span><span style='color:windowtext;display:none;
\r
8693 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
8694 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500320035000000</w:data>
\r
8695 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
8696 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8697 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
8698 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
8699 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
8701 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
8702 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
8703 href="#_Toc235958526">-mode<span style='color:windowtext;display:none;
\r
8704 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8705 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
8706 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8707 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
8708 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8709 text-underline:none'> PAGEREF _Toc235958526 \h </span><span style='color:windowtext;
\r
8710 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8711 style='mso-element:field-separator'></span></span><![endif]--><span
\r
8712 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8713 text-underline:none'>33</span><span style='color:windowtext;display:none;
\r
8714 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
8715 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500320036000000</w:data>
\r
8716 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
8717 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8718 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
8719 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
8720 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
8722 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
8723 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
8724 href="#_Toc235958527">-score [Deprecated]<span style='color:windowtext;
\r
8725 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8726 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
8727 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8728 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
8729 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8730 text-underline:none'> PAGEREF _Toc235958527 \h </span><span style='color:windowtext;
\r
8731 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8732 style='mso-element:field-separator'></span></span><![endif]--><span
\r
8733 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8734 text-underline:none'>34</span><span style='color:windowtext;display:none;
\r
8735 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
8736 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500320037000000</w:data>
\r
8737 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
8738 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8739 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
8740 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
8741 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
8743 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
8744 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
8745 href="#_Toc235958528">-evaluate<span style='color:windowtext;display:none;
\r
8746 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8747 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
8748 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8749 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
8750 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8751 text-underline:none'> PAGEREF _Toc235958528 \h </span><span style='color:windowtext;
\r
8752 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8753 style='mso-element:field-separator'></span></span><![endif]--><span
\r
8754 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8755 text-underline:none'>34</span><span style='color:windowtext;display:none;
\r
8756 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
8757 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500320038000000</w:data>
\r
8758 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
8759 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8760 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
8761 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
8762 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
8764 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
8765 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
8766 href="#_Toc235958529">-convert [cw]<span style='color:windowtext;display:none;
\r
8767 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8768 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
8769 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8770 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
8771 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8772 text-underline:none'> PAGEREF _Toc235958529 \h </span><span style='color:windowtext;
\r
8773 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8774 style='mso-element:field-separator'></span></span><![endif]--><span
\r
8775 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8776 text-underline:none'>34</span><span style='color:windowtext;display:none;
\r
8777 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
8778 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500320039000000</w:data>
\r
8779 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
8780 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8781 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
8782 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
8783 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
8785 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
8786 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
8787 href="#_Toc235958530">-do_align [cw]<span style='color:windowtext;display:none;
\r
8788 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8789 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
8790 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8791 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
8792 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8793 text-underline:none'> PAGEREF _Toc235958530 \h </span><span style='color:windowtext;
\r
8794 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8795 style='mso-element:field-separator'></span></span><![endif]--><span
\r
8796 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8797 text-underline:none'>34</span><span style='color:windowtext;display:none;
\r
8798 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
8799 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500330030000000</w:data>
\r
8800 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
8801 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8802 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
8803 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
8804 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
8806 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
\r
8807 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
8808 href="#_Toc235958531">Special Parameters<span style='color:windowtext;
\r
8809 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8810 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
8811 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8812 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
8813 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8814 text-underline:none'> PAGEREF _Toc235958531 \h </span><span style='color:windowtext;
\r
8815 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8816 style='mso-element:field-separator'></span></span><![endif]--><span
\r
8817 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8818 text-underline:none'>35</span><span style='color:windowtext;display:none;
\r
8819 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
8820 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500330031000000</w:data>
\r
8821 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
8822 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8823 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
8824 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
8825 FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
8827 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
8828 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
8829 href="#_Toc235958532">-version<span style='color:windowtext;display:none;
\r
8830 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8831 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
8832 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8833 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
8834 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8835 text-underline:none'> PAGEREF _Toc235958532 \h </span><span style='color:windowtext;
\r
8836 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8837 style='mso-element:field-separator'></span></span><![endif]--><span
\r
8838 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8839 text-underline:none'>35</span><span style='color:windowtext;display:none;
\r
8840 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
8841 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500330032000000</w:data>
\r
8842 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
8843 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8844 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
8845 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
8846 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
8848 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
8849 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
8850 href="#_Toc235958533">-proxy<span style='color:windowtext;display:none;
\r
8851 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8852 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
8853 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8854 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
8855 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8856 text-underline:none'> PAGEREF _Toc235958533 \h </span><span style='color:windowtext;
\r
8857 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8858 style='mso-element:field-separator'></span></span><![endif]--><span
\r
8859 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8860 text-underline:none'>35</span><span style='color:windowtext;display:none;
\r
8861 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
8862 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500330033000000</w:data>
\r
8863 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
8864 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8865 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
8866 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
8867 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
8869 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
8870 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
8871 href="#_Toc235958534">-email<span style='color:windowtext;display:none;
\r
8872 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8873 style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span
\r
8874 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8875 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
8876 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8877 text-underline:none'> PAGEREF _Toc235958534 \h </span><span style='color:windowtext;
\r
8878 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8879 style='mso-element:field-separator'></span></span><![endif]--><span
\r
8880 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8881 text-underline:none'>35</span><span style='color:windowtext;display:none;
\r
8882 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
8883 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500330034000000</w:data>
\r
8884 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
8885 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8886 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
8887 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
8888 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
8890 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
8891 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
8892 href="#_Toc235958535">-check_configuration<span style='color:windowtext;
\r
8893 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8894 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
8895 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8896 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
8897 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8898 text-underline:none'> PAGEREF _Toc235958535 \h </span><span style='color:windowtext;
\r
8899 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8900 style='mso-element:field-separator'></span></span><![endif]--><span
\r
8901 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8902 text-underline:none'>35</span><span style='color:windowtext;display:none;
\r
8903 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
8904 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500330035000000</w:data>
\r
8905 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
8906 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8907 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
8908 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
8909 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
8911 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
8912 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
8913 href="#_Toc235958536">-cache<span style='color:windowtext;display:none;
\r
8914 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8915 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
8916 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8917 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
8918 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8919 text-underline:none'> PAGEREF _Toc235958536 \h </span><span style='color:windowtext;
\r
8920 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8921 style='mso-element:field-separator'></span></span><![endif]--><span
\r
8922 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8923 text-underline:none'>35</span><span style='color:windowtext;display:none;
\r
8924 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
8925 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500330036000000</w:data>
\r
8926 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
8927 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8928 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
8929 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
8930 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
8932 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
8933 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
8934 href="#_Toc235958537">-update<span style='color:windowtext;display:none;
\r
8935 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8936 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
8937 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8938 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
8939 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8940 text-underline:none'> PAGEREF _Toc235958537 \h </span><span style='color:windowtext;
\r
8941 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8942 style='mso-element:field-separator'></span></span><![endif]--><span
\r
8943 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8944 text-underline:none'>35</span><span style='color:windowtext;display:none;
\r
8945 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
8946 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500330037000000</w:data>
\r
8947 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
8948 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8949 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
8950 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
8951 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
8953 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
8954 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
8955 href="#_Toc235958538">-full_log<span style='color:windowtext;display:none;
\r
8956 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8957 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
8958 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8959 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
8960 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8961 text-underline:none'> PAGEREF _Toc235958538 \h </span><span style='color:windowtext;
\r
8962 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8963 style='mso-element:field-separator'></span></span><![endif]--><span
\r
8964 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8965 text-underline:none'>35</span><span style='color:windowtext;display:none;
\r
8966 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
8967 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500330038000000</w:data>
\r
8968 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
8969 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8970 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
8971 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
8972 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
8974 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
8975 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
8976 href="#_Toc235958539">-other_pg<span style='color:windowtext;display:none;
\r
8977 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8978 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
8979 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8980 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
8981 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8982 text-underline:none'> PAGEREF _Toc235958539 \h </span><span style='color:windowtext;
\r
8983 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8984 style='mso-element:field-separator'></span></span><![endif]--><span
\r
8985 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
8986 text-underline:none'>36</span><span style='color:windowtext;display:none;
\r
8987 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
8988 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500330039000000</w:data>
\r
8989 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
8990 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8991 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
8992 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
8993 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
8995 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
\r
8996 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
8997 href="#_Toc235958540">Input<span style='color:windowtext;display:none;
\r
8998 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
8999 style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span
\r
9000 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9001 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
9002 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9003 text-underline:none'> PAGEREF _Toc235958540 \h </span><span style='color:windowtext;
\r
9004 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9005 style='mso-element:field-separator'></span></span><![endif]--><span
\r
9006 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9007 text-underline:none'>36</span><span style='color:windowtext;display:none;
\r
9008 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
9009 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500340030000000</w:data>
\r
9010 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
9011 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9012 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
9013 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
9014 FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
9016 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
9017 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
9018 href="#_Toc235958541">Sequence Input<span style='color:windowtext;display:none;
\r
9019 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9020 style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span
\r
9021 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9022 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
9023 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9024 text-underline:none'> PAGEREF _Toc235958541 \h </span><span style='color:windowtext;
\r
9025 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9026 style='mso-element:field-separator'></span></span><![endif]--><span
\r
9027 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9028 text-underline:none'>36</span><span style='color:windowtext;display:none;
\r
9029 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
9030 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500340031000000</w:data>
\r
9031 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
9032 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9033 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
9034 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
9035 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
9037 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
9038 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
9039 href="#_Toc235958542">-infile [cw]<span style='color:windowtext;display:none;
\r
9040 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9041 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
9042 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9043 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
9044 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9045 text-underline:none'> PAGEREF _Toc235958542 \h </span><span style='color:windowtext;
\r
9046 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9047 style='mso-element:field-separator'></span></span><![endif]--><span
\r
9048 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9049 text-underline:none'>36</span><span style='color:windowtext;display:none;
\r
9050 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
9051 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500340032000000</w:data>
\r
9052 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
9053 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9054 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
9055 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
9056 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
9058 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
9059 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
9060 href="#_Toc235958543">-in (Cf
\96in from the Method and Library Input section)<span
\r
9061 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9062 text-underline:none'><span style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span
\r
9063 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9064 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
9065 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9066 text-underline:none'> PAGEREF _Toc235958543 \h </span><span style='color:windowtext;
\r
9067 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9068 style='mso-element:field-separator'></span></span><![endif]--><span
\r
9069 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9070 text-underline:none'>36</span><span style='color:windowtext;display:none;
\r
9071 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
9072 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500340033000000</w:data>
\r
9073 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
9074 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9075 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
9076 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
9077 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
9079 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
9080 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
9081 href="#_Toc235958544">-get_type<span style='color:windowtext;display:none;
\r
9082 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9083 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
9084 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9085 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
9086 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9087 text-underline:none'> PAGEREF _Toc235958544 \h </span><span style='color:windowtext;
\r
9088 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9089 style='mso-element:field-separator'></span></span><![endif]--><span
\r
9090 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9091 text-underline:none'>36</span><span style='color:windowtext;display:none;
\r
9092 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
9093 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500340034000000</w:data>
\r
9094 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
9095 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9096 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
9097 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
9098 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
9100 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
9101 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
9102 href="#_Toc235958545">-type [cw]<span style='color:windowtext;display:none;
\r
9103 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9104 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
9105 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9106 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
9107 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9108 text-underline:none'> PAGEREF _Toc235958545 \h </span><span style='color:windowtext;
\r
9109 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9110 style='mso-element:field-separator'></span></span><![endif]--><span
\r
9111 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9112 text-underline:none'>36</span><span style='color:windowtext;display:none;
\r
9113 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
9114 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500340035000000</w:data>
\r
9115 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
9116 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9117 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
9118 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
9119 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
9121 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
9122 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
9123 href="#_Toc235958546">-seq<span style='color:windowtext;display:none;
\r
9124 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9125 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
9126 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9127 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
9128 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9129 text-underline:none'> PAGEREF _Toc235958546 \h </span><span style='color:windowtext;
\r
9130 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9131 style='mso-element:field-separator'></span></span><![endif]--><span
\r
9132 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9133 text-underline:none'>37</span><span style='color:windowtext;display:none;
\r
9134 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
9135 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500340036000000</w:data>
\r
9136 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
9137 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9138 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
9139 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
9140 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
9142 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
9143 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
9144 href="#_Toc235958547">-seq_source<span style='color:windowtext;display:none;
\r
9145 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9146 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
9147 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9148 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
9149 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9150 text-underline:none'> PAGEREF _Toc235958547 \h </span><span style='color:windowtext;
\r
9151 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9152 style='mso-element:field-separator'></span></span><![endif]--><span
\r
9153 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9154 text-underline:none'>37</span><span style='color:windowtext;display:none;
\r
9155 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
9156 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500340037000000</w:data>
\r
9157 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
9158 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9159 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
9160 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
9161 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
9163 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
9164 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
9165 href="#_Toc235958548">Structure Input<span style='color:windowtext;display:
\r
9166 none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9167 style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span
\r
9168 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9169 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
9170 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9171 text-underline:none'> PAGEREF _Toc235958548 \h </span><span style='color:windowtext;
\r
9172 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9173 style='mso-element:field-separator'></span></span><![endif]--><span
\r
9174 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9175 text-underline:none'>37</span><span style='color:windowtext;display:none;
\r
9176 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
9177 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500340038000000</w:data>
\r
9178 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
9179 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9180 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
9181 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
9182 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
9184 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
9185 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
9186 href="#_Toc235958549">-pdb<span style='color:windowtext;display:none;
\r
9187 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9188 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
9189 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9190 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
9191 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9192 text-underline:none'> PAGEREF _Toc235958549 \h </span><span style='color:windowtext;
\r
9193 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9194 style='mso-element:field-separator'></span></span><![endif]--><span
\r
9195 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9196 text-underline:none'>37</span><span style='color:windowtext;display:none;
\r
9197 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
9198 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500340039000000</w:data>
\r
9199 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
9200 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9201 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
9202 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
9203 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
9205 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
9206 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
9207 href="#_Toc235958550">Tree Input<span style='color:windowtext;display:none;
\r
9208 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9209 style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span
\r
9210 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9211 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
9212 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9213 text-underline:none'> PAGEREF _Toc235958550 \h </span><span style='color:windowtext;
\r
9214 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9215 style='mso-element:field-separator'></span></span><![endif]--><span
\r
9216 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9217 text-underline:none'>37</span><span style='color:windowtext;display:none;
\r
9218 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
9219 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500350030000000</w:data>
\r
9220 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
9221 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9222 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
9223 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
9224 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
9226 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
9227 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
9228 href="#_Toc235958551">-usetree<span style='color:windowtext;display:none;
\r
9229 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9230 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
9231 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9232 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
9233 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9234 text-underline:none'> PAGEREF _Toc235958551 \h </span><span style='color:windowtext;
\r
9235 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9236 style='mso-element:field-separator'></span></span><![endif]--><span
\r
9237 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9238 text-underline:none'>37</span><span style='color:windowtext;display:none;
\r
9239 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
9240 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500350031000000</w:data>
\r
9241 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
9242 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9243 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
9244 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
9245 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
9247 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
9248 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
9249 href="#_Toc235958552">Structures, Sequences Methods and Library Input via the
\r
9250 in Flag<span style='color:windowtext;display:none;mso-hide:screen;
\r
9251 text-decoration:none;text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
9252 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9253 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
9254 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9255 text-underline:none'> PAGEREF _Toc235958552 \h </span><span style='color:windowtext;
\r
9256 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9257 style='mso-element:field-separator'></span></span><![endif]--><span
\r
9258 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9259 text-underline:none'>38</span><span style='color:windowtext;display:none;
\r
9260 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
9261 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500350032000000</w:data>
\r
9262 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
9263 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9264 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
9265 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
9266 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
9268 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
9269 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
9270 href="#_Toc235958553">-in<span style='color:windowtext;display:none;mso-hide:
\r
9271 screen;text-decoration:none;text-underline:none'><span style='mso-tab-count:
\r
9272 1 dotted'>. </span></span><!--[if supportFields]><span style='color:windowtext;
\r
9273 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9274 style='mso-element:field-begin'></span></span><span style='color:windowtext;
\r
9275 display:none;mso-hide:screen;text-decoration:none;text-underline:none'> PAGEREF
\r
9276 _Toc235958553 \h </span><span style='color:windowtext;display:none;mso-hide:
\r
9277 screen;text-decoration:none;text-underline:none'><span style='mso-element:field-separator'></span></span><![endif]--><span
\r
9278 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9279 text-underline:none'>38</span><span style='color:windowtext;display:none;
\r
9280 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
9281 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500350033000000</w:data>
\r
9282 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
9283 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9284 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
9285 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
9286 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
9288 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
9289 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
9290 href="#_Toc235958554">Profile Input<span style='color:windowtext;display:none;
\r
9291 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9292 style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span
\r
9293 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9294 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
9295 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9296 text-underline:none'> PAGEREF _Toc235958554 \h </span><span style='color:windowtext;
\r
9297 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9298 style='mso-element:field-separator'></span></span><![endif]--><span
\r
9299 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9300 text-underline:none'>40</span><span style='color:windowtext;display:none;
\r
9301 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
9302 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500350034000000</w:data>
\r
9303 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
9304 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9305 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
9306 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
9307 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
9309 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
9310 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
9311 href="#_Toc235958555">-profile<span style='color:windowtext;display:none;
\r
9312 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9313 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
9314 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9315 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
9316 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9317 text-underline:none'> PAGEREF _Toc235958555 \h </span><span style='color:windowtext;
\r
9318 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9319 style='mso-element:field-separator'></span></span><![endif]--><span
\r
9320 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9321 text-underline:none'>40</span><span style='color:windowtext;display:none;
\r
9322 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
9323 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500350035000000</w:data>
\r
9324 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
9325 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9326 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
9327 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
9328 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
9330 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
9331 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
9332 href="#_Toc235958556">-profile1 [cw]<span style='color:windowtext;display:none;
\r
9333 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9334 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
9335 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9336 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
9337 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9338 text-underline:none'> PAGEREF _Toc235958556 \h </span><span style='color:windowtext;
\r
9339 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9340 style='mso-element:field-separator'></span></span><![endif]--><span
\r
9341 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9342 text-underline:none'>40</span><span style='color:windowtext;display:none;
\r
9343 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
9344 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500350036000000</w:data>
\r
9345 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
9346 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9347 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
9348 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
9349 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
9351 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
9352 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
9353 href="#_Toc235958557">-profile2 [cw]<span style='color:windowtext;display:none;
\r
9354 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9355 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
9356 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9357 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
9358 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9359 text-underline:none'> PAGEREF _Toc235958557 \h </span><span style='color:windowtext;
\r
9360 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9361 style='mso-element:field-separator'></span></span><![endif]--><span
\r
9362 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9363 text-underline:none'>40</span><span style='color:windowtext;display:none;
\r
9364 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
9365 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500350037000000</w:data>
\r
9366 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
9367 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9368 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
9369 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
9370 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
9372 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
\r
9373 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
9374 href="#_Toc235958558">Alignment Computation<span style='color:windowtext;
\r
9375 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9376 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
9377 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9378 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
9379 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9380 text-underline:none'> PAGEREF _Toc235958558 \h </span><span style='color:windowtext;
\r
9381 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9382 style='mso-element:field-separator'></span></span><![endif]--><span
\r
9383 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9384 text-underline:none'>40</span><span style='color:windowtext;display:none;
\r
9385 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
9386 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500350038000000</w:data>
\r
9387 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
9388 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9389 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
9390 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
9391 FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
9393 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
9394 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
9395 href="#_Toc235958559">Library Computation: Methods<span style='color:windowtext;
\r
9396 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9397 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
9398 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9399 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
9400 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9401 text-underline:none'> PAGEREF _Toc235958559 \h </span><span style='color:windowtext;
\r
9402 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9403 style='mso-element:field-separator'></span></span><![endif]--><span
\r
9404 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9405 text-underline:none'>40</span><span style='color:windowtext;display:none;
\r
9406 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
9407 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500350039000000</w:data>
\r
9408 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
9409 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9410 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
9411 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
9412 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
9414 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
9415 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
9416 href="#_Toc235958560">-lalign_n_top<span style='color:windowtext;display:none;
\r
9417 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9418 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
9419 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9420 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
9421 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9422 text-underline:none'> PAGEREF _Toc235958560 \h </span><span style='color:windowtext;
\r
9423 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9424 style='mso-element:field-separator'></span></span><![endif]--><span
\r
9425 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9426 text-underline:none'>40</span><span style='color:windowtext;display:none;
\r
9427 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
9428 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500360030000000</w:data>
\r
9429 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
9430 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9431 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
9432 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
9433 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
9435 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
9436 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
9437 href="#_Toc235958561">-align_pdb_param_file<span style='color:windowtext;
\r
9438 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9439 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
9440 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9441 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
9442 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9443 text-underline:none'> PAGEREF _Toc235958561 \h </span><span style='color:windowtext;
\r
9444 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9445 style='mso-element:field-separator'></span></span><![endif]--><span
\r
9446 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9447 text-underline:none'>41</span><span style='color:windowtext;display:none;
\r
9448 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
9449 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500360031000000</w:data>
\r
9450 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
9451 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9452 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
9453 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
9454 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
9456 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
9457 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
9458 href="#_Toc235958562">-align_pdb_hasch_mode<span style='color:windowtext;
\r
9459 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9460 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
9461 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9462 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
9463 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9464 text-underline:none'> PAGEREF _Toc235958562 \h </span><span style='color:windowtext;
\r
9465 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9466 style='mso-element:field-separator'></span></span><![endif]--><span
\r
9467 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9468 text-underline:none'>41</span><span style='color:windowtext;display:none;
\r
9469 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
9470 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500360032000000</w:data>
\r
9471 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
9472 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9473 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
9474 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
9475 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
9477 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
9478 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
9479 href="#_Toc235958563">Library Computation: Extension<span style='color:windowtext;
\r
9480 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9481 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
9482 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9483 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
9484 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9485 text-underline:none'> PAGEREF _Toc235958563 \h </span><span style='color:windowtext;
\r
9486 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9487 style='mso-element:field-separator'></span></span><![endif]--><span
\r
9488 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9489 text-underline:none'>41</span><span style='color:windowtext;display:none;
\r
9490 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
9491 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500360033000000</w:data>
\r
9492 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
9493 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9494 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
9495 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
9496 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
9498 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
9499 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
9500 href="#_Toc235958564">-lib_list [Unsupported]<span style='color:windowtext;
\r
9501 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9502 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
9503 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9504 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
9505 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9506 text-underline:none'> PAGEREF _Toc235958564 \h </span><span style='color:windowtext;
\r
9507 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9508 style='mso-element:field-separator'></span></span><![endif]--><span
\r
9509 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9510 text-underline:none'>41</span><span style='color:windowtext;display:none;
\r
9511 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
9512 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500360034000000</w:data>
\r
9513 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
9514 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9515 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
9516 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
9517 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
9519 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
9520 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
9521 href="#_Toc235958565">-do_normalise<span style='color:windowtext;display:none;
\r
9522 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9523 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
9524 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9525 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
9526 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9527 text-underline:none'> PAGEREF _Toc235958565 \h </span><span style='color:windowtext;
\r
9528 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9529 style='mso-element:field-separator'></span></span><![endif]--><span
\r
9530 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9531 text-underline:none'>41</span><span style='color:windowtext;display:none;
\r
9532 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
9533 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500360035000000</w:data>
\r
9534 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
9535 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9536 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
9537 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
9538 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
9540 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
9541 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
9542 href="#_Toc235958566">-extend<span style='color:windowtext;display:none;
\r
9543 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9544 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
9545 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9546 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
9547 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9548 text-underline:none'> PAGEREF _Toc235958566 \h </span><span style='color:windowtext;
\r
9549 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9550 style='mso-element:field-separator'></span></span><![endif]--><span
\r
9551 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9552 text-underline:none'>41</span><span style='color:windowtext;display:none;
\r
9553 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
9554 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500360036000000</w:data>
\r
9555 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
9556 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9557 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
9558 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
9559 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
9561 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
9562 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
9563 href="#_Toc235958567">-extend_mode<span style='color:windowtext;display:none;
\r
9564 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9565 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
9566 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9567 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
9568 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9569 text-underline:none'> PAGEREF _Toc235958567 \h </span><span style='color:windowtext;
\r
9570 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9571 style='mso-element:field-separator'></span></span><![endif]--><span
\r
9572 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9573 text-underline:none'>41</span><span style='color:windowtext;display:none;
\r
9574 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
9575 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500360037000000</w:data>
\r
9576 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
9577 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9578 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
9579 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
9580 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
9582 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
9583 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
9584 href="#_Toc235958568">-max_n_pair<span style='color:windowtext;display:none;
\r
9585 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9586 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
9587 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9588 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
9589 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9590 text-underline:none'> PAGEREF _Toc235958568 \h </span><span style='color:windowtext;
\r
9591 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9592 style='mso-element:field-separator'></span></span><![endif]--><span
\r
9593 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9594 text-underline:none'>42</span><span style='color:windowtext;display:none;
\r
9595 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
9596 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500360038000000</w:data>
\r
9597 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
9598 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9599 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
9600 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
9601 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
9603 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
9604 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
9605 href="#_Toc235958569">-seq_name_for_quadruplet<span style='color:windowtext;
\r
9606 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9607 style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span
\r
9608 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9609 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
9610 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9611 text-underline:none'> PAGEREF _Toc235958569 \h </span><span style='color:windowtext;
\r
9612 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9613 style='mso-element:field-separator'></span></span><![endif]--><span
\r
9614 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9615 text-underline:none'>42</span><span style='color:windowtext;display:none;
\r
9616 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
9617 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500360039000000</w:data>
\r
9618 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
9619 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9620 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
9621 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
9622 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
9624 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
9625 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
9626 href="#_Toc235958570">-compact<span style='color:windowtext;display:none;
\r
9627 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9628 style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span
\r
9629 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9630 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
9631 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9632 text-underline:none'> PAGEREF _Toc235958570 \h </span><span style='color:windowtext;
\r
9633 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9634 style='mso-element:field-separator'></span></span><![endif]--><span
\r
9635 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9636 text-underline:none'>42</span><span style='color:windowtext;display:none;
\r
9637 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
9638 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500370030000000</w:data>
\r
9639 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
9640 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9641 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
9642 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
9643 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
9645 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
9646 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
9647 href="#_Toc235958571">-clean<span style='color:windowtext;display:none;
\r
9648 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9649 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
9650 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9651 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
9652 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9653 text-underline:none'> PAGEREF _Toc235958571 \h </span><span style='color:windowtext;
\r
9654 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9655 style='mso-element:field-separator'></span></span><![endif]--><span
\r
9656 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9657 text-underline:none'>42</span><span style='color:windowtext;display:none;
\r
9658 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
9659 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500370031000000</w:data>
\r
9660 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
9661 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9662 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
9663 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
9664 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
9666 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
9667 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
9668 href="#_Toc235958572">-maximise<span style='color:windowtext;display:none;
\r
9669 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9670 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
9671 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9672 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
9673 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9674 text-underline:none'> PAGEREF _Toc235958572 \h </span><span style='color:windowtext;
\r
9675 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9676 style='mso-element:field-separator'></span></span><![endif]--><span
\r
9677 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9678 text-underline:none'>42</span><span style='color:windowtext;display:none;
\r
9679 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
9680 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500370032000000</w:data>
\r
9681 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
9682 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9683 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
9684 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
9685 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
9687 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
9688 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
9689 href="#_Toc235958573">-do_self<span style='color:windowtext;display:none;
\r
9690 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9691 style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span
\r
9692 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9693 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
9694 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9695 text-underline:none'> PAGEREF _Toc235958573 \h </span><span style='color:windowtext;
\r
9696 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9697 style='mso-element:field-separator'></span></span><![endif]--><span
\r
9698 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9699 text-underline:none'>42</span><span style='color:windowtext;display:none;
\r
9700 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
9701 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500370033000000</w:data>
\r
9702 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
9703 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9704 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
9705 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
9706 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
9708 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
9709 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
9710 href="#_Toc235958574">-seq_name_for_quadruplet<span style='color:windowtext;
\r
9711 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9712 style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span
\r
9713 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9714 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
9715 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9716 text-underline:none'> PAGEREF _Toc235958574 \h </span><span style='color:windowtext;
\r
9717 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9718 style='mso-element:field-separator'></span></span><![endif]--><span
\r
9719 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9720 text-underline:none'>42</span><span style='color:windowtext;display:none;
\r
9721 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
9722 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500370034000000</w:data>
\r
9723 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
9724 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9725 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
9726 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
9727 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
9729 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
9730 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
9731 href="#_Toc235958575">-weight<span style='color:windowtext;display:none;
\r
9732 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9733 style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span
\r
9734 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9735 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
9736 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9737 text-underline:none'> PAGEREF _Toc235958575 \h </span><span style='color:windowtext;
\r
9738 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9739 style='mso-element:field-separator'></span></span><![endif]--><span
\r
9740 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9741 text-underline:none'>43</span><span style='color:windowtext;display:none;
\r
9742 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
9743 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500370035000000</w:data>
\r
9744 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
9745 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9746 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
9747 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
9748 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
9750 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
9751 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
9752 href="#_Toc235958576">Tree Computation<span style='color:windowtext;display:
\r
9753 none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9754 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
9755 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9756 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
9757 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9758 text-underline:none'> PAGEREF _Toc235958576 \h </span><span style='color:windowtext;
\r
9759 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9760 style='mso-element:field-separator'></span></span><![endif]--><span
\r
9761 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9762 text-underline:none'>43</span><span style='color:windowtext;display:none;
\r
9763 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
9764 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500370036000000</w:data>
\r
9765 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
9766 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9767 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
9768 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
9769 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
9771 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
9772 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
9773 href="#_Toc235958577">-distance_matrix_mode<span style='color:windowtext;
\r
9774 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9775 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
9776 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9777 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
9778 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9779 text-underline:none'> PAGEREF _Toc235958577 \h </span><span style='color:windowtext;
\r
9780 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9781 style='mso-element:field-separator'></span></span><![endif]--><span
\r
9782 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9783 text-underline:none'>43</span><span style='color:windowtext;display:none;
\r
9784 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
9785 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500370037000000</w:data>
\r
9786 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
9787 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9788 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
9789 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
9790 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
9792 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
9793 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
9794 href="#_Toc235958578">-quicktree [CW]<span style='color:windowtext;display:
\r
9795 none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9796 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
9797 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9798 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
9799 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9800 text-underline:none'> PAGEREF _Toc235958578 \h </span><span style='color:windowtext;
\r
9801 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9802 style='mso-element:field-separator'></span></span><![endif]--><span
\r
9803 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9804 text-underline:none'>44</span><span style='color:windowtext;display:none;
\r
9805 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
9806 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500370038000000</w:data>
\r
9807 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
9808 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9809 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
9810 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
9811 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
9813 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
9814 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
9815 href="#_Toc235958579">Pair-wise Alignment Computation<span style='color:windowtext;
\r
9816 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9817 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
9818 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9819 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
9820 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9821 text-underline:none'> PAGEREF _Toc235958579 \h </span><span style='color:windowtext;
\r
9822 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9823 style='mso-element:field-separator'></span></span><![endif]--><span
\r
9824 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9825 text-underline:none'>44</span><span style='color:windowtext;display:none;
\r
9826 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
9827 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500370039000000</w:data>
\r
9828 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
9829 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9830 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
9831 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
9832 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
9834 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
9835 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
9836 href="#_Toc235958580">-dp_mode<span style='color:windowtext;display:none;
\r
9837 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9838 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
9839 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9840 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
9841 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9842 text-underline:none'> PAGEREF _Toc235958580 \h </span><span style='color:windowtext;
\r
9843 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9844 style='mso-element:field-separator'></span></span><![endif]--><span
\r
9845 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9846 text-underline:none'>44</span><span style='color:windowtext;display:none;
\r
9847 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
9848 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500380030000000</w:data>
\r
9849 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
9850 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9851 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
9852 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
9853 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
9855 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
9856 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
9857 href="#_Toc235958581">-ktuple<span style='color:windowtext;display:none;
\r
9858 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9859 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
9860 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9861 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
9862 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9863 text-underline:none'> PAGEREF _Toc235958581 \h </span><span style='color:windowtext;
\r
9864 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9865 style='mso-element:field-separator'></span></span><![endif]--><span
\r
9866 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9867 text-underline:none'>45</span><span style='color:windowtext;display:none;
\r
9868 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
9869 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500380031000000</w:data>
\r
9870 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
9871 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9872 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
9873 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
9874 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
9876 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
9877 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
9878 href="#_Toc235958582">-ndiag<span style='color:windowtext;display:none;
\r
9879 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9880 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
9881 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9882 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
9883 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9884 text-underline:none'> PAGEREF _Toc235958582 \h </span><span style='color:windowtext;
\r
9885 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9886 style='mso-element:field-separator'></span></span><![endif]--><span
\r
9887 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9888 text-underline:none'>45</span><span style='color:windowtext;display:none;
\r
9889 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
9890 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500380032000000</w:data>
\r
9891 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
9892 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9893 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
9894 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
9895 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
9897 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
9898 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
9899 href="#_Toc235958583">-diag_mode<span style='color:windowtext;display:none;
\r
9900 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9901 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
9902 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9903 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
9904 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9905 text-underline:none'> PAGEREF _Toc235958583 \h </span><span style='color:windowtext;
\r
9906 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9907 style='mso-element:field-separator'></span></span><![endif]--><span
\r
9908 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9909 text-underline:none'>45</span><span style='color:windowtext;display:none;
\r
9910 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
9911 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500380033000000</w:data>
\r
9912 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
9913 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9914 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
9915 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
9916 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
9918 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
9919 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
9920 href="#_Toc235958584">-diag_threshold<span style='color:windowtext;display:
\r
9921 none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9922 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
9923 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9924 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
9925 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9926 text-underline:none'> PAGEREF _Toc235958584 \h </span><span style='color:windowtext;
\r
9927 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9928 style='mso-element:field-separator'></span></span><![endif]--><span
\r
9929 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9930 text-underline:none'>46</span><span style='color:windowtext;display:none;
\r
9931 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
9932 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500380034000000</w:data>
\r
9933 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
9934 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9935 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
9936 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
9937 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
9939 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
9940 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
9941 href="#_Toc235958585">-sim_matrix<span style='color:windowtext;display:none;
\r
9942 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9943 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
9944 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9945 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
9946 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9947 text-underline:none'> PAGEREF _Toc235958585 \h </span><span style='color:windowtext;
\r
9948 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9949 style='mso-element:field-separator'></span></span><![endif]--><span
\r
9950 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9951 text-underline:none'>46</span><span style='color:windowtext;display:none;
\r
9952 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
9953 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500380035000000</w:data>
\r
9954 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
9955 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9956 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
9957 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
9958 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
9960 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
9961 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
9962 href="#_Toc235958586">-matrix [CW]<span style='color:windowtext;display:none;
\r
9963 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9964 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
9965 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9966 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
9967 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9968 text-underline:none'> PAGEREF _Toc235958586 \h </span><span style='color:windowtext;
\r
9969 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9970 style='mso-element:field-separator'></span></span><![endif]--><span
\r
9971 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9972 text-underline:none'>46</span><span style='color:windowtext;display:none;
\r
9973 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
9974 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500380036000000</w:data>
\r
9975 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
9976 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9977 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
9978 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
9979 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
9981 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
9982 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
9983 href="#_Toc235958587">-nomatch<span style='color:windowtext;display:none;
\r
9984 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9985 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
9986 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9987 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
9988 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9989 text-underline:none'> PAGEREF _Toc235958587 \h </span><span style='color:windowtext;
\r
9990 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9991 style='mso-element:field-separator'></span></span><![endif]--><span
\r
9992 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
9993 text-underline:none'>46</span><span style='color:windowtext;display:none;
\r
9994 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
9995 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500380037000000</w:data>
\r
9996 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
9997 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
9998 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
9999 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
10000 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
10002 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
10003 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
10004 href="#_Toc235958588">-gapopen<span style='color:windowtext;display:none;
\r
10005 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10006 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
10007 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10008 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
10009 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10010 text-underline:none'> PAGEREF _Toc235958588 \h </span><span style='color:windowtext;
\r
10011 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10012 style='mso-element:field-separator'></span></span><![endif]--><span
\r
10013 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10014 text-underline:none'>46</span><span style='color:windowtext;display:none;
\r
10015 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
10016 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500380038000000</w:data>
\r
10017 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
10018 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10019 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
10020 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
10021 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
10023 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
10024 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
10025 href="#_Toc235958589">-gapext<span style='color:windowtext;display:none;
\r
10026 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10027 style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span
\r
10028 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10029 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
10030 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10031 text-underline:none'> PAGEREF _Toc235958589 \h </span><span style='color:windowtext;
\r
10032 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10033 style='mso-element:field-separator'></span></span><![endif]--><span
\r
10034 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10035 text-underline:none'>47</span><span style='color:windowtext;display:none;
\r
10036 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
10037 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500380039000000</w:data>
\r
10038 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
10039 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10040 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
10041 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
10042 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
10044 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
10045 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
10046 href="#_Toc235958590">-fgapopen<span style='color:windowtext;display:none;
\r
10047 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10048 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
10049 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10050 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
10051 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10052 text-underline:none'> PAGEREF _Toc235958590 \h </span><span style='color:windowtext;
\r
10053 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10054 style='mso-element:field-separator'></span></span><![endif]--><span
\r
10055 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10056 text-underline:none'>47</span><span style='color:windowtext;display:none;
\r
10057 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
10058 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500390030000000</w:data>
\r
10059 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
10060 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10061 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
10062 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
10063 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
10065 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
10066 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
10067 href="#_Toc235958591">-fgapext<span style='color:windowtext;display:none;
\r
10068 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10069 style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span
\r
10070 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10071 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
10072 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10073 text-underline:none'> PAGEREF _Toc235958591 \h </span><span style='color:windowtext;
\r
10074 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10075 style='mso-element:field-separator'></span></span><![endif]--><span
\r
10076 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10077 text-underline:none'>47</span><span style='color:windowtext;display:none;
\r
10078 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
10079 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500390031000000</w:data>
\r
10080 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
10081 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10082 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
10083 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
10084 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
10086 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
10087 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
10088 href="#_Toc235958592">-cosmetic_penalty<span style='color:windowtext;
\r
10089 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10090 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
10091 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10092 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
10093 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10094 text-underline:none'> PAGEREF _Toc235958592 \h </span><span style='color:windowtext;
\r
10095 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10096 style='mso-element:field-separator'></span></span><![endif]--><span
\r
10097 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10098 text-underline:none'>47</span><span style='color:windowtext;display:none;
\r
10099 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
10100 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500390032000000</w:data>
\r
10101 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
10102 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10103 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
10104 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
10105 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
10107 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
10108 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
10109 href="#_Toc235958593">-tg_mode<span style='color:windowtext;display:none;
\r
10110 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10111 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
10112 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10113 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
10114 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10115 text-underline:none'> PAGEREF _Toc235958593 \h </span><span style='color:windowtext;
\r
10116 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10117 style='mso-element:field-separator'></span></span><![endif]--><span
\r
10118 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10119 text-underline:none'>47</span><span style='color:windowtext;display:none;
\r
10120 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
10121 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500390033000000</w:data>
\r
10122 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
10123 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10124 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
10125 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
10126 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
10128 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
10129 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
10130 href="#_Toc235958594">Weighting Schemes<span style='color:windowtext;
\r
10131 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10132 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
10133 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10134 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
10135 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10136 text-underline:none'> PAGEREF _Toc235958594 \h </span><span style='color:windowtext;
\r
10137 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10138 style='mso-element:field-separator'></span></span><![endif]--><span
\r
10139 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10140 text-underline:none'>47</span><span style='color:windowtext;display:none;
\r
10141 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
10142 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500390034000000</w:data>
\r
10143 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
10144 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10145 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
10146 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
10147 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
10149 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
10150 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
10151 href="#_Toc235958595">-seq_weight<span style='color:windowtext;display:none;
\r
10152 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10153 style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span
\r
10154 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10155 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
10156 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10157 text-underline:none'> PAGEREF _Toc235958595 \h </span><span style='color:windowtext;
\r
10158 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10159 style='mso-element:field-separator'></span></span><![endif]--><span
\r
10160 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10161 text-underline:none'>47</span><span style='color:windowtext;display:none;
\r
10162 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
10163 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500390035000000</w:data>
\r
10164 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
10165 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10166 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
10167 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
10168 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
10170 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
10171 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
10172 href="#_Toc235958596">Multiple Alignment Computation<span style='color:windowtext;
\r
10173 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10174 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
10175 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10176 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
10177 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10178 text-underline:none'> PAGEREF _Toc235958596 \h </span><span style='color:windowtext;
\r
10179 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10180 style='mso-element:field-separator'></span></span><![endif]--><span
\r
10181 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10182 text-underline:none'>48</span><span style='color:windowtext;display:none;
\r
10183 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
10184 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500390036000000</w:data>
\r
10185 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
10186 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10187 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
10188 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
10189 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
10191 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
10192 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
10193 href="#_Toc235958597">-msa_mode<span style='color:windowtext;display:none;
\r
10194 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10195 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
10196 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10197 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
10198 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10199 text-underline:none'> PAGEREF _Toc235958597 \h </span><span style='color:windowtext;
\r
10200 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10201 style='mso-element:field-separator'></span></span><![endif]--><span
\r
10202 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10203 text-underline:none'>48</span><span style='color:windowtext;display:none;
\r
10204 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
10205 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500390037000000</w:data>
\r
10206 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
10207 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10208 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
10209 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
10210 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
10212 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
10213 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
10214 href="#_Toc235958598">-one2all<span style='color:windowtext;display:none;
\r
10215 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10216 style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span
\r
10217 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10218 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
10219 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10220 text-underline:none'> PAGEREF _Toc235958598 \h </span><span style='color:windowtext;
\r
10221 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10222 style='mso-element:field-separator'></span></span><![endif]--><span
\r
10223 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10224 text-underline:none'>48</span><span style='color:windowtext;display:none;
\r
10225 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
10226 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500390038000000</w:data>
\r
10227 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
10228 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10229 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
10230 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
10231 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
10233 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
10234 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
10235 href="#_Toc235958599">-profile_comparison<span style='color:windowtext;
\r
10236 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10237 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
10238 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10239 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
10240 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10241 text-underline:none'> PAGEREF _Toc235958599 \h </span><span style='color:windowtext;
\r
10242 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10243 style='mso-element:field-separator'></span></span><![endif]--><span
\r
10244 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10245 text-underline:none'>48</span><span style='color:windowtext;display:none;
\r
10246 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
10247 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003500390039000000</w:data>
\r
10248 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
10249 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10250 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
10251 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
10252 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
10254 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
10255 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
10256 href="#_Toc235958600">-profile_mode<span style='color:windowtext;display:none;
\r
10257 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10258 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
10259 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10260 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
10261 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10262 text-underline:none'> PAGEREF _Toc235958600 \h </span><span style='color:windowtext;
\r
10263 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10264 style='mso-element:field-separator'></span></span><![endif]--><span
\r
10265 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10266 text-underline:none'>49</span><span style='color:windowtext;display:none;
\r
10267 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
10268 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600300030000000</w:data>
\r
10269 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
10270 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10271 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
10272 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
10273 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
10275 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
10276 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
10277 href="#_Toc235958601">Alignment Post-Processing<span style='color:windowtext;
\r
10278 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10279 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
10280 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10281 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
10282 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10283 text-underline:none'> PAGEREF _Toc235958601 \h </span><span style='color:windowtext;
\r
10284 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10285 style='mso-element:field-separator'></span></span><![endif]--><span
\r
10286 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10287 text-underline:none'>49</span><span style='color:windowtext;display:none;
\r
10288 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
10289 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600300031000000</w:data>
\r
10290 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
10291 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10292 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
10293 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
10294 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
10296 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
10297 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
10298 href="#_Toc235958602">-clean_aln<span style='color:windowtext;display:none;
\r
10299 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10300 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
10301 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10302 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
10303 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10304 text-underline:none'> PAGEREF _Toc235958602 \h </span><span style='color:windowtext;
\r
10305 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10306 style='mso-element:field-separator'></span></span><![endif]--><span
\r
10307 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10308 text-underline:none'>49</span><span style='color:windowtext;display:none;
\r
10309 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
10310 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600300032000000</w:data>
\r
10311 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
10312 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10313 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
10314 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
10315 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
10317 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
10318 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
10319 href="#_Toc235958603">-clean_threshold<span style='color:windowtext;display:
\r
10320 none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10321 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
10322 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10323 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
10324 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10325 text-underline:none'> PAGEREF _Toc235958603 \h </span><span style='color:windowtext;
\r
10326 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10327 style='mso-element:field-separator'></span></span><![endif]--><span
\r
10328 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10329 text-underline:none'>49</span><span style='color:windowtext;display:none;
\r
10330 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
10331 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600300033000000</w:data>
\r
10332 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
10333 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10334 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
10335 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
10336 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
10338 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
10339 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
10340 href="#_Toc235958604">-clean_iteration<span style='color:windowtext;display:
\r
10341 none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10342 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
10343 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10344 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
10345 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10346 text-underline:none'> PAGEREF _Toc235958604 \h </span><span style='color:windowtext;
\r
10347 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10348 style='mso-element:field-separator'></span></span><![endif]--><span
\r
10349 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10350 text-underline:none'>49</span><span style='color:windowtext;display:none;
\r
10351 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
10352 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600300034000000</w:data>
\r
10353 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
10354 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10355 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
10356 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
10357 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
10359 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
10360 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
10361 href="#_Toc235958605">-clean_evaluation_mode<span style='color:windowtext;
\r
10362 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10363 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
10364 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10365 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
10366 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10367 text-underline:none'> PAGEREF _Toc235958605 \h </span><span style='color:windowtext;
\r
10368 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10369 style='mso-element:field-separator'></span></span><![endif]--><span
\r
10370 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10371 text-underline:none'>49</span><span style='color:windowtext;display:none;
\r
10372 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
10373 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600300035000000</w:data>
\r
10374 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
10375 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10376 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
10377 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
10378 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
10380 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
10381 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
10382 href="#_Toc235958606">-iterate<span style='color:windowtext;display:none;
\r
10383 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10384 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
10385 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10386 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
10387 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10388 text-underline:none'> PAGEREF _Toc235958606 \h </span><span style='color:windowtext;
\r
10389 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10390 style='mso-element:field-separator'></span></span><![endif]--><span
\r
10391 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10392 text-underline:none'>49</span><span style='color:windowtext;display:none;
\r
10393 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
10394 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600300036000000</w:data>
\r
10395 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
10396 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10397 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
10398 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
10399 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
10401 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
\r
10402 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
10403 href="#_Toc235958607">CPU Control<span style='color:windowtext;display:none;
\r
10404 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10405 style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span
\r
10406 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10407 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
10408 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10409 text-underline:none'> PAGEREF _Toc235958607 \h </span><span style='color:windowtext;
\r
10410 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10411 style='mso-element:field-separator'></span></span><![endif]--><span
\r
10412 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10413 text-underline:none'>50</span><span style='color:windowtext;display:none;
\r
10414 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
10415 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600300037000000</w:data>
\r
10416 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
10417 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10418 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
10419 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
10420 FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
10422 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
10423 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
10424 href="#_Toc235958608">Multithreading<span style='color:windowtext;display:none;
\r
10425 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10426 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
10427 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10428 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
10429 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10430 text-underline:none'> PAGEREF _Toc235958608 \h </span><span style='color:windowtext;
\r
10431 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10432 style='mso-element:field-separator'></span></span><![endif]--><span
\r
10433 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10434 text-underline:none'>50</span><span style='color:windowtext;display:none;
\r
10435 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
10436 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600300038000000</w:data>
\r
10437 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
10438 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10439 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
10440 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
10441 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
10443 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
10444 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
10445 href="#_Toc235958609">-multi_thread [NOT Supported]<span style='color:windowtext;
\r
10446 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10447 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
10448 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10449 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
10450 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10451 text-underline:none'> PAGEREF _Toc235958609 \h </span><span style='color:windowtext;
\r
10452 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10453 style='mso-element:field-separator'></span></span><![endif]--><span
\r
10454 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10455 text-underline:none'>50</span><span style='color:windowtext;display:none;
\r
10456 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
10457 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600300039000000</w:data>
\r
10458 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
10459 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10460 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
10461 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
10462 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
10464 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
10465 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
10466 href="#_Toc235958610">Limits<span style='color:windowtext;display:none;
\r
10467 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10468 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
10469 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10470 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
10471 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10472 text-underline:none'> PAGEREF _Toc235958610 \h </span><span style='color:windowtext;
\r
10473 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10474 style='mso-element:field-separator'></span></span><![endif]--><span
\r
10475 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10476 text-underline:none'>50</span><span style='color:windowtext;display:none;
\r
10477 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
10478 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600310030000000</w:data>
\r
10479 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
10480 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10481 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
10482 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
10483 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
10485 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
10486 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
10487 href="#_Toc235958611">-mem_mode<span style='color:windowtext;display:none;
\r
10488 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10489 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
10490 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10491 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
10492 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10493 text-underline:none'> PAGEREF _Toc235958611 \h </span><span style='color:windowtext;
\r
10494 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10495 style='mso-element:field-separator'></span></span><![endif]--><span
\r
10496 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10497 text-underline:none'>50</span><span style='color:windowtext;display:none;
\r
10498 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
10499 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600310031000000</w:data>
\r
10500 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
10501 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10502 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
10503 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
10504 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
10506 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
10507 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
10508 href="#_Toc235958612">-ulimit<span style='color:windowtext;display:none;
\r
10509 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10510 style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span
\r
10511 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10512 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
10513 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10514 text-underline:none'> PAGEREF _Toc235958612 \h </span><span style='color:windowtext;
\r
10515 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10516 style='mso-element:field-separator'></span></span><![endif]--><span
\r
10517 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10518 text-underline:none'>50</span><span style='color:windowtext;display:none;
\r
10519 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
10520 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600310032000000</w:data>
\r
10521 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
10522 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10523 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
10524 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
10525 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
10527 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
10528 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
10529 href="#_Toc235958613">-maxlen<span style='color:windowtext;display:none;
\r
10530 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10531 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
10532 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10533 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
10534 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10535 text-underline:none'> PAGEREF _Toc235958613 \h </span><span style='color:windowtext;
\r
10536 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10537 style='mso-element:field-separator'></span></span><![endif]--><span
\r
10538 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10539 text-underline:none'>50</span><span style='color:windowtext;display:none;
\r
10540 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
10541 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600310033000000</w:data>
\r
10542 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
10543 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10544 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
10545 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
10546 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
10548 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
10549 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
10550 href="#_Toc235958614">Aligning more than 100 sequences with DPA<span
\r
10551 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10552 text-underline:none'><span style='mso-tab-count:1 dotted'>.. </span></span><!--[if supportFields]><span
\r
10553 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10554 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
10555 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10556 text-underline:none'> PAGEREF _Toc235958614 \h </span><span style='color:windowtext;
\r
10557 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10558 style='mso-element:field-separator'></span></span><![endif]--><span
\r
10559 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10560 text-underline:none'>50</span><span style='color:windowtext;display:none;
\r
10561 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
10562 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600310034000000</w:data>
\r
10563 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
10564 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10565 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
10566 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
10567 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
10569 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
10570 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
10571 href="#_Toc235958615">-maxnseq<span style='color:windowtext;display:none;
\r
10572 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10573 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
10574 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10575 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
10576 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10577 text-underline:none'> PAGEREF _Toc235958615 \h </span><span style='color:windowtext;
\r
10578 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10579 style='mso-element:field-separator'></span></span><![endif]--><span
\r
10580 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10581 text-underline:none'>50</span><span style='color:windowtext;display:none;
\r
10582 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
10583 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600310035000000</w:data>
\r
10584 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
10585 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10586 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
10587 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
10588 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
10590 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
10591 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
10592 href="#_Toc235958616">-dpa_master_aln<span style='color:windowtext;display:
\r
10593 none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10594 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
10595 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10596 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
10597 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10598 text-underline:none'> PAGEREF _Toc235958616 \h </span><span style='color:windowtext;
\r
10599 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10600 style='mso-element:field-separator'></span></span><![endif]--><span
\r
10601 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10602 text-underline:none'>50</span><span style='color:windowtext;display:none;
\r
10603 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
10604 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600310036000000</w:data>
\r
10605 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
10606 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10607 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
10608 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
10609 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
10611 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
10612 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
10613 href="#_Toc235958617">-dpa_maxnseq<span style='color:windowtext;display:none;
\r
10614 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10615 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
10616 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10617 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
10618 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10619 text-underline:none'> PAGEREF _Toc235958617 \h </span><span style='color:windowtext;
\r
10620 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10621 style='mso-element:field-separator'></span></span><![endif]--><span
\r
10622 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10623 text-underline:none'>51</span><span style='color:windowtext;display:none;
\r
10624 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
10625 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600310037000000</w:data>
\r
10626 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
10627 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10628 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
10629 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
10630 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
10632 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
10633 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
10634 href="#_Toc235958618">-dpa_min_score1<span style='color:windowtext;display:
\r
10635 none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10636 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
10637 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10638 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
10639 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10640 text-underline:none'> PAGEREF _Toc235958618 \h </span><span style='color:windowtext;
\r
10641 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10642 style='mso-element:field-separator'></span></span><![endif]--><span
\r
10643 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10644 text-underline:none'>51</span><span style='color:windowtext;display:none;
\r
10645 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
10646 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600310038000000</w:data>
\r
10647 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
10648 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10649 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
10650 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
10651 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
10653 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
10654 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
10655 href="#_Toc235958619">-dpa_min_score2<span style='color:windowtext;display:
\r
10656 none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10657 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
10658 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10659 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
10660 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10661 text-underline:none'> PAGEREF _Toc235958619 \h </span><span style='color:windowtext;
\r
10662 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10663 style='mso-element:field-separator'></span></span><![endif]--><span
\r
10664 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10665 text-underline:none'>51</span><span style='color:windowtext;display:none;
\r
10666 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
10667 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600310039000000</w:data>
\r
10668 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
10669 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10670 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
10671 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
10672 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
10674 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
10675 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
10676 href="#_Toc235958620">-dap_tree [NOT IMPLEMENTED]<span style='color:windowtext;
\r
10677 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10678 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
10679 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10680 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
10681 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10682 text-underline:none'> PAGEREF _Toc235958620 \h </span><span style='color:windowtext;
\r
10683 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10684 style='mso-element:field-separator'></span></span><![endif]--><span
\r
10685 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10686 text-underline:none'>51</span><span style='color:windowtext;display:none;
\r
10687 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
10688 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600320030000000</w:data>
\r
10689 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
10690 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10691 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
10692 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
10693 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
10695 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
\r
10696 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
10697 href="#_Toc235958621">Using Structures<span style='color:windowtext;display:
\r
10698 none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10699 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
10700 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10701 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
10702 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10703 text-underline:none'> PAGEREF _Toc235958621 \h </span><span style='color:windowtext;
\r
10704 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10705 style='mso-element:field-separator'></span></span><![endif]--><span
\r
10706 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10707 text-underline:none'>51</span><span style='color:windowtext;display:none;
\r
10708 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
10709 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600320031000000</w:data>
\r
10710 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
10711 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10712 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
10713 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
10714 FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
10716 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
10717 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
10718 href="#_Toc235958622">Generic<span style='color:windowtext;display:none;
\r
10719 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10720 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
10721 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10722 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
10723 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10724 text-underline:none'> PAGEREF _Toc235958622 \h </span><span style='color:windowtext;
\r
10725 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10726 style='mso-element:field-separator'></span></span><![endif]--><span
\r
10727 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10728 text-underline:none'>51</span><span style='color:windowtext;display:none;
\r
10729 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
10730 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600320032000000</w:data>
\r
10731 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
10732 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10733 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
10734 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
10735 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
10737 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
10738 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
10739 href="#_Toc235958623">-mode<span style='color:windowtext;display:none;
\r
10740 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10741 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
10742 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10743 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
10744 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10745 text-underline:none'> PAGEREF _Toc235958623 \h </span><span style='color:windowtext;
\r
10746 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10747 style='mso-element:field-separator'></span></span><![endif]--><span
\r
10748 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10749 text-underline:none'>51</span><span style='color:windowtext;display:none;
\r
10750 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
10751 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600320033000000</w:data>
\r
10752 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
10753 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10754 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
10755 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
10756 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
10758 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
10759 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
10760 href="#_Toc235958624">-check_pdb_status<span style='color:windowtext;
\r
10761 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10762 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
10763 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10764 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
10765 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10766 text-underline:none'> PAGEREF _Toc235958624 \h </span><span style='color:windowtext;
\r
10767 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10768 style='mso-element:field-separator'></span></span><![endif]--><span
\r
10769 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10770 text-underline:none'>52</span><span style='color:windowtext;display:none;
\r
10771 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
10772 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600320034000000</w:data>
\r
10773 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
10774 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10775 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
10776 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
10777 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
10779 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
10780 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
10781 href="#_Toc235958625">3D Coffee: Using SAP<span style='color:windowtext;
\r
10782 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10783 style='mso-tab-count:1 dotted'>.. </span></span><!--[if supportFields]><span
\r
10784 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10785 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
10786 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10787 text-underline:none'> PAGEREF _Toc235958625 \h </span><span style='color:windowtext;
\r
10788 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10789 style='mso-element:field-separator'></span></span><![endif]--><span
\r
10790 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10791 text-underline:none'>52</span><span style='color:windowtext;display:none;
\r
10792 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
10793 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600320035000000</w:data>
\r
10794 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
10795 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10796 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
10797 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
10798 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
10800 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
10801 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
10802 href="#_Toc235958626">Using/finding PDB templates for the Sequences<span
\r
10803 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10804 text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
10805 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10806 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
10807 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10808 text-underline:none'> PAGEREF _Toc235958626 \h </span><span style='color:windowtext;
\r
10809 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10810 style='mso-element:field-separator'></span></span><![endif]--><span
\r
10811 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10812 text-underline:none'>52</span><span style='color:windowtext;display:none;
\r
10813 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
10814 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600320036000000</w:data>
\r
10815 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
10816 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10817 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
10818 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
10819 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
10821 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
10822 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
10823 href="#_Toc235958627">-template_file<span style='color:windowtext;display:none;
\r
10824 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10825 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
10826 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10827 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
10828 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10829 text-underline:none'> PAGEREF _Toc235958627 \h </span><span style='color:windowtext;
\r
10830 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10831 style='mso-element:field-separator'></span></span><![endif]--><span
\r
10832 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10833 text-underline:none'>52</span><span style='color:windowtext;display:none;
\r
10834 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
10835 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600320037000000</w:data>
\r
10836 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
10837 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10838 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
10839 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
10840 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
10842 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
10843 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
10844 href="#_Toc235958628">-struc_to_use<span style='color:windowtext;display:none;
\r
10845 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10846 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
10847 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10848 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
10849 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10850 text-underline:none'> PAGEREF _Toc235958628 \h </span><span style='color:windowtext;
\r
10851 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10852 style='mso-element:field-separator'></span></span><![endif]--><span
\r
10853 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10854 text-underline:none'>54</span><span style='color:windowtext;display:none;
\r
10855 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
10856 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600320038000000</w:data>
\r
10857 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
10858 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10859 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
10860 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
10861 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
10863 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
\r
10864 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
10865 href="#_Toc235958629">Multiple Local Alignments<span style='color:windowtext;
\r
10866 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10867 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
10868 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10869 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
10870 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10871 text-underline:none'> PAGEREF _Toc235958629 \h </span><span style='color:windowtext;
\r
10872 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10873 style='mso-element:field-separator'></span></span><![endif]--><span
\r
10874 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10875 text-underline:none'>54</span><span style='color:windowtext;display:none;
\r
10876 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
10877 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600320039000000</w:data>
\r
10878 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
10879 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10880 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
10881 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
10882 FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
10884 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
10885 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
10886 href="#_Toc235958630">-domain/-mocca<span style='color:windowtext;display:none;
\r
10887 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10888 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
10889 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10890 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
10891 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10892 text-underline:none'> PAGEREF _Toc235958630 \h </span><span style='color:windowtext;
\r
10893 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10894 style='mso-element:field-separator'></span></span><![endif]--><span
\r
10895 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10896 text-underline:none'>55</span><span style='color:windowtext;display:none;
\r
10897 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
10898 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600330030000000</w:data>
\r
10899 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
10900 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10901 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
10902 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
10903 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
10905 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
10906 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
10907 href="#_Toc235958631">-start<span style='color:windowtext;display:none;
\r
10908 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10909 style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span
\r
10910 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10911 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
10912 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10913 text-underline:none'> PAGEREF _Toc235958631 \h </span><span style='color:windowtext;
\r
10914 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10915 style='mso-element:field-separator'></span></span><![endif]--><span
\r
10916 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10917 text-underline:none'>55</span><span style='color:windowtext;display:none;
\r
10918 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
10919 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600330031000000</w:data>
\r
10920 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
10921 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10922 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
10923 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
10924 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
10926 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
10927 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
10928 href="#_Toc235958632">-len<span style='color:windowtext;display:none;
\r
10929 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10930 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
10931 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10932 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
10933 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10934 text-underline:none'> PAGEREF _Toc235958632 \h </span><span style='color:windowtext;
\r
10935 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10936 style='mso-element:field-separator'></span></span><![endif]--><span
\r
10937 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10938 text-underline:none'>55</span><span style='color:windowtext;display:none;
\r
10939 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
10940 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600330032000000</w:data>
\r
10941 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
10942 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10943 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
10944 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
10945 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
10947 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
10948 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
10949 href="#_Toc235958633">-scale<span style='color:windowtext;display:none;
\r
10950 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10951 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
10952 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10953 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
10954 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10955 text-underline:none'> PAGEREF _Toc235958633 \h </span><span style='color:windowtext;
\r
10956 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10957 style='mso-element:field-separator'></span></span><![endif]--><span
\r
10958 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10959 text-underline:none'>55</span><span style='color:windowtext;display:none;
\r
10960 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
10961 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600330033000000</w:data>
\r
10962 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
10963 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10964 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
10965 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
10966 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
10968 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
10969 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
10970 href="#_Toc235958634">-domain_interactive [Examples]<span style='color:windowtext;
\r
10971 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10972 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
10973 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10974 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
10975 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10976 text-underline:none'> PAGEREF _Toc235958634 \h </span><span style='color:windowtext;
\r
10977 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10978 style='mso-element:field-separator'></span></span><![endif]--><span
\r
10979 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10980 text-underline:none'>56</span><span style='color:windowtext;display:none;
\r
10981 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
10982 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600330034000000</w:data>
\r
10983 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
10984 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10985 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
10986 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
10987 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
10989 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
\r
10990 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
10991 href="#_Toc235958635">Output Control<span style='color:windowtext;display:none;
\r
10992 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10993 style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span
\r
10994 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10995 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
10996 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
10997 text-underline:none'> PAGEREF _Toc235958635 \h </span><span style='color:windowtext;
\r
10998 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
10999 style='mso-element:field-separator'></span></span><![endif]--><span
\r
11000 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11001 text-underline:none'>57</span><span style='color:windowtext;display:none;
\r
11002 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
11003 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600330035000000</w:data>
\r
11004 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
11005 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11006 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
11007 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
11008 FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
11010 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
11011 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
11012 href="#_Toc235958636">Generic<span style='color:windowtext;display:none;
\r
11013 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11014 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
11015 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11016 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
11017 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11018 text-underline:none'> PAGEREF _Toc235958636 \h </span><span style='color:windowtext;
\r
11019 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11020 style='mso-element:field-separator'></span></span><![endif]--><span
\r
11021 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11022 text-underline:none'>57</span><span style='color:windowtext;display:none;
\r
11023 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
11024 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600330036000000</w:data>
\r
11025 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
11026 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11027 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
11028 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
11029 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
11031 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
11032 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
11033 href="#_Toc235958637">Conventions Regarding Filenames<span style='color:windowtext;
\r
11034 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11035 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
11036 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11037 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
11038 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11039 text-underline:none'> PAGEREF _Toc235958637 \h </span><span style='color:windowtext;
\r
11040 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11041 style='mso-element:field-separator'></span></span><![endif]--><span
\r
11042 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11043 text-underline:none'>57</span><span style='color:windowtext;display:none;
\r
11044 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
11045 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600330037000000</w:data>
\r
11046 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
11047 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11048 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
11049 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
11050 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
11052 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
11053 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
11054 href="#_Toc235958638">Identifying the Output files automatically<span
\r
11055 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11056 text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
11057 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11058 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
11059 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11060 text-underline:none'> PAGEREF _Toc235958638 \h </span><span style='color:windowtext;
\r
11061 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11062 style='mso-element:field-separator'></span></span><![endif]--><span
\r
11063 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11064 text-underline:none'>57</span><span style='color:windowtext;display:none;
\r
11065 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
11066 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600330038000000</w:data>
\r
11067 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
11068 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11069 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
11070 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
11071 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
11073 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
11074 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
11075 href="#_Toc235958639">-no_warning<span style='color:windowtext;display:none;
\r
11076 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11077 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
11078 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11079 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
11080 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11081 text-underline:none'> PAGEREF _Toc235958639 \h </span><span style='color:windowtext;
\r
11082 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11083 style='mso-element:field-separator'></span></span><![endif]--><span
\r
11084 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11085 text-underline:none'>57</span><span style='color:windowtext;display:none;
\r
11086 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
11087 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600330039000000</w:data>
\r
11088 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
11089 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11090 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
11091 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
11092 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
11094 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
11095 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
11096 href="#_Toc235958640">Alignments<span style='color:windowtext;display:none;
\r
11097 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11098 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
11099 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11100 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
11101 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11102 text-underline:none'> PAGEREF _Toc235958640 \h </span><span style='color:windowtext;
\r
11103 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11104 style='mso-element:field-separator'></span></span><![endif]--><span
\r
11105 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11106 text-underline:none'>57</span><span style='color:windowtext;display:none;
\r
11107 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
11108 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600340030000000</w:data>
\r
11109 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
11110 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11111 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
11112 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
11113 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
11115 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
11116 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
11117 href="#_Toc235958641">-outfile<span style='color:windowtext;display:none;
\r
11118 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11119 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
11120 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11121 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
11122 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11123 text-underline:none'> PAGEREF _Toc235958641 \h </span><span style='color:windowtext;
\r
11124 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11125 style='mso-element:field-separator'></span></span><![endif]--><span
\r
11126 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11127 text-underline:none'>57</span><span style='color:windowtext;display:none;
\r
11128 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
11129 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600340031000000</w:data>
\r
11130 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
11131 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11132 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
11133 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
11134 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
11136 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
11137 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
11138 href="#_Toc235958642">-output<span style='color:windowtext;display:none;
\r
11139 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11140 style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span
\r
11141 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11142 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
11143 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11144 text-underline:none'> PAGEREF _Toc235958642 \h </span><span style='color:windowtext;
\r
11145 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11146 style='mso-element:field-separator'></span></span><![endif]--><span
\r
11147 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11148 text-underline:none'>57</span><span style='color:windowtext;display:none;
\r
11149 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
11150 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600340032000000</w:data>
\r
11151 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
11152 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11153 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
11154 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
11155 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
11157 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
11158 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
11159 href="#_Toc235958643">-outseqweight<span style='color:windowtext;display:none;
\r
11160 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11161 style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span
\r
11162 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11163 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
11164 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11165 text-underline:none'> PAGEREF _Toc235958643 \h </span><span style='color:windowtext;
\r
11166 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11167 style='mso-element:field-separator'></span></span><![endif]--><span
\r
11168 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11169 text-underline:none'>58</span><span style='color:windowtext;display:none;
\r
11170 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
11171 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600340033000000</w:data>
\r
11172 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
11173 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11174 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
11175 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
11176 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
11178 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
11179 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
11180 href="#_Toc235958644">-case<span style='color:windowtext;display:none;
\r
11181 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11182 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
11183 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11184 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
11185 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11186 text-underline:none'> PAGEREF _Toc235958644 \h </span><span style='color:windowtext;
\r
11187 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11188 style='mso-element:field-separator'></span></span><![endif]--><span
\r
11189 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11190 text-underline:none'>58</span><span style='color:windowtext;display:none;
\r
11191 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
11192 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600340034000000</w:data>
\r
11193 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
11194 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11195 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
11196 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
11197 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
11199 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
11200 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
11201 href="#_Toc235958645">-cpu<span style='color:windowtext;display:none;
\r
11202 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11203 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
11204 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11205 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
11206 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11207 text-underline:none'> PAGEREF _Toc235958645 \h </span><span style='color:windowtext;
\r
11208 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11209 style='mso-element:field-separator'></span></span><![endif]--><span
\r
11210 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11211 text-underline:none'>58</span><span style='color:windowtext;display:none;
\r
11212 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
11213 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600340035000000</w:data>
\r
11214 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
11215 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11216 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
11217 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
11218 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
11220 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
11221 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
11222 href="#_Toc235958646">-outseqweight<span style='color:windowtext;display:none;
\r
11223 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11224 style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span
\r
11225 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11226 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
11227 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11228 text-underline:none'> PAGEREF _Toc235958646 \h </span><span style='color:windowtext;
\r
11229 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11230 style='mso-element:field-separator'></span></span><![endif]--><span
\r
11231 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11232 text-underline:none'>58</span><span style='color:windowtext;display:none;
\r
11233 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
11234 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600340036000000</w:data>
\r
11235 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
11236 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11237 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
11238 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
11239 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
11241 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
11242 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
11243 href="#_Toc235958647">-outorder [cw]<span style='color:windowtext;display:none;
\r
11244 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11245 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
11246 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11247 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
11248 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11249 text-underline:none'> PAGEREF _Toc235958647 \h </span><span style='color:windowtext;
\r
11250 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11251 style='mso-element:field-separator'></span></span><![endif]--><span
\r
11252 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11253 text-underline:none'>59</span><span style='color:windowtext;display:none;
\r
11254 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
11255 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600340037000000</w:data>
\r
11256 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
11257 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11258 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
11259 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
11260 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
11262 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
11263 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
11264 href="#_Toc235958648">-inorder [cw]<span style='color:windowtext;display:none;
\r
11265 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11266 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
11267 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11268 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
11269 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11270 text-underline:none'> PAGEREF _Toc235958648 \h </span><span style='color:windowtext;
\r
11271 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11272 style='mso-element:field-separator'></span></span><![endif]--><span
\r
11273 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11274 text-underline:none'>59</span><span style='color:windowtext;display:none;
\r
11275 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
11276 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600340038000000</w:data>
\r
11277 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
11278 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11279 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
11280 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
11281 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
11283 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
11284 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
11285 href="#_Toc235958649">-seqnos<span style='color:windowtext;display:none;
\r
11286 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11287 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
11288 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11289 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
11290 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11291 text-underline:none'> PAGEREF _Toc235958649 \h </span><span style='color:windowtext;
\r
11292 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11293 style='mso-element:field-separator'></span></span><![endif]--><span
\r
11294 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11295 text-underline:none'>59</span><span style='color:windowtext;display:none;
\r
11296 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
11297 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600340039000000</w:data>
\r
11298 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
11299 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11300 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
11301 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
11302 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
11304 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
11305 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
11306 href="#_Toc235958650">Libraries<span style='color:windowtext;display:none;
\r
11307 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11308 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
11309 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11310 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
11311 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11312 text-underline:none'> PAGEREF _Toc235958650 \h </span><span style='color:windowtext;
\r
11313 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11314 style='mso-element:field-separator'></span></span><![endif]--><span
\r
11315 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11316 text-underline:none'>59</span><span style='color:windowtext;display:none;
\r
11317 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
11318 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600350030000000</w:data>
\r
11319 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
11320 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11321 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
11322 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
11323 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
11325 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
11326 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
11327 href="#_Toc235958651">-out_lib<span style='color:windowtext;display:none;
\r
11328 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11329 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
11330 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11331 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
11332 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11333 text-underline:none'> PAGEREF _Toc235958651 \h </span><span style='color:windowtext;
\r
11334 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11335 style='mso-element:field-separator'></span></span><![endif]--><span
\r
11336 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11337 text-underline:none'>59</span><span style='color:windowtext;display:none;
\r
11338 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
11339 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600350031000000</w:data>
\r
11340 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
11341 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11342 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
11343 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
11344 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
11346 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
11347 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
11348 href="#_Toc235958652">-lib_only<span style='color:windowtext;display:none;
\r
11349 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11350 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
11351 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11352 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
11353 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11354 text-underline:none'> PAGEREF _Toc235958652 \h </span><span style='color:windowtext;
\r
11355 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11356 style='mso-element:field-separator'></span></span><![endif]--><span
\r
11357 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11358 text-underline:none'>59</span><span style='color:windowtext;display:none;
\r
11359 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
11360 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600350032000000</w:data>
\r
11361 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
11362 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11363 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
11364 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
11365 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
11367 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
11368 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
11369 href="#_Toc235958653">Trees<span style='color:windowtext;display:none;
\r
11370 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11371 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
11372 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11373 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
11374 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11375 text-underline:none'> PAGEREF _Toc235958653 \h </span><span style='color:windowtext;
\r
11376 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11377 style='mso-element:field-separator'></span></span><![endif]--><span
\r
11378 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11379 text-underline:none'>60</span><span style='color:windowtext;display:none;
\r
11380 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
11381 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600350033000000</w:data>
\r
11382 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
11383 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11384 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
11385 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
11386 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
11388 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
11389 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
11390 href="#_Toc235958654">-newtree<span style='color:windowtext;display:none;
\r
11391 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11392 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
11393 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11394 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
11395 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11396 text-underline:none'> PAGEREF _Toc235958654 \h </span><span style='color:windowtext;
\r
11397 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11398 style='mso-element:field-separator'></span></span><![endif]--><span
\r
11399 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11400 text-underline:none'>60</span><span style='color:windowtext;display:none;
\r
11401 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
11402 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600350034000000</w:data>
\r
11403 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
11404 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11405 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
11406 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
11407 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
11409 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
\r
11410 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
11411 href="#_Toc235958655">Reliability Estimation<span style='color:windowtext;
\r
11412 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11413 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
11414 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11415 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
11416 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11417 text-underline:none'> PAGEREF _Toc235958655 \h </span><span style='color:windowtext;
\r
11418 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11419 style='mso-element:field-separator'></span></span><![endif]--><span
\r
11420 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11421 text-underline:none'>60</span><span style='color:windowtext;display:none;
\r
11422 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
11423 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600350035000000</w:data>
\r
11424 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
11425 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11426 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
11427 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
11428 FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
11430 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
11431 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
11432 href="#_Toc235958656">CORE Computation<span style='color:windowtext;display:
\r
11433 none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11434 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
11435 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11436 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
11437 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11438 text-underline:none'> PAGEREF _Toc235958656 \h </span><span style='color:windowtext;
\r
11439 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11440 style='mso-element:field-separator'></span></span><![endif]--><span
\r
11441 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11442 text-underline:none'>60</span><span style='color:windowtext;display:none;
\r
11443 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
11444 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600350036000000</w:data>
\r
11445 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
11446 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11447 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
11448 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
11449 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
11451 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
11452 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
11453 href="#_Toc235958657">-evaluate_mode<span style='color:windowtext;display:none;
\r
11454 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11455 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
11456 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11457 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
11458 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11459 text-underline:none'> PAGEREF _Toc235958657 \h </span><span style='color:windowtext;
\r
11460 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11461 style='mso-element:field-separator'></span></span><![endif]--><span
\r
11462 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11463 text-underline:none'>60</span><span style='color:windowtext;display:none;
\r
11464 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
11465 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600350037000000</w:data>
\r
11466 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
11467 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11468 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
11469 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
11470 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
11472 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
\r
11473 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
11474 href="#_Toc235958658">Generic Output<span style='color:windowtext;display:none;
\r
11475 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11476 style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span
\r
11477 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11478 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
11479 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11480 text-underline:none'> PAGEREF _Toc235958658 \h </span><span style='color:windowtext;
\r
11481 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11482 style='mso-element:field-separator'></span></span><![endif]--><span
\r
11483 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11484 text-underline:none'>61</span><span style='color:windowtext;display:none;
\r
11485 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
11486 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600350038000000</w:data>
\r
11487 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
11488 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11489 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
11490 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
11491 FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
11493 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
11494 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
11495 href="#_Toc235958659">-run_name<span style='color:windowtext;display:none;
\r
11496 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11497 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
11498 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11499 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
11500 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11501 text-underline:none'> PAGEREF _Toc235958659 \h </span><span style='color:windowtext;
\r
11502 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11503 style='mso-element:field-separator'></span></span><![endif]--><span
\r
11504 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11505 text-underline:none'>61</span><span style='color:windowtext;display:none;
\r
11506 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
11507 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600350039000000</w:data>
\r
11508 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
11509 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11510 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
11511 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
11512 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
11514 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
11515 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
11516 href="#_Toc235958660">-quiet<span style='color:windowtext;display:none;
\r
11517 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11518 style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span
\r
11519 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11520 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
11521 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11522 text-underline:none'> PAGEREF _Toc235958660 \h </span><span style='color:windowtext;
\r
11523 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11524 style='mso-element:field-separator'></span></span><![endif]--><span
\r
11525 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11526 text-underline:none'>61</span><span style='color:windowtext;display:none;
\r
11527 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
11528 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600360030000000</w:data>
\r
11529 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
11530 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11531 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
11532 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
11533 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
11535 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
11536 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
11537 href="#_Toc235958661">-align [CW]<span style='color:windowtext;display:none;
\r
11538 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11539 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
11540 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11541 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
11542 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11543 text-underline:none'> PAGEREF _Toc235958661 \h </span><span style='color:windowtext;
\r
11544 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11545 style='mso-element:field-separator'></span></span><![endif]--><span
\r
11546 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11547 text-underline:none'>61</span><span style='color:windowtext;display:none;
\r
11548 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
11549 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600360031000000</w:data>
\r
11550 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
11551 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11552 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
11553 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
11554 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
11556 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
\r
11557 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
11558 href="#_Toc235958662">APDB, iRMSD and tRMSD Parameters<span style='color:windowtext;
\r
11559 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11560 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
11561 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11562 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
11563 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11564 text-underline:none'> PAGEREF _Toc235958662 \h </span><span style='color:windowtext;
\r
11565 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11566 style='mso-element:field-separator'></span></span><![endif]--><span
\r
11567 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11568 text-underline:none'>61</span><span style='color:windowtext;display:none;
\r
11569 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
11570 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600360032000000</w:data>
\r
11571 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
11572 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11573 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
11574 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
11575 FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
11577 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
11578 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
11579 href="#_Toc235958663">-quiet [Same as T-Coffee]<span style='color:windowtext;
\r
11580 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11581 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
11582 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11583 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
11584 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11585 text-underline:none'> PAGEREF _Toc235958663 \h </span><span style='color:windowtext;
\r
11586 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11587 style='mso-element:field-separator'></span></span><![endif]--><span
\r
11588 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11589 text-underline:none'>61</span><span style='color:windowtext;display:none;
\r
11590 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
11591 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600360033000000</w:data>
\r
11592 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
11593 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11594 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
11595 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
11596 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
11598 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
11599 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
11600 href="#_Toc235958664">-run_name [Same as T-Coffee]<span style='color:windowtext;
\r
11601 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11602 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
11603 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11604 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
11605 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11606 text-underline:none'> PAGEREF _Toc235958664 \h </span><span style='color:windowtext;
\r
11607 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11608 style='mso-element:field-separator'></span></span><![endif]--><span
\r
11609 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11610 text-underline:none'>61</span><span style='color:windowtext;display:none;
\r
11611 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
11612 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600360034000000</w:data>
\r
11613 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
11614 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11615 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
11616 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
11617 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
11619 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
11620 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
11621 href="#_Toc235958665">-aln<span style='color:windowtext;display:none;
\r
11622 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11623 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
11624 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11625 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
11626 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11627 text-underline:none'> PAGEREF _Toc235958665 \h </span><span style='color:windowtext;
\r
11628 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11629 style='mso-element:field-separator'></span></span><![endif]--><span
\r
11630 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11631 text-underline:none'>61</span><span style='color:windowtext;display:none;
\r
11632 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
11633 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600360035000000</w:data>
\r
11634 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
11635 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11636 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
11637 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
11638 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
11640 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
11641 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
11642 href="#_Toc235958666">-n_excluded_nb<span style='color:windowtext;display:none;
\r
11643 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11644 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
11645 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11646 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
11647 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11648 text-underline:none'> PAGEREF _Toc235958666 \h </span><span style='color:windowtext;
\r
11649 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11650 style='mso-element:field-separator'></span></span><![endif]--><span
\r
11651 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11652 text-underline:none'>62</span><span style='color:windowtext;display:none;
\r
11653 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
11654 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600360036000000</w:data>
\r
11655 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
11656 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11657 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
11658 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
11659 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
11661 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
11662 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
11663 href="#_Toc235958667">-maximum_distance<span style='color:windowtext;
\r
11664 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11665 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
11666 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11667 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
11668 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11669 text-underline:none'> PAGEREF _Toc235958667 \h </span><span style='color:windowtext;
\r
11670 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11671 style='mso-element:field-separator'></span></span><![endif]--><span
\r
11672 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11673 text-underline:none'>62</span><span style='color:windowtext;display:none;
\r
11674 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
11675 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600360037000000</w:data>
\r
11676 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
11677 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11678 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
11679 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
11680 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
11682 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
11683 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
11684 href="#_Toc235958668">-similarity_threshold<span style='color:windowtext;
\r
11685 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11686 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
11687 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11688 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
11689 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11690 text-underline:none'> PAGEREF _Toc235958668 \h </span><span style='color:windowtext;
\r
11691 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11692 style='mso-element:field-separator'></span></span><![endif]--><span
\r
11693 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11694 text-underline:none'>62</span><span style='color:windowtext;display:none;
\r
11695 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
11696 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600360038000000</w:data>
\r
11697 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
11698 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11699 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
11700 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
11701 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
11703 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
11704 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
11705 href="#_Toc235958669">-local_mode<span style='color:windowtext;display:none;
\r
11706 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11707 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
11708 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11709 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
11710 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11711 text-underline:none'> PAGEREF _Toc235958669 \h </span><span style='color:windowtext;
\r
11712 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11713 style='mso-element:field-separator'></span></span><![endif]--><span
\r
11714 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11715 text-underline:none'>62</span><span style='color:windowtext;display:none;
\r
11716 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
11717 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600360039000000</w:data>
\r
11718 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
11719 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11720 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
11721 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
11722 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
11724 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
11725 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
11726 href="#_Toc235958670">-filter<span style='color:windowtext;display:none;
\r
11727 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11728 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
11729 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11730 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
11731 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11732 text-underline:none'> PAGEREF _Toc235958670 \h </span><span style='color:windowtext;
\r
11733 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11734 style='mso-element:field-separator'></span></span><![endif]--><span
\r
11735 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11736 text-underline:none'>62</span><span style='color:windowtext;display:none;
\r
11737 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
11738 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600370030000000</w:data>
\r
11739 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
11740 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11741 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
11742 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
11743 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
11745 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
11746 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
11747 href="#_Toc235958671">-print_rapdb [Unsupported]<span style='color:windowtext;
\r
11748 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11749 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
11750 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11751 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
11752 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11753 text-underline:none'> PAGEREF _Toc235958671 \h </span><span style='color:windowtext;
\r
11754 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11755 style='mso-element:field-separator'></span></span><![endif]--><span
\r
11756 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11757 text-underline:none'>63</span><span style='color:windowtext;display:none;
\r
11758 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
11759 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600370031000000</w:data>
\r
11760 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
11761 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11762 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
11763 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
11764 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
11766 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
11767 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
11768 href="#_Toc235958672">-outfile [Same as T-Coffee]<span style='color:windowtext;
\r
11769 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11770 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
11771 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11772 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
11773 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11774 text-underline:none'> PAGEREF _Toc235958672 \h </span><span style='color:windowtext;
\r
11775 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11776 style='mso-element:field-separator'></span></span><![endif]--><span
\r
11777 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11778 text-underline:none'>63</span><span style='color:windowtext;display:none;
\r
11779 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
11780 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600370032000000</w:data>
\r
11781 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
11782 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11783 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
11784 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
11785 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
11787 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
11788 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
11789 href="#_Toc235958673">-color_mode<span style='color:windowtext;display:none;
\r
11790 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11791 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
11792 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11793 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
11794 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11795 text-underline:none'> PAGEREF _Toc235958673 \h </span><span style='color:windowtext;
\r
11796 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11797 style='mso-element:field-separator'></span></span><![endif]--><span
\r
11798 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11799 text-underline:none'>63</span><span style='color:windowtext;display:none;
\r
11800 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
11801 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600370033000000</w:data>
\r
11802 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
11803 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11804 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
11805 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
11806 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
11808 <p class=MsoToc1 style='tab-stops:right dotted 474.85pt'><span
\r
11809 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
11810 href="#_Toc235958674">Building a Server<span style='color:black;display:none;
\r
11811 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11812 style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span
\r
11813 style='color:black;display:none;mso-hide:screen;text-decoration:none;
\r
11814 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
11815 style='color:black;display:none;mso-hide:screen;text-decoration:none;
\r
11816 text-underline:none'> PAGEREF _Toc235958674 \h </span><span style='color:black;
\r
11817 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11818 style='mso-element:field-separator'></span></span><![endif]--><span
\r
11819 style='color:black;display:none;mso-hide:screen;text-decoration:none;
\r
11820 text-underline:none'>64</span><span style='color:black;display:none;mso-hide:
\r
11821 screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
11822 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600370034000000</w:data>
\r
11823 </xml><![endif]--></span><!--[if supportFields]><span style='color:black;
\r
11824 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11825 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
11826 style='font-size:12.0pt;font-family:"Times New Roman";mso-fareast-font-family:
\r
11827 "MS Mincho";color:windowtext;mso-ansi-language:FR;mso-fareast-language:JA;
\r
11828 font-weight:normal;mso-bidi-font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
11830 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
11831 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
11832 href="#_Toc235958675">Environment Variables<span style='color:windowtext;
\r
11833 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11834 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
11835 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11836 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
11837 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11838 text-underline:none'> PAGEREF _Toc235958675 \h </span><span style='color:windowtext;
\r
11839 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11840 style='mso-element:field-separator'></span></span><![endif]--><span
\r
11841 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11842 text-underline:none'>64</span><span style='color:windowtext;display:none;
\r
11843 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
11844 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600370035000000</w:data>
\r
11845 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
11846 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11847 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
11848 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
11849 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
11851 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
11852 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
11853 href="#_Toc235958676">Output of the .dnd file.<span style='color:windowtext;
\r
11854 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11855 style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span
\r
11856 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11857 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
11858 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11859 text-underline:none'> PAGEREF _Toc235958676 \h </span><span style='color:windowtext;
\r
11860 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11861 style='mso-element:field-separator'></span></span><![endif]--><span
\r
11862 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11863 text-underline:none'>65</span><span style='color:windowtext;display:none;
\r
11864 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
11865 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600370036000000</w:data>
\r
11866 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
11867 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11868 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
11869 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
11870 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
11872 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
11873 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
11874 href="#_Toc235958677">Permissions<span style='color:windowtext;display:none;
\r
11875 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11876 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
11877 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11878 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
11879 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11880 text-underline:none'> PAGEREF _Toc235958677 \h </span><span style='color:windowtext;
\r
11881 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11882 style='mso-element:field-separator'></span></span><![endif]--><span
\r
11883 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11884 text-underline:none'>65</span><span style='color:windowtext;display:none;
\r
11885 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
11886 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600370037000000</w:data>
\r
11887 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
11888 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11889 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
11890 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
11891 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
11893 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
11894 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
11895 href="#_Toc235958678">Other Programs<span style='color:windowtext;display:none;
\r
11896 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11897 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
11898 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11899 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
11900 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11901 text-underline:none'> PAGEREF _Toc235958678 \h </span><span style='color:windowtext;
\r
11902 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11903 style='mso-element:field-separator'></span></span><![endif]--><span
\r
11904 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11905 text-underline:none'>65</span><span style='color:windowtext;display:none;
\r
11906 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
11907 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600370038000000</w:data>
\r
11908 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
11909 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11910 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
11911 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
11912 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
11914 <p class=MsoToc1 style='tab-stops:right dotted 474.85pt'><span
\r
11915 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
11916 href="#_Toc235958679">Formats<span style='color:black;display:none;mso-hide:
\r
11917 screen;text-decoration:none;text-underline:none'><span style='mso-tab-count:
\r
11918 1 dotted'>. </span></span><!--[if supportFields]><span style='color:black;
\r
11919 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11920 style='mso-element:field-begin'></span></span><span style='color:black;
\r
11921 display:none;mso-hide:screen;text-decoration:none;text-underline:none'> PAGEREF
\r
11922 _Toc235958679 \h </span><span style='color:black;display:none;mso-hide:screen;
\r
11923 text-decoration:none;text-underline:none'><span style='mso-element:field-separator'></span></span><![endif]--><span
\r
11924 style='color:black;display:none;mso-hide:screen;text-decoration:none;
\r
11925 text-underline:none'>66</span><span style='color:black;display:none;mso-hide:
\r
11926 screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
11927 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600370039000000</w:data>
\r
11928 </xml><![endif]--></span><!--[if supportFields]><span style='color:black;
\r
11929 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11930 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
11931 style='font-size:12.0pt;font-family:"Times New Roman";mso-fareast-font-family:
\r
11932 "MS Mincho";color:windowtext;mso-ansi-language:FR;mso-fareast-language:JA;
\r
11933 font-weight:normal;mso-bidi-font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
11935 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
\r
11936 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
11937 href="#_Toc235958680">Parameter files<span style='color:windowtext;display:
\r
11938 none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11939 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
11940 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11941 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
11942 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11943 text-underline:none'> PAGEREF _Toc235958680 \h </span><span style='color:windowtext;
\r
11944 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11945 style='mso-element:field-separator'></span></span><![endif]--><span
\r
11946 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11947 text-underline:none'>66</span><span style='color:windowtext;display:none;
\r
11948 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
11949 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600380030000000</w:data>
\r
11950 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
11951 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11952 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
11953 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
11954 FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
11956 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
\r
11957 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
11958 href="#_Toc235958681">Sequence Name Handling<span style='color:windowtext;
\r
11959 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11960 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
11961 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11962 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
11963 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11964 text-underline:none'> PAGEREF _Toc235958681 \h </span><span style='color:windowtext;
\r
11965 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11966 style='mso-element:field-separator'></span></span><![endif]--><span
\r
11967 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11968 text-underline:none'>66</span><span style='color:windowtext;display:none;
\r
11969 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
11970 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600380031000000</w:data>
\r
11971 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
11972 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11973 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
11974 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
11975 FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
11977 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
\r
11978 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
11979 href="#_Toc235958682">Automatic Format Recognition<span style='color:windowtext;
\r
11980 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11981 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
11982 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11983 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
11984 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11985 text-underline:none'> PAGEREF _Toc235958682 \h </span><span style='color:windowtext;
\r
11986 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11987 style='mso-element:field-separator'></span></span><![endif]--><span
\r
11988 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
11989 text-underline:none'>67</span><span style='color:windowtext;display:none;
\r
11990 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
11991 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600380032000000</w:data>
\r
11992 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
11993 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
11994 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
11995 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
11996 FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
11998 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
\r
11999 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
12000 href="#_Toc235958683">Structures<span style='color:windowtext;display:none;
\r
12001 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
12002 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
12003 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
12004 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
12005 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
12006 text-underline:none'> PAGEREF _Toc235958683 \h </span><span style='color:windowtext;
\r
12007 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
12008 style='mso-element:field-separator'></span></span><![endif]--><span
\r
12009 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
12010 text-underline:none'>67</span><span style='color:windowtext;display:none;
\r
12011 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
12012 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600380033000000</w:data>
\r
12013 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
12014 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
12015 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
12016 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
12017 FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
12019 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
\r
12020 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
12021 href="#_Toc235958684">RNA Structures<span style='color:windowtext;display:none;
\r
12022 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
12023 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
12024 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
12025 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
12026 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
12027 text-underline:none'> PAGEREF _Toc235958684 \h </span><span style='color:windowtext;
\r
12028 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
12029 style='mso-element:field-separator'></span></span><![endif]--><span
\r
12030 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
12031 text-underline:none'>67</span><span style='color:windowtext;display:none;
\r
12032 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
12033 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600380034000000</w:data>
\r
12034 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
12035 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
12036 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
12037 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
12038 FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
12040 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
\r
12041 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
12042 href="#_Toc235958685">Sequences<span style='color:windowtext;display:none;
\r
12043 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
12044 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
12045 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
12046 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
12047 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
12048 text-underline:none'> PAGEREF _Toc235958685 \h </span><span style='color:windowtext;
\r
12049 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
12050 style='mso-element:field-separator'></span></span><![endif]--><span
\r
12051 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
12052 text-underline:none'>67</span><span style='color:windowtext;display:none;
\r
12053 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
12054 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600380035000000</w:data>
\r
12055 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
12056 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
12057 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
12058 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
12059 FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
12061 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
\r
12062 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
12063 href="#_Toc235958686">Alignments<span style='color:windowtext;display:none;
\r
12064 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
12065 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
12066 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
12067 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
12068 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
12069 text-underline:none'> PAGEREF _Toc235958686 \h </span><span style='color:windowtext;
\r
12070 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
12071 style='mso-element:field-separator'></span></span><![endif]--><span
\r
12072 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
12073 text-underline:none'>67</span><span style='color:windowtext;display:none;
\r
12074 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
12075 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600380036000000</w:data>
\r
12076 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
12077 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
12078 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
12079 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
12080 FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
12082 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
\r
12083 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
12084 href="#_Toc235958687">Libraries<span style='color:windowtext;display:none;
\r
12085 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
12086 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
12087 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
12088 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
12089 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
12090 text-underline:none'> PAGEREF _Toc235958687 \h </span><span style='color:windowtext;
\r
12091 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
12092 style='mso-element:field-separator'></span></span><![endif]--><span
\r
12093 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
12094 text-underline:none'>68</span><span style='color:windowtext;display:none;
\r
12095 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
12096 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600380037000000</w:data>
\r
12097 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
12098 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
12099 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
12100 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
12101 FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
12103 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
12104 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
12105 href="#_Toc235958688">T-COFFEE_LIB_FORMAT_01<span style='color:windowtext;
\r
12106 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
12107 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
12108 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
12109 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
12110 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
12111 text-underline:none'> PAGEREF _Toc235958688 \h </span><span style='color:windowtext;
\r
12112 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
12113 style='mso-element:field-separator'></span></span><![endif]--><span
\r
12114 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
12115 text-underline:none'>68</span><span style='color:windowtext;display:none;
\r
12116 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
12117 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600380038000000</w:data>
\r
12118 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
12119 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
12120 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
12121 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
12122 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
12124 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
12125 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
12126 href="#_Toc235958689">T-COFFEE_LIB_FORMAT_02<span style='color:windowtext;
\r
12127 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
12128 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
12129 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
12130 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
12131 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
12132 text-underline:none'> PAGEREF _Toc235958689 \h </span><span style='color:windowtext;
\r
12133 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
12134 style='mso-element:field-separator'></span></span><![endif]--><span
\r
12135 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
12136 text-underline:none'>69</span><span style='color:windowtext;display:none;
\r
12137 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
12138 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600380039000000</w:data>
\r
12139 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
12140 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
12141 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
12142 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
12143 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
12145 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
\r
12146 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
12147 href="#_Toc235958690">Library List<span style='color:windowtext;display:none;
\r
12148 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
12149 style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span
\r
12150 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
12151 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
12152 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
12153 text-underline:none'> PAGEREF _Toc235958690 \h </span><span style='color:windowtext;
\r
12154 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
12155 style='mso-element:field-separator'></span></span><![endif]--><span
\r
12156 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
12157 text-underline:none'>69</span><span style='color:windowtext;display:none;
\r
12158 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
12159 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600390030000000</w:data>
\r
12160 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
12161 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
12162 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
12163 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
12164 FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
12166 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
\r
12167 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
12168 href="#_Toc235958691">Substitution matrices.<span style='color:windowtext;
\r
12169 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
12170 style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span
\r
12171 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
12172 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
12173 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
12174 text-underline:none'> PAGEREF _Toc235958691 \h </span><span style='color:windowtext;
\r
12175 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
12176 style='mso-element:field-separator'></span></span><![endif]--><span
\r
12177 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
12178 text-underline:none'>69</span><span style='color:windowtext;display:none;
\r
12179 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
12180 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600390031000000</w:data>
\r
12181 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
12182 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
12183 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
12184 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
12185 FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
12187 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
12188 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
12189 href="#_Toc235958692">ClustalW Style [Deprecated]<span style='color:windowtext;
\r
12190 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
12191 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
12192 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
12193 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
12194 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
12195 text-underline:none'> PAGEREF _Toc235958692 \h </span><span style='color:windowtext;
\r
12196 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
12197 style='mso-element:field-separator'></span></span><![endif]--><span
\r
12198 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
12199 text-underline:none'>69</span><span style='color:windowtext;display:none;
\r
12200 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
12201 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600390032000000</w:data>
\r
12202 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
12203 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
12204 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
12205 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
12206 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
12208 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
12209 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
12210 href="#_Toc235958693">BLAST Format [Recommended]<span style='color:windowtext;
\r
12211 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
12212 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
12213 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
12214 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
12215 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
12216 text-underline:none'> PAGEREF _Toc235958693 \h </span><span style='color:windowtext;
\r
12217 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
12218 style='mso-element:field-separator'></span></span><![endif]--><span
\r
12219 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
12220 text-underline:none'>70</span><span style='color:windowtext;display:none;
\r
12221 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
12222 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600390033000000</w:data>
\r
12223 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
12224 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
12225 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
12226 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
12227 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
12229 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
\r
12230 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
12231 href="#_Toc235958694">Sequences Weights<span style='color:windowtext;
\r
12232 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
12233 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
12234 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
12235 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
12236 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
12237 text-underline:none'> PAGEREF _Toc235958694 \h </span><span style='color:windowtext;
\r
12238 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
12239 style='mso-element:field-separator'></span></span><![endif]--><span
\r
12240 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
12241 text-underline:none'>70</span><span style='color:windowtext;display:none;
\r
12242 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
12243 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600390034000000</w:data>
\r
12244 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
12245 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
12246 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
12247 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
12248 FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
12250 <p class=MsoToc1 style='tab-stops:right dotted 474.85pt'><span
\r
12251 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
12252 href="#_Toc235958695">Known Problems<span style='color:black;display:none;
\r
12253 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
12254 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
12255 style='color:black;display:none;mso-hide:screen;text-decoration:none;
\r
12256 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
12257 style='color:black;display:none;mso-hide:screen;text-decoration:none;
\r
12258 text-underline:none'> PAGEREF _Toc235958695 \h </span><span style='color:black;
\r
12259 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
12260 style='mso-element:field-separator'></span></span><![endif]--><span
\r
12261 style='color:black;display:none;mso-hide:screen;text-decoration:none;
\r
12262 text-underline:none'>71</span><span style='color:black;display:none;mso-hide:
\r
12263 screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
12264 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600390035000000</w:data>
\r
12265 </xml><![endif]--></span><!--[if supportFields]><span style='color:black;
\r
12266 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
12267 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
12268 style='font-size:12.0pt;font-family:"Times New Roman";mso-fareast-font-family:
\r
12269 "MS Mincho";color:windowtext;mso-ansi-language:FR;mso-fareast-language:JA;
\r
12270 font-weight:normal;mso-bidi-font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
12272 <p class=MsoToc1 style='tab-stops:right dotted 474.85pt'><span
\r
12273 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
12274 href="#_Toc235958696">Technical Notes<span style='color:black;display:none;
\r
12275 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
12276 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
12277 style='color:black;display:none;mso-hide:screen;text-decoration:none;
\r
12278 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
12279 style='color:black;display:none;mso-hide:screen;text-decoration:none;
\r
12280 text-underline:none'> PAGEREF _Toc235958696 \h </span><span style='color:black;
\r
12281 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
12282 style='mso-element:field-separator'></span></span><![endif]--><span
\r
12283 style='color:black;display:none;mso-hide:screen;text-decoration:none;
\r
12284 text-underline:none'>72</span><span style='color:black;display:none;mso-hide:
\r
12285 screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
12286 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600390036000000</w:data>
\r
12287 </xml><![endif]--></span><!--[if supportFields]><span style='color:black;
\r
12288 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
12289 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
12290 style='font-size:12.0pt;font-family:"Times New Roman";mso-fareast-font-family:
\r
12291 "MS Mincho";color:windowtext;mso-ansi-language:FR;mso-fareast-language:JA;
\r
12292 font-weight:normal;mso-bidi-font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
12294 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
\r
12295 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
12296 href="#_Toc235958697">Development<span style='color:windowtext;display:none;
\r
12297 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
12298 style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span
\r
12299 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
12300 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
12301 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
12302 text-underline:none'> PAGEREF _Toc235958697 \h </span><span style='color:windowtext;
\r
12303 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
12304 style='mso-element:field-separator'></span></span><![endif]--><span
\r
12305 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
12306 text-underline:none'>72</span><span style='color:windowtext;display:none;
\r
12307 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
12308 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600390037000000</w:data>
\r
12309 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
12310 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
12311 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
12312 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
12313 FR;mso-fareast-language:JA;font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
12315 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
\r
12316 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
12317 href="#_Toc235958698">Command Line List<span style='color:windowtext;
\r
12318 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
12319 style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span
\r
12320 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
12321 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
12322 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
12323 text-underline:none'> PAGEREF _Toc235958698 \h </span><span style='color:windowtext;
\r
12324 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
12325 style='mso-element:field-separator'></span></span><![endif]--><span
\r
12326 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
12327 text-underline:none'>72</span><span style='color:windowtext;display:none;
\r
12328 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
12329 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600390038000000</w:data>
\r
12330 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
12331 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
12332 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
12333 style='font-size:12.0pt;mso-fareast-font-family:"MS Mincho";mso-ansi-language:
\r
12334 FR;mso-fareast-language:JA;font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
12336 <p class=MsoToc1 style='tab-stops:right dotted 474.85pt'><span
\r
12337 class=MsoHyperlink><span lang=EN-US style='mso-no-proof:yes'><a
\r
12338 href="#_Toc235958699">To Do
\85<span style='color:black;display:none;mso-hide:
\r
12339 screen;text-decoration:none;text-underline:none'><span style='mso-tab-count:
\r
12340 1 dotted'>.. </span></span><!--[if supportFields]><span style='color:black;
\r
12341 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
12342 style='mso-element:field-begin'></span></span><span style='color:black;
\r
12343 display:none;mso-hide:screen;text-decoration:none;text-underline:none'> PAGEREF
\r
12344 _Toc235958699 \h </span><span style='color:black;display:none;mso-hide:screen;
\r
12345 text-decoration:none;text-underline:none'><span style='mso-element:field-separator'></span></span><![endif]--><span
\r
12346 style='color:black;display:none;mso-hide:screen;text-decoration:none;
\r
12347 text-underline:none'>74</span><span style='color:black;display:none;mso-hide:
\r
12348 screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
12349 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003200330035003900350038003600390039000000</w:data>
\r
12350 </xml><![endif]--></span><!--[if supportFields]><span style='color:black;
\r
12351 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
12352 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
12353 style='font-size:12.0pt;font-family:"Times New Roman";mso-fareast-font-family:
\r
12354 "MS Mincho";color:windowtext;mso-ansi-language:FR;mso-fareast-language:JA;
\r
12355 font-weight:normal;mso-bidi-font-style:normal;mso-no-proof:yes'><o:p></o:p></span></p>
\r
12357 <p class=MsoNormal><!--[if supportFields]><i><span lang=EN-US style='font-size:
\r
12358 11.0pt;font-family:"Times New Roman"'><span style='mso-element:field-end'></span></span></i><![endif]--></p>
\r
12362 <span lang=EN-US style='font-size:8.0pt;mso-bidi-font-size:10.0pt;font-family:
\r
12363 Garamond;mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:"Times New Roman";
\r
12364 mso-ansi-language:EN-US;mso-fareast-language:EN-US;mso-bidi-language:AR-SA'><br
\r
12365 clear=all style='page-break-before:auto;mso-break-type:section-break'>
\r
12368 <div class=Section4>
\r
12370 <div style='mso-element:para-border-div;border:solid windowtext 3.0pt;
\r
12371 padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#CCCCCC;margin-left:0mm;margin-right:
\r
12374 <p class=ChapterTitle><a name="_Toc235958452"></a><a name="_Toc102494650"></a><a
\r
12375 name="_Toc101065185"><span style='mso-bookmark:_Toc102494650'><span
\r
12376 style='mso-bookmark:_Toc235958452'><span lang=EN-US>License and Terms of Use</span></span></span></a></p>
\r
12380 <p class=MyNormal><span lang=AF><o:p> </o:p></span></p>
\r
12382 <h2><a name="_Toc235958453"></a><a name="_Toc102494651"></a><a
\r
12383 name="_Toc102494275"><span style='mso-bookmark:_Toc102494651'><span
\r
12384 style='mso-bookmark:_Toc235958453'><span lang=EN-US>T-Coffee is distributed
\r
12385 under the Gnu Public License</span></span></span></a></h2>
\r
12387 <p class=MyNormal><span lang=AF><o:p> </o:p></span></p>
\r
12389 <p class=MyNormal><span lang=AF>Please make sure you have agreed with the terms
\r
12390 of the license attached to the package before using the T-Coffee package or its
\r
12391 documentation. T-Coffee is a freeware open source distributed under a GPL license.
\r
12392 This means that there are very little restrictions to its use, either in an
\r
12393 academic or a non academic environment.</span></p>
\r
12395 <h2><a name="_Toc235958454"></a><a name="_Toc102494652"></a><a
\r
12396 name="_Toc102494276"><span style='mso-bookmark:_Toc102494652'><span
\r
12397 style='mso-bookmark:_Toc235958454'><span lang=EN-US>T-Coffee code can be
\r
12398 re-used freely</span></span></span></a></h2>
\r
12400 <p class=MyNormal><span lang=AF>Our philosophy is that code is meant to be re-used,
\r
12401 including ours. No permission is needed for the cut and paste of a few
\r
12402 functions, although we are always happy to receive pieces of improved code.</span></p>
\r
12404 <h2><a name="_Toc102494653"></a><a name="_Toc101065186"></a><a
\r
12405 name="_Toc235958455"><span style='mso-bookmark:_Toc101065186'><span
\r
12406 style='mso-bookmark:_Toc102494653'><span lang=EN-US>T-Coffee can be
\r
12407 incorporated in most pipelines: Plug-in/Plug-out
\85</span></span></span></a><span
\r
12408 style='mso-bookmark:_Toc101065186'><span style='mso-bookmark:_Toc102494653'></span></span></h2>
\r
12410 <p class=MyNormal><span style='mso-bookmark:_Toc101065186'><span
\r
12411 style='mso-bookmark:_Toc102494653'><span lang=AF>Our philosophy is to insure
\r
12412 that as many methods as possible can be used as plug-ins within T-Coffee.
\r
12413 Likewise, we will give as much support as possible to anyone wishing to turn
\r
12414 T-Coffee into a plug-in for another method. For more details on how to do this,
\r
12415 see the plug-in and the plug-out sections of the Tutorial Manual.</span></span></span></p>
\r
12417 <p class=MyNormal><span style='mso-bookmark:_Toc101065186'><span
\r
12418 style='mso-bookmark:_Toc102494653'><span lang=AF>Again, you do not need our
\r
12419 permission to either use T-Coffee (or your method as a plug-in/out) but if you
\r
12420 let us know, we will insure the stability of T-Coffee within your system
\r
12421 through future releases. </span></span></span></p>
\r
12423 <p class=MyNormal><span style='mso-bookmark:_Toc101065186'><span
\r
12424 style='mso-bookmark:_Toc102494653'><span lang=AF>The current license only
\r
12425 allows for the incorporation of T-Coffee in non-commercial pipelines (i.e.
\r
12426 where you do not sell the pipeline, or access to it). If your pipeline is
\r
12427 commercial, please get in touch with us. </span></span></span></p>
\r
12429 <p class=MyNormal><span style='mso-bookmark:_Toc101065186'><span
\r
12430 style='mso-bookmark:_Toc102494653'><span lang=AF><o:p> </o:p></span></span></span></p>
\r
12432 <div style='mso-element:para-border-div;border:solid windowtext 3.0pt;
\r
12433 padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#CCCCCC;margin-left:0mm;margin-right:
\r
12436 <p class=ChapterTitle><span style='mso-bookmark:_Toc101065186'><span
\r
12437 style='mso-bookmark:_Toc102494653'><a name="_Toc235958456"><span lang=EN-US>Addresses
\r
12438 and Contacts</span></a></span></span><span style='mso-bookmark:_Toc235958456'></span><span
\r
12439 style='mso-bookmark:_Toc102494653'></span><span style='mso-bookmark:_Toc101065186'></span><span
\r
12440 lang=EN-US style='font-size:98.0pt;mso-bidi-font-size:48.0pt'><o:p></o:p></span></p>
\r
12444 <h2><a name="_Toc235958457"><span lang=EN-US>Contributors</span></a></h2>
\r
12446 <p class=MsoBodyText><span lang=EN-US>T-coffee is developed, maintained,
\r
12447 monitored, used and debugged by a dedicated team that include or have included:</span></p>
\r
12449 <p class=MsoBodyText><span lang=EN-US><span style='mso-tab-count:1'> </span>Cédric
\r
12450 Notredame, Fabrice Armougom, Des Higgins, Sebastien Moretti, Orla O
\92Sullivan. Eamon
\r
12451 O
\92Toole, Olivier Poirot, Karsten Suhre, Iain Wallace, Andreas Wilm</span></p>
\r
12453 <h2><a name="_Toc235958458"><span lang=EN-US>Addresses</span></a></h2>
\r
12455 <p class=MyNormal><span lang=AF>We are always very eager to get some user
\r
12456 feedback. Please do not hesitate to drop us a line<span
\r
12457 style='mso-spacerun:yes'> </span>at: <a
\r
12458 href="mailto:cedric.notredame@europe.com"><span lang=EN-US style='mso-ansi-language:
\r
12459 EN-US'>cedric.notredame@europe.com</span></a> The latest updates of T-Coffee
\r
12460 are always available<span style='mso-spacerun:yes'> </span>on: www.tcoffee.org
\r
12461 . On this address you will also find a link to some of the online T-Coffee
\r
12462 servers, including Tcoffee@igs </span></p>
\r
12464 <p class=MyNormal><span lang=AF><o:p> </o:p></span></p>
\r
12466 <p class=MyNormal><span lang=AF>T-Coffee can be used to automatically check if
\r
12467 an updated version is available, however the program will not update
\r
12468 automatically, as this can cause endless reproducibility problems.</span></p>
\r
12470 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
12471 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
12472 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
12473 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
12475 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:
\r
12476 t_coffee
\96update</span></p>
\r
12480 <p class=MyNormal><span lang=AF><o:p> </o:p></span></p>
\r
12482 <div style='mso-element:para-border-div;border:solid windowtext 3.0pt;
\r
12483 padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#CCCCCC;margin-left:0mm;margin-right:
\r
12486 <p class=ChapterTitle><a name="_Toc235958459"></a><a name="_Toc102494654"></a><a
\r
12487 name="_Toc101065187"><span style='mso-bookmark:_Toc102494654'><span
\r
12488 style='mso-bookmark:_Toc235958459'><span lang=EN-US>Citations</span></span></span></a></p>
\r
12492 <p class=MyNormal><span lang=AF>It is important that you cite T-Coffee when you
\r
12493 use it. Citing us is (almost) like giving us money: it helps us convincing our
\r
12494 institutions that what we do is useful and that they should keep paying our
\r
12495 salaries and deliver Donuts to our offices from time to time (Not that they
\r
12496 ever did it, but it would be nice anyway). </span></p>
\r
12498 <p class=MyNormal><span lang=AF><o:p> </o:p></span></p>
\r
12500 <p class=MyNormal><span lang=AF>Cite the server if you used it, otherwise, cite
\r
12501 the original paper from 2000 (No, it was never named "T-Coffee 2000").</span></p>
\r
12503 <table class=MsoNormalTable border=0 cellspacing=5 cellpadding=0 width="81%"
\r
12504 style='width:81.78%;mso-cellspacing:3.7pt;mso-padding-alt:0mm 0mm 0mm 0mm'>
\r
12505 <tr style='mso-yfti-irow:0;mso-yfti-firstrow:yes'>
\r
12506 <td width="53%" style='width:53.48%;padding:0mm 0mm 0mm 0mm'>
\r
12507 <p class=MyNormalJustified><span lang=EN-US><a
\r
12508 href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10964570">Notredame
\r
12509 C, Higgins DG, Heringa J.</a></span><span lang=EN-US style='mso-bidi-font-size:
\r
12510 12.0pt;color:black'><o:p></o:p></span></p>
\r
12512 <td width="43%" nowrap valign=top style='width:43.3%;padding:0mm 0mm 0mm 0mm'>
\r
12513 <p class=MyNormalJustified><span lang=EN-US><a
\r
12514 href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Display&dopt=pubmed_pubmed&from_uid=10964570"><span
\r
12515 style='mso-bidi-font-size:9.0pt;color:#336699'>Related Articles,</span></a> <script language="JavaScript1.2">
\r
12517 var PopUpMenu2_LocalConfig_jsmenu3Config = [
12518 ["ShowCloseIcon","yes"],
12519 ["Help","window.open('/entrez/query/static/popup.html','Links_Help','resizable=no,scrollbars=yes,toolbar=no,location=no,directories=no,status=no,menubar=no,copyhistory=no,alwaysRaised=no,depend=no,width=400,height=500');"],
12520 ["TitleText"," Links "]
12523 </script><script language="JavaScript1.2">
\r
12525 var Menu10964570 = [
12526 ["UseLocalConfig","jsmenu3Config","",""],
12527 ["Cited in PMC","window.top.location='http://www.pubmedcentral.gov/tocrender.fcgi?action=cited&tool=pubmed&pubmedid=10964570'","",""],
12528 ["Cited in Books","window.top.location='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Display&dopt=pubmed_books_refs&from_uid=10964570'","",""],
12529 ["Books","window.top.location='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&list_uids=10964570&dopt=Books'","",""],
12530 ["LinkOut","window.top.location='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&list_uids=10964570&dopt=ExternalLink'","",""]
12533 </script><a href="javascript:PopUpMenu2_Set(Menu10964570);" target="_self"><span
\r
12534 style='mso-bidi-font-size:9.0pt;color:#336699'>Links</span></a> </span><span
\r
12535 lang=EN-US style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>
\r
12538 <tr style='mso-yfti-irow:1;mso-yfti-lastrow:yes'>
\r
12539 <td width="97%" colspan=2 style='width:97.86%;padding:0mm 0mm 0mm 0mm'>
\r
12540 <p class=MyNormalJustified><span lang=EN-US>T-Coffee: A novel method for fast
\r
12541 and accurate multiple sequence alignment.<br>
\r
12542 J Mol Biol. 2000 Sep 8;302(1):205-17. <br>
\r
12543 PMID: 10964570 [PubMed - indexed for MEDLINE]</span><span lang=EN-US
\r
12544 style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>
\r
12549 <p class=MyNormal><span lang=AF>Other useful publications include:</span></p>
\r
12551 <h2><a name="_Toc235958460"></a><a name="_Toc102494655"></a><a
\r
12552 name="_Toc102494277"></a><a name="_Toc101065188"><span style='mso-bookmark:
\r
12553 _Toc102494277'><span style='mso-bookmark:_Toc102494655'><span style='mso-bookmark:
\r
12554 _Toc235958460'><span lang=EN-US>T-Coffee</span></span></span></span></a></h2>
\r
12556 <table class=MsoNormalTable border=0 cellspacing=5 cellpadding=0 width="81%"
\r
12557 style='width:81.78%;mso-cellspacing:3.7pt;mso-padding-alt:0mm 0mm 0mm 0mm'>
\r
12558 <tr style='mso-yfti-irow:0;mso-yfti-firstrow:yes'>
\r
12559 <td width="53%" style='width:53.48%;padding:0mm 0mm 0mm 0mm'>
\r
12560 <p class=MyNormalJustified><span lang=EN-US><a
\r
12561 href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15215460">Claude
\r
12562 JB, Suhre K, Notredame C, Claverie JM, Abergel C.</a></span><span lang=EN-US
\r
12563 style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>
\r
12565 <td width="43%" nowrap valign=top style='width:43.3%;padding:0mm 0mm 0mm 0mm'>
\r
12566 <p class=MyNormalJustified><span lang=EN-US><a
\r
12567 href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Display&dopt=pubmed_pubmed&from_uid=15215460"><span
\r
12568 style='mso-bidi-font-size:9.0pt;color:#336699'>Related Articles,</span></a> <script language="JavaScript1.2">
\r
12570 var PopUpMenu2_LocalConfig_jsmenu3Config = [
12571 ["ShowCloseIcon","yes"],
12572 ["Help","window.open('/entrez/query/static/popup.html','Links_Help','resizable=no,scrollbars=yes,toolbar=no,location=no,directories=no,status=no,menubar=no,copyhistory=no,alwaysRaised=no,depend=no,width=400,height=500');"],
12573 ["TitleText"," Links "]
12576 </script><script language="JavaScript1.2">
\r
12578 var Menu15215460 = [
12579 ["UseLocalConfig","jsmenu3Config","",""],
12580 ["Free in PMC","window.top.location='http://www.pubmedcentral.gov/articlerender.fcgi?tool=pubmed&pubmedid=15215460'","",""],
12581 ["Books","window.top.location='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&list_uids=15215460&dopt=Books'","",""],
12582 ["LinkOut","window.top.location='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&list_uids=15215460&dopt=ExternalLink'","",""]
12585 </script><a href="javascript:PopUpMenu2_Set(Menu15215460);" target="_self"><span
\r
12586 style='mso-bidi-font-size:9.0pt;color:#336699'>Links</span></a> </span><span
\r
12587 lang=EN-US style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>
\r
12590 <tr style='mso-yfti-irow:1;mso-yfti-lastrow:yes'>
\r
12591 <td width="97%" colspan=2 style='width:97.86%;padding:0mm 0mm 0mm 0mm'>
\r
12592 <p class=MyNormalJustified><span lang=EN-US>CaspR: a web server for automated
\r
12593 molecular replacement using homology modelling.<br>
\r
12594 Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W606-9. <br>
\r
12595 PMID: 15215460 [PubMed - indexed for MEDLINE]</span><span lang=EN-US
\r
12596 style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>
\r
12601 <p class=MyNormalJustified><span lang=EN-US><o:p> </o:p></span></p>
\r
12603 <table class=MsoNormalTable border=0 cellspacing=5 cellpadding=0 width="81%"
\r
12604 style='width:81.98%;mso-cellspacing:3.7pt;mso-padding-alt:0mm 0mm 0mm 0mm'>
\r
12605 <tr style='mso-yfti-irow:0;mso-yfti-firstrow:yes'>
\r
12606 <td width="53%" style='width:53.5%;padding:0mm 0mm 0mm 0mm'>
\r
12607 <p class=MyNormalJustified><span lang=EN-US><a
\r
12608 href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15215345">Poirot
\r
12609 O, Suhre K, Abergel C, O'Toole E, Notredame C.</a></span><span lang=EN-US
\r
12610 style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>
\r
12612 <td nowrap valign=top style='padding:0mm 0mm 0mm 0mm'>
\r
12613 <p class=MyNormalJustified><span lang=EN-US><a
\r
12614 href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Display&dopt=pubmed_pubmed&from_uid=15215345"><span
\r
12615 style='mso-bidi-font-size:9.0pt;color:#336699'>Related Articles,</span></a> <script language="JavaScript1.2">
\r
12617 var Menu15215345 = [
12618 ["UseLocalConfig","jsmenu3Config","",""],
12619 ["Free in PMC","window.top.location='http://www.pubmedcentral.gov/articlerender.fcgi?tool=pubmed&pubmedid=15215345'","",""],
12620 ["Cited in PMC","window.top.location='http://www.pubmedcentral.gov/tocrender.fcgi?action=cited&tool=pubmed&pubmedid=15215345'","",""],
12621 ["Books","window.top.location='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&list_uids=15215345&dopt=Books'","",""],
12622 ["LinkOut","window.top.location='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&list_uids=15215345&dopt=ExternalLink'","",""]
12625 </script><a href="javascript:PopUpMenu2_Set(Menu15215345);" target="_self"><span
\r
12626 style='mso-bidi-font-size:9.0pt;color:#336699'>Links</span></a> </span><span
\r
12627 lang=EN-US style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>
\r
12630 <tr style='mso-yfti-irow:1;mso-yfti-lastrow:yes'>
\r
12631 <td colspan=2 style='padding:0mm 0mm 0mm 0mm'>
\r
12632 <p class=MyNormalJustified><span lang=EN-US>3DCoffee@igs: a web server for
\r
12633 combining sequences and structures into a multiple sequence alignment.<br>
\r
12634 Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W37-40. <br>
\r
12635 PMID: 15215345 [PubMed - indexed for MEDLINE]</span><span lang=EN-US
\r
12636 style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>
\r
12641 <p class=MyNormalJustified><span lang=EN-US><o:p> </o:p></span></p>
\r
12643 <table class=MsoNormalTable border=0 cellspacing=5 cellpadding=0 width="81%"
\r
12644 style='width:81.98%;mso-cellspacing:3.7pt;mso-padding-alt:0mm 0mm 0mm 0mm'>
\r
12645 <tr style='mso-yfti-irow:0;mso-yfti-firstrow:yes'>
\r
12646 <td width="53%" style='width:53.5%;padding:0mm 0mm 0mm 0mm'>
\r
12647 <p class=MyNormalJustified><span lang=EN-US><a
\r
12648 href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15201059">O'Sullivan
\r
12649 O, Suhre K, Abergel C, Higgins DG, Notredame C.</a></span><span lang=EN-US
\r
12650 style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>
\r
12652 <td nowrap valign=top style='padding:0mm 0mm 0mm 0mm'>
\r
12653 <p class=MyNormalJustified><span lang=EN-US><a
\r
12654 href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Display&dopt=pubmed_pubmed&from_uid=15201059"><span
\r
12655 style='mso-bidi-font-size:9.0pt;color:#336699'>Related Articles,</span></a> <script language="JavaScript1.2">
\r
12657 var Menu15201059 = [
12658 ["UseLocalConfig","jsmenu3Config","",""],
12659 ["Cited in PMC","window.top.location='http://www.pubmedcentral.gov/tocrender.fcgi?action=cited&tool=pubmed&pubmedid=15201059'","",""],
12660 ["Books","window.top.location='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&list_uids=15201059&dopt=Books'","",""],
12661 ["LinkOut","window.top.location='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&list_uids=15201059&dopt=ExternalLink'","",""]
12664 </script><a href="javascript:PopUpMenu2_Set(Menu15201059);" target="_self"><span
\r
12665 style='mso-bidi-font-size:9.0pt;color:#336699'>Links</span></a> </span><span
\r
12666 lang=EN-US style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>
\r
12669 <tr style='mso-yfti-irow:1;mso-yfti-lastrow:yes'>
\r
12670 <td colspan=2 style='padding:0mm 0mm 0mm 0mm'>
\r
12671 <p class=MyNormalJustified><span lang=EN-US>3DCoffee: combining protein
\r
12672 sequences and structures within multiple sequence alignments.<br>
\r
12673 J Mol Biol. 2004 Jul 2;340(2):385-95. <br>
\r
12674 PMID: 15201059 [PubMed - indexed for MEDLINE]</span><span lang=EN-US
\r
12675 style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>
\r
12680 <p class=MyNormalJustified><span lang=EN-US><o:p> </o:p></span></p>
\r
12682 <table class=MsoNormalTable border=0 cellspacing=5 cellpadding=0 width="81%"
\r
12683 style='width:81.98%;mso-cellspacing:3.7pt;mso-padding-alt:0mm 0mm 0mm 0mm'>
\r
12684 <tr style='mso-yfti-irow:0;mso-yfti-firstrow:yes'>
\r
12685 <td width="53%" style='width:53.5%;padding:0mm 0mm 0mm 0mm'>
\r
12686 <p class=MyNormalJustified><span lang=EN-US><a
\r
12687 href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12824354">Poirot
\r
12688 O, O'Toole E, Notredame C.</a></span><span lang=EN-US style='mso-bidi-font-size:
\r
12689 12.0pt;color:black'><o:p></o:p></span></p>
\r
12691 <td nowrap valign=top style='padding:0mm 0mm 0mm 0mm'>
\r
12692 <p class=MyNormalJustified><span lang=EN-US><a
\r
12693 href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Display&dopt=pubmed_pubmed&from_uid=12824354"><span
\r
12694 style='mso-bidi-font-size:9.0pt;color:#336699'>Related Articles,</span></a> <script language="JavaScript1.2">
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12696 var Menu12824354 = [
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12704 </script><a href="javascript:PopUpMenu2_Set(Menu12824354);" target="_self"><span
\r
12705 style='mso-bidi-font-size:9.0pt;color:#336699'>Links</span></a> </span><span
\r
12706 lang=EN-US style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>
\r
12709 <tr style='mso-yfti-irow:1;mso-yfti-lastrow:yes'>
\r
12710 <td colspan=2 style='padding:0mm 0mm 0mm 0mm'>
\r
12711 <p class=MyNormalJustified><span lang=EN-US>Tcoffee@igs: A web server for
\r
12712 computing, evaluating and combining multiple sequence alignments.<br>
\r
12713 Nucleic Acids Res. 2003 Jul 1;31(13):3503-6. <br>
\r
12714 PMID: 12824354 [PubMed - indexed for MEDLINE]</span><span lang=EN-US
\r
12715 style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>
\r
12720 <p class=MyNormalJustified><span lang=EN-US><o:p> </o:p></span></p>
\r
12722 <table class=MsoNormalTable border=0 cellspacing=5 cellpadding=0 width="81%"
\r
12723 style='width:81.98%;mso-cellspacing:3.7pt;mso-padding-alt:0mm 0mm 0mm 0mm'>
\r
12724 <tr style='mso-yfti-irow:0;mso-yfti-firstrow:yes'>
\r
12725 <td width="53%" style='width:53.5%;padding:0mm 0mm 0mm 0mm'>
\r
12726 <p class=MyNormalJustified><span lang=EN-US><a
\r
12727 href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11301309">Notredame
\r
12728 C.</a></span><span lang=EN-US style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>
\r
12730 <td nowrap valign=top style='padding:0mm 0mm 0mm 0mm'>
\r
12731 <p class=MyNormalJustified><span lang=EN-US><a
\r
12732 href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Display&dopt=pubmed_pubmed&from_uid=11301309"><span
\r
12733 style='mso-bidi-font-size:9.0pt;color:#336699'>Related Articles,</span></a> <script language="JavaScript1.2">
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12735 var Menu11301309 = [
12736 ["UseLocalConfig","jsmenu3Config","",""],
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12742 </script><a href="javascript:PopUpMenu2_Set(Menu11301309);" target="_self"><span
\r
12743 style='mso-bidi-font-size:9.0pt;color:#336699'>Links</span></a> </span><span
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12744 lang=EN-US style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>
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12747 <tr style='mso-yfti-irow:1;mso-yfti-lastrow:yes'>
\r
12748 <td colspan=2 style='padding:0mm 0mm 0mm 0mm'>
\r
12749 <p class=MyNormalJustified><span lang=EN-US>Mocca: semi-automatic method for
\r
12750 domain hunting.<br>
\r
12751 Bioinformatics. 2001 Apr;17(4):373-4. <br>
\r
12752 PMID: 11301309 [PubMed - indexed for MEDLINE]</span><span lang=EN-US
\r
12753 style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>
\r
12758 <p class=MyNormalJustified><span lang=EN-US><o:p> </o:p></span></p>
\r
12760 <table class=MsoNormalTable border=0 cellspacing=5 cellpadding=0 width="81%"
\r
12761 style='width:81.98%;mso-cellspacing:3.7pt;mso-padding-alt:0mm 0mm 0mm 0mm'>
\r
12762 <tr style='mso-yfti-irow:0;mso-yfti-firstrow:yes'>
\r
12763 <td width="53%" style='width:53.5%;padding:0mm 0mm 0mm 0mm'>
\r
12764 <p class=MyNormalJustified><span lang=EN-US><a
\r
12765 href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10964570">Notredame
\r
12766 C, Higgins DG, Heringa J.</a></span><span lang=EN-US style='mso-bidi-font-size:
\r
12767 12.0pt;color:black'><o:p></o:p></span></p>
\r
12769 <td nowrap valign=top style='padding:0mm 0mm 0mm 0mm'>
\r
12770 <p class=MyNormalJustified><span lang=EN-US><a
\r
12771 href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Display&dopt=pubmed_pubmed&from_uid=10964570"><span
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12772 style='mso-bidi-font-size:9.0pt;color:#336699'>Related Articles,</span></a> <script language="JavaScript1.2">
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12774 var Menu10964570 = [
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12778 ["Books","window.top.location='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&list_uids=10964570&dopt=Books'","",""],
12779 ["LinkOut","window.top.location='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&list_uids=10964570&dopt=ExternalLink'","",""]
12782 </script><a href="javascript:PopUpMenu2_Set(Menu10964570);" target="_self"><span
\r
12783 style='mso-bidi-font-size:9.0pt;color:#336699'>Links</span></a> </span><span
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12784 lang=EN-US style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>
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12787 <tr style='mso-yfti-irow:1;mso-yfti-lastrow:yes'>
\r
12788 <td colspan=2 style='padding:0mm 0mm 0mm 0mm'>
\r
12789 <p class=MyNormalJustified><span lang=EN-US>T-Coffee: A novel method for fast
\r
12790 and accurate multiple sequence alignment.<br>
\r
12791 J Mol Biol. 2000 Sep 8;302(1):205-17. <br>
\r
12792 PMID: 10964570 [PubMed - indexed for MEDLINE]</span><span lang=EN-US
\r
12793 style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>
\r
12798 <p class=MyNormalJustified><span lang=EN-US><o:p> </o:p></span></p>
\r
12800 <table class=MsoNormalTable border=0 cellspacing=5 cellpadding=0 width="81%"
\r
12801 style='width:81.98%;mso-cellspacing:3.7pt;mso-padding-alt:0mm 0mm 0mm 0mm'>
\r
12802 <tr style='mso-yfti-irow:0;mso-yfti-firstrow:yes'>
\r
12803 <td width="53%" style='width:53.5%;padding:0mm 0mm 0mm 0mm'>
\r
12804 <p class=MyNormalJustified><span lang=EN-US><a
\r
12805 href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=9682054">Notredame
\r
12806 C, Holm L, Higgins DG.</a></span><span lang=EN-US style='mso-bidi-font-size:
\r
12807 12.0pt;color:black'><o:p></o:p></span></p>
\r
12809 <td nowrap valign=top style='padding:0mm 0mm 0mm 0mm'>
\r
12810 <p class=MyNormalJustified><span lang=EN-US><a
\r
12811 href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Display&dopt=pubmed_pubmed&from_uid=9682054"><span
\r
12812 style='mso-bidi-font-size:9.0pt;color:#336699'>Related Articles,</span></a> <script language="JavaScript1.2">
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12814 var Menu9682054 = [
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12817 ["Books","window.top.location='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&list_uids=9682054&dopt=Books'","",""],
12818 ["LinkOut","window.top.location='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&list_uids=9682054&dopt=ExternalLink'","",""]
12821 </script><a href="javascript:PopUpMenu2_Set(Menu9682054);" target="_self"><span
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12822 style='mso-bidi-font-size:9.0pt;color:#336699'>Links</span></a> </span><span
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12823 lang=EN-US style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>
\r
12826 <tr style='mso-yfti-irow:1;mso-yfti-lastrow:yes'>
\r
12827 <td colspan=2 style='padding:0mm 0mm 0mm 0mm'>
\r
12828 <p class=MyNormalJustified><span lang=EN-US>COFFEE: an objective function for
\r
12829 multiple sequence alignments.<br>
\r
12830 Bioinformatics. 1998 Jun;14(5):407-22. <br>
\r
12831 PMID: 9682054 [PubMed - indexed for MEDLINE]</span><span lang=EN-US
\r
12832 style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>
\r
12837 <p class=MyNormal><span lang=AF><o:p> </o:p></span></p>
\r
12839 <h2><a name="_Toc235958461"></a><a name="_Toc102494656"></a><a
\r
12840 name="_Toc102494278"></a><a name="_Toc101065189"><span style='mso-bookmark:
\r
12841 _Toc102494278'><span style='mso-bookmark:_Toc102494656'><span style='mso-bookmark:
\r
12842 _Toc235958461'><span lang=EN-US>Mocca</span></span></span></span></a></h2>
\r
12844 <table class=MsoNormalTable border=0 cellspacing=5 cellpadding=0 width="81%"
\r
12845 style='width:81.98%;mso-cellspacing:3.7pt;mso-padding-alt:0mm 0mm 0mm 0mm'>
\r
12846 <tr style='mso-yfti-irow:0;mso-yfti-firstrow:yes'>
\r
12847 <td width="53%" style='width:53.5%;padding:0mm 0mm 0mm 0mm'>
\r
12848 <p class=MyNormal><span lang=AF><a
\r
12849 href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11301309"><span
\r
12850 lang=EN-US style='mso-ansi-language:EN-US'>Notredame C.</span></a></span><span
\r
12851 lang=AF style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>
\r
12853 <td nowrap valign=top style='padding:0mm 0mm 0mm 0mm'>
\r
12854 <p class=MyNormal><span lang=AF><a
\r
12855 href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Display&dopt=pubmed_pubmed&from_uid=11301309&tool=ExternalSearch"><span
\r
12856 lang=EN-US style='mso-bidi-font-size:9.0pt;color:#336699;mso-ansi-language:
\r
12857 EN-US'>Related Articles,</span></a> <script language="JavaScript1.2">
\r
12859 var Menu11301309 = [
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12862 ["Books","window.top.location='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&list_uids=11301309&dopt=Books'","",""],
12863 ["LinkOut","window.top.location='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&list_uids=11301309&dopt=ExternalLink'","",""]
12866 </script><a href="javascript:PopUpMenu2_Set(Menu11301309);" target="_self"><span
\r
12867 lang=EN-US style='mso-bidi-font-size:9.0pt;color:#336699;mso-ansi-language:
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12868 EN-US'>Links</span></a> </span><span lang=AF style='mso-bidi-font-size:12.0pt;
\r
12869 color:black'><o:p></o:p></span></p>
\r
12872 <tr style='mso-yfti-irow:1;mso-yfti-lastrow:yes'>
\r
12873 <td colspan=2 style='padding:0mm 0mm 0mm 0mm'>
\r
12874 <p class=MyNormal><span lang=AF>Mocca: semi-automatic method for domain
\r
12876 Bioinformatics. 2001 Apr;17(4):373-4. <br>
\r
12877 PMID: 11301309 [PubMed - indexed for MEDLINE]</span><span lang=AF
\r
12878 style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>
\r
12883 <h2><a name="_Toc235958462"></a><a name="_Toc102494657"></a><a
\r
12884 name="_Toc102494279"><span style='mso-bookmark:_Toc102494657'><span
\r
12885 style='mso-bookmark:_Toc235958462'><span lang=EN-US>CORE</span></span></span></a></h2>
\r
12887 <p class=MyNormal><span lang=AF><a
\r
12888 href="http://www.tcoffee.org/Publications/Pdf/core.pp.pdf"><span lang=EN-US
\r
12889 style='mso-ansi-language:EN-US'>http://www.tcoffee.org/Publications/Pdf/core.pp.pdf<o:p></o:p></span></a></span></p>
\r
12891 <h2><a name="_Toc102494658"></a><a name="_Toc102494280"></a><a
\r
12892 name="_Toc101065367"><span style='mso-bookmark:_Toc102494280'><span
\r
12893 style='mso-bookmark:_Toc102494658'></span></span></a><a name="_Toc235958463"><span
\r
12894 style='mso-bookmark:_Toc102494658'><span style='mso-bookmark:_Toc102494280'><span
\r
12895 style='mso-bookmark:_Toc101065367'><span lang=EN-US>Other Contributions</span></span></span></span></a></h2>
\r
12897 <p class=MyNormal><span lang=AF>We do not mean to steal code, but we will always
\r
12898 try to re-use pre-existing code whenever that code exists, free of copyright,
\r
12899 just like we expect people to do with our code. However, whenever this happens,
\r
12900 we make a point at properly citing the source of the original contribution. If
\r
12901 ever you recognize a piece of your code improperly cited, please drop us a note
\r
12902 and we will be happy to correct that.</span></p>
\r
12904 <p class=MyNormal><span lang=AF>In the mean time, here are some important pieces
\r
12905 of code from other packages that have been incorporated within the T-Coffee
\r
12906 package. These include: </span></p>
\r
12908 <p class=MyNormal><span lang=AF><span style='mso-tab-count:1'> </span>-The
\r
12909 Sim algorithm of Huang and Miller that given two sequences computes the N best
\r
12910 scoring local alignments.</span></p>
\r
12912 <p class=MyNormal><span lang=AF><span style='mso-tab-count:1'> </span>-The
\r
12913 tree reading/computing routines are taken from the ClustalW Package, courtesy
\r
12914 of Julie Thompson, Des Higgins and Toby Gibson (Thompson, Higgins, Gibson,
\r
12915 1994, 4673-4680,vol. 22, Nucleic Acid Research).</span></p>
\r
12917 <p class=MyNormal><span lang=AF><span style='mso-tab-count:1'> </span>-The
\r
12918 implementation of the algorithm for aligning two sequences in linear space was
\r
12919 adapted from Myers and Miller, in CABIOS, 1988, 11-17, vol. 1)</span></p>
\r
12921 <p class=MyNormal><span lang=AF><span style='mso-spacerun:yes'> </span><span
\r
12922 style='mso-tab-count:1'> </span>-Various techniques and algorithms have
\r
12923 been implemented. Whenever relevant, the source of the code/algorithm/idea is
\r
12924 indicated in the corresponding function.</span></p>
\r
12926 <p class=MyNormal><span lang=AF><span style='mso-tab-count:1'> </span>-64
\r
12927 Bits compliance was implemented by Benjamin Sohn, Performance Computing Center
\r
12928 Stuttgart (HLRS), <st1:place w:st="on"><st1:country-region w:st="on">Germany</st1:country-region></st1:place></span></p>
\r
12930 <p class=MyNormal><span lang=AF><span style='mso-tab-count:1'> </span>-David
\r
12931 Mathog (Caltech) provided many fixes and useful feedback for improving the code
\r
12932 and making the whole soft behaving more rationally</span></p>
\r
12934 <h2><a name="_Toc235958464"><span lang=EN-US>Bug Reports and Feedback</span></a></h2>
\r
12936 <p class=MyNormal><span lang=AF><span style='mso-tab-count:1'> </span>-Prof
\r
12937 David Jones (UCL) reported and corrected the PDB1K bug (now t_coffee/sap can
\r
12938 align PDB sequences longer than 1000 AA).</span></p>
\r
12940 <p class=MyNormal><span lang=AF><span style='mso-tab-count:1'> </span>-Johan
\r
12941 Leckner reported several bugs related to the treatment of PDB structures,
\r
12942 insuring a consistent behavior between version 1.37 and current ones.</span></p>
\r
12944 <p class=MyNormal><span lang=AF><span style='mso-spacerun:yes'> </span></span></p>
\r
12946 <p class=MyNormal><span lang=AF><o:p> </o:p></span></p>
\r
12948 <div style='mso-element:para-border-div;border:solid windowtext 3.0pt;
\r
12949 padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#CCCCCC;margin-left:0mm;margin-right:
\r
12952 <p class=ChapterTitle><a name="_Toc235958465"></a><a name="_Toc102494673"></a><a
\r
12953 name="_Toc101065204"><span style='mso-bookmark:_Toc102494673'><span
\r
12954 style='mso-bookmark:_Toc235958465'><span lang=EN-US>I</span></span></span></a><span
\r
12955 style='mso-bookmark:_Toc235958465'><span lang=EN-US>nstallation of The T-Coffee
\r
12956 Packages</span></span></p>
\r
12960 <h2><a name="_Toc102494674"></a><a name="_Toc102494294"></a><a
\r
12961 name="_Toc101065205"></a><a name="_Toc235958466"><span style='mso-bookmark:
\r
12962 _Toc101065205'><span style='mso-bookmark:_Toc102494294'><span style='mso-bookmark:
\r
12963 _Toc102494674'><span lang=EN-US>Third Party Packages and On Demand
\r
12964 Installations</span></span></span></span></a><span style='mso-bookmark:_Toc101065205'><span
\r
12965 style='mso-bookmark:_Toc102494294'><span style='mso-bookmark:_Toc102494674'></span></span></span></h2>
\r
12967 <p class=MyNormaBoldl><span style='mso-bookmark:_Toc101065205'><span
\r
12968 style='mso-bookmark:_Toc102494294'><span style='mso-bookmark:_Toc102494674'><span
\r
12969 lang=AF>T-Coffee is a complex package that interacts with many other third part
\r
12970 software. If you only want a standalone version of T-Coffee, you may install
\r
12971 that package on its own. If you want to use a most sophisticated flavor
\r
12972 (3dcoffee, expresso, rcofeee, etc...), the installer will try to install all
\r
12973 the third paparty packages required.</span></span></span></span></p>
\r
12975 <p class=MyNormaBoldl><span style='mso-bookmark:_Toc101065205'><span
\r
12976 style='mso-bookmark:_Toc102494294'><span style='mso-bookmark:_Toc102494674'><span
\r
12977 lang=AF><o:p> </o:p></span></span></span></span></p>
\r
12979 <p class=MyNormaBoldl><span style='mso-bookmark:_Toc101065205'><span
\r
12980 style='mso-bookmark:_Toc102494294'><span style='mso-bookmark:_Toc102494674'><span
\r
12981 lang=AF>Note that since version 7.56, T-Coffee will use 'on demand'
\r
12982 installation and install the third party packages it needs *when* it needs
\r
12983 them. This only works for packages not requiring specific licenses and that can
\r
12984 be installed by the regular installer. Please let us know if you would like
\r
12985 another third party package to be included. </span></span></span></span></p>
\r
12987 <p class=MyNormaBoldl><span style='mso-bookmark:_Toc101065205'><span
\r
12988 style='mso-bookmark:_Toc102494294'><span style='mso-bookmark:_Toc102494674'><span
\r
12989 lang=AF>Whenver on-demand installation or automated installation fails because
\r
12990 of unforessen system specificities, users should install the third party
\r
12991 package manually. In this documentation gives some tips we have found useful,
\r
12992 but users are encouraged to check the original documentation.</span></span></span></span></p>
\r
12994 <h2><span style='mso-bookmark:_Toc101065205'><span style='mso-bookmark:_Toc102494294'><span
\r
12995 style='mso-bookmark:_Toc102494674'><a name="_Toc235958467"><span lang=EN-US>Standard
\r
12996 Installation</span></a></span></span></span><span style='mso-bookmark:_Toc235958467'><span
\r
12997 lang=EN-US> of T-Coffee</span></span></h2>
\r
12999 <h3><a name="_Toc235958468"><span lang=EN-US>Unix</span></a></h3>
\r
13001 <p class=MyNormaBoldl><span lang=AF>You need to have: gcc, g77, CPAN and an internet
\r
13002 connection and your root password (to install SOAP). If you cannot log as root,
\r
13003 ask (kindly) your system manager to install <a
\r
13004 href="http://search.cpan.org/%7Ebyrne/SOAP-Lite-0.60a/"><span lang=EN-US
\r
13005 style='mso-ansi-language:EN-US'>SOAP::Lite</span></a> for you. You may do this
\r
13006 before or after the installation of T-Coffee. Even without SOAP you will still
\r
13007 be able to use the basic functions of T-Coffee (simplest usage).</span></p>
\r
13009 <p class=MsoNormal style='margin-left:72.0pt'><span lang=EN-US><o:p> </o:p></span></p>
\r
13011 <p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
\r
13012 margin-left:72.0pt;text-indent:-18.0pt;mso-list:l24 level2 lfo39;tab-stops:
\r
13013 list 72.0pt'><![if !supportLists]><span lang=EN-US style='font-family:Arial;
\r
13014 mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>1.<span
\r
13015 style='font:7.0pt "Times New Roman"'>
\r
13016 </span></span></span><![endif]><span dir=LTR><code><span lang=EN-US
\r
13017 style='font-size:10.0pt'>gunzip t_coffee.tar.gz</span></code></span><span
\r
13018 lang=EN-US style='font-family:Arial'><o:p></o:p></span></p>
\r
13020 <p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
\r
13021 margin-left:72.0pt;text-indent:-18.0pt;mso-list:l24 level2 lfo39;tab-stops:
\r
13022 list 72.0pt'><![if !supportLists]><span lang=EN-US style='font-family:Arial;
\r
13023 mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>2.<span
\r
13024 style='font:7.0pt "Times New Roman"'>
\r
13025 </span></span></span><![endif]><span dir=LTR><code><span lang=EN-US
\r
13026 style='font-size:10.0pt'>tar -xvf t_coffee.tar</span></code></span><span
\r
13027 lang=EN-US style='font-family:Arial'><o:p></o:p></span></p>
\r
13029 <p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
\r
13030 margin-left:72.0pt;text-indent:-18.0pt;mso-list:l24 level2 lfo39;tab-stops:
\r
13031 list 72.0pt'><![if !supportLists]><span lang=EN-US style='font-family:Arial;
\r
13032 mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>3.<span
\r
13033 style='font:7.0pt "Times New Roman"'>
\r
13034 </span></span></span><![endif]><span dir=LTR><code><span lang=EN-US
\r
13035 style='font-size:10.0pt'>cd t_coffee</span></code></span><span lang=EN-US
\r
13036 style='font-family:Arial'><o:p></o:p></span></p>
\r
13038 <p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
\r
13039 margin-left:72.0pt;text-indent:-18.0pt;mso-list:l24 level2 lfo39;tab-stops:
\r
13040 list 72.0pt'><![if !supportLists]><span lang=EN-US style='font-family:Arial;
\r
13041 mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>4.<span
\r
13042 style='font:7.0pt "Times New Roman"'>
\r
13043 </span></span></span><![endif]><span dir=LTR><code><span lang=EN-US
\r
13044 style='font-size:10.0pt'>./install t_coffee</span></code></span><span
\r
13045 lang=EN-US style='font-family:Arial'><o:p></o:p></span></p>
\r
13047 <p class=MyNormal><span lang=AF>This installation will try to install EVERY
\r
13048 flavor of T-Coffee along with the packages it requires. It will not re-install
\r
13049 the packages that are already on your computer.</span></p>
\r
13051 <p class=MyNormal><span lang=AF>If you want a more specific installation, you
\r
13052 can try:</span></p>
\r
13054 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
13055 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
13056 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
13057 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
13059 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US><span
\r
13060 style='mso-tab-count:1'> </span>./install t_coffee</span></p>
\r
13062 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US><span
\r
13063 style='mso-tab-count:1'> </span>./install mcoffee</span></p>
\r
13065 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US><span
\r
13066 style='mso-tab-count:1'> </span>./install 3dcoffee</span></p>
\r
13068 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US><span
\r
13069 style='mso-tab-count:1'> </span>./install rcoffee</span></p>
\r
13071 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US><span
\r
13072 style='mso-tab-count:1'> </span>./install psicoffee</span></p>
\r
13074 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US><o:p> </o:p></span></p>
\r
13078 <p class=MyNormal><span lang=AF><o:p> </o:p></span></p>
\r
13080 <p class=MyNormal><span lang=AF>Or even</span></p>
\r
13082 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
13083 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
13084 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
13085 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
13087 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US><span
\r
13088 style='mso-tab-count:1'> </span>./install all</span></p>
\r
13092 <p class=MyNormal><span lang=AF><o:p> </o:p></span></p>
\r
13094 <p class=MyNormal><span lang=AF>-All the corresponding executables will be
\r
13095 downloaded automatically and installed in</span></p>
\r
13097 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
13098 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
13099 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
13100 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
13102 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US><span
\r
13103 style='mso-tab-count:1'> </span>$HOME/.t_coffee/plugins</span></p>
\r
13107 <p class=MyNormal><span lang=AF><o:p> </o:p></span></p>
\r
13109 <p class=MyNormal><span lang=AF>-if you executables are in a different
\r
13110 location, give it to T-Coffee using the -plugins flag.</span></p>
\r
13112 <p class=MyNormal><span lang=AF>-If the installation of any of the companion
\r
13113 package fails, you should install it yourself using the provided link (see
\r
13114 below) and following the authors instructions.<span style='mso-tab-count:1'> </span></span></p>
\r
13116 <p class=MyNormal><span lang=AF>-If you have not managed to install SOAP::Lite,
\r
13117 you can re-install it later (from anywhere) following steps 1-2.</span></p>
\r
13119 <p class=MsoNormal style='margin-left:72.0pt'><span lang=EN-US><o:p> </o:p></span></p>
\r
13121 <p class=MyNormaBoldl><span lang=AF>-This procedure attempts 3 things:
\r
13122 installing and Compiling T-Coffee (C program), Installing and compiling <a
\r
13123 href="http://zhang.bioinformatics.ku.edu/TM-align/"><span lang=EN-US
\r
13124 style='mso-ansi-language:EN-US'>TMalign</span></a> (Fortran), Installing and
\r
13125 compiling <a href="http://search.cpan.org/%7Ebyrne/SOAP-Lite-0.60a/"><span
\r
13126 lang=EN-US style='mso-ansi-language:EN-US'>SOAP::Lite</span></a>(Perl Module).</span></p>
\r
13128 <p class=MyNormaBoldl><span lang=AF><o:p> </o:p></span></p>
\r
13130 <p class=MyNormaBoldl><span lang=AF>-If you have never installed SOAP::Lite,
\r
13131 CPAN will ask you many questions: say Yes to all </span></p>
\r
13133 <p class=MyNormaBoldl><span lang=AF>-If everything went well, the procedure has
\r
13134 created in the <b>bin</b> directory two executables: t_coffee and TMalign (<b>Make
\r
13135 sure these executables are on your $PATH!</b>)</span></p>
\r
13137 <p class=MyNormaBoldl><span lang=AF><o:p> </o:p></span></p>
\r
13139 <h3><a name="_Toc235958469"><span lang=EN-US>Microsoft Windows/Cygwin</span></a></h3>
\r
13141 <p class=MyNormaBoldl><span lang=AF>Install <a href="http://www.cygwin.com"><span
\r
13142 lang=EN-US style='color:windowtext;mso-ansi-language:EN-US;text-decoration:
\r
13143 none;text-underline:none'>Cygwin</span></a></span></p>
\r
13145 <p class=MyNormaBoldl><span lang=AF>Download The Installer (NOT Cygwin/X)</span></p>
\r
13147 <p class=MyNormaBoldl><span lang=AF>Click on view to list ALL the packages</span></p>
\r
13149 <p class=MyNormaBoldl><span lang=AF>Select: gcc-core, make, wget</span></p>
\r
13151 <p class=MyNormaBoldl><span lang=AF>Optional: ssh, xemacs, nano</span></p>
\r
13153 <p class=MyNormaBoldl><span lang=AF>Run mkpasswd in Cywin (as requested when
\r
13154 you start cygwin)</span></p>
\r
13156 <p class=MyNormaBoldl><span lang=AF>Install T-Coffee within Cygwin using the
\r
13157 Unix procedure</span></p>
\r
13159 <h3><a name="_Toc235958470"><span lang=EN-US>MAC osX, Linux</span></a></h3>
\r
13161 <p class=MyNormaBoldl><span lang=AF>Make sure you have the Developer's kit installed
\r
13162 (compilers and makefile)</span></p>
\r
13164 <p class=MyNormaBoldl><span lang=AF>Follow the Unix Procedure</span></p>
\r
13166 <p class=Mylist><span lang=AF><o:p> </o:p></span></p>
\r
13168 <h3><a name="_Toc235958471"><span lang=EN-US>CLUSTER Installation</span></a></h3>
\r
13170 <p class=MyNormal><span lang=AF>In order to run, T-Coffee must have a value for
\r
13171 the http_proxy and for the E-mail. In order to do so you can either:</span></p>
\r
13173 <p class=MyNormaBoldl><span lang=AF>export the following values:</span></p>
\r
13175 <p class=MyNormaBoldl><span lang=AF>export
\r
13176 http_proxy_4_TCOFFEE="proxy" or "" if no proxy</span></p>
\r
13178 <p class=MyNormaBoldl><span lang=AF>export EMAIL_4_TCOFFEE="your
\r
13179 email"</span></p>
\r
13181 <p class=MyNormaBoldl><span lang=AF>OR </span></p>
\r
13183 <p class=MyNormaBoldl><span lang=AF>modify the file ~/.t_coffee/t_coffee_env</span></p>
\r
13185 <p class=MyNormaBoldl><span lang=AF>OR</span></p>
\r
13187 <p class=MyNormaBoldl><span lang=AF>add to your command line: t_coffee
\85.
\r
13188 -proxy=<proxy> -email=<email</span></p>
\r
13190 <p class=MyNormaBoldl><span lang=AF>if you have no proxy: t_coffee
\85 -proxy
\r
13191 -email=<email></span></p>
\r
13193 <p class=MyNormal><span lang=AF><o:p> </o:p></span></p>
\r
13195 <p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p>
\r
13197 <h3><a name="_Toc235958472"><span lang=EN-US>If you have PDB installed:</span></a></h3>
\r
13199 <p class=MyNormal><span lang=AF>Assuming you have a standard PDB installation
\r
13200 in your file system</span></p>
\r
13202 <p class=example2CxSpFirst><span lang=EN-US>setenv (or export)<span
\r
13203 style='mso-spacerun:yes'> </span>PDB_DIR <abs path>/data/structures/all/pdb/</span></p>
\r
13205 <p class=example2CxSpMiddle><span lang=EN-US>OR</span></p>
\r
13207 <p class=example2CxSpLast><span lang=EN-US>setenv (or export)<span
\r
13208 style='mso-spacerun:yes'> </span>PDB_DIR <abs
\r
13209 path>/structures/divided/pdb/</span></p>
\r
13211 <p class=MyNormal><span lang=AF>If you do not have PDB installed, don't worry,
\r
13212 t_coffee will go and fetch any structure it needs directly from the PDB
\r
13213 repository. It will simply be a bit slower than if you had PDB locally. </span></p>
\r
13215 <h2><a name="_Toc102494675"></a><a name="_Toc102494295"></a><a
\r
13216 name="_Toc101065206"></a><a name="_Toc235958473"><span style='mso-bookmark:
\r
13217 _Toc101065206'><span style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:
\r
13218 _Toc102494675'><span lang=EN-US>Installing BLAST for T-Coffee</span></span></span></span></a><span
\r
13219 style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span
\r
13220 style='mso-bookmark:_Toc102494675'></span></span></span></h2>
\r
13222 <p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span
\r
13223 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13224 lang=AF>BLAST is a program that search sequence databases for homologues of a
\r
13225 query sequence. It works for proteins and Nucleic Acids. In theory BLAST is
\r
13226 just a package like any, but in practice things are a bit more complex. To run
\r
13227 well, BLST requires up to date databases (that can be fairly large, like NR or
\r
13228 UNIPROT) and a powerful computer.</span></span></span></span></p>
\r
13230 <p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span
\r
13231 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13232 lang=AF>Fortunately, an increasing number of institutes or companies are now providing
\r
13233 BLAST clients that run over the net. It means that all you need is a small
\r
13234 program that send your query to the big server and gets the results back. This
\r
13235 prevents you from the hassle of installing and maintaining BLAST, but of course
\r
13236 it is less private and you rely on the network and the current load of these
\r
13237 busy servers.</span></span></span></span></p>
\r
13239 <p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span
\r
13240 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13241 lang=AF>Thanks to its interaction with BLAST, T-Coffee can gather structures
\r
13242 and protein profiles and deliver an alignment significantly more accurate than
\r
13243 the default you would get with T-Coffee or any similar method.</span></span></span></span></p>
\r
13245 <p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span
\r
13246 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13247 lang=AF>Let us go through the various modes available for T-Coffee</span></span></span></span></p>
\r
13249 <p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span
\r
13250 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13251 lang=AF><o:p> </o:p></span></span></span></span></p>
\r
13253 <h3><span style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span
\r
13254 style='mso-bookmark:_Toc102494675'><a name="_Toc235958474"><span lang=EN-US>Why
\r
13255 Do I need BLAST with T-Coffee?</span></a></span></span></span></h3>
\r
13257 <p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span
\r
13258 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13259 lang=AF>The most accurate modes of T-Coffe scan the databases for templates
\r
13260 that they use to align the sequences. There are currently two types of templates
\r
13261 for proteins:</span></span></span></span></p>
\r
13263 <p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span
\r
13264 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13265 lang=AF>structures (PDB) that can be found by a blastp against the PDB database
\r
13266 and profiles that can be constructed with eiether a blastp or a psiblast
\r
13267 against nr or uniprot.</span></span></span></span></p>
\r
13269 <p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span
\r
13270 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13271 lang=AF>These templates are automatically built if you use:</span></span></span></span></p>
\r
13273 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
13274 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
13275 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
13276 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
13278 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span
\r
13279 style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span
\r
13280 style='mso-bookmark:_Toc102494675'><span lang=EN-US><span style='mso-tab-count:
\r
13281 1'> </span>t_coffee <yourseq> -mode expresso</span></span></span></span></p>
\r
13285 <p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span
\r
13286 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13287 lang=AF><span style='mso-tab-count:1'> </span>that fetches aand uses
\r
13288 pdb templates, or</span></span></span></span></p>
\r
13290 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
13291 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
13292 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
13293 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
13295 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span
\r
13296 style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span
\r
13297 style='mso-bookmark:_Toc102494675'><span lang=EN-US><span style='mso-tab-count:
\r
13298 1'> </span><span style='mso-tab-count:1'> </span>t_coffee <your
\r
13299 seq> -mode psicoffee</span></span></span></span></p>
\r
13303 <p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span
\r
13304 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13305 lang=AF><span style='mso-tab-count:1'> </span>that fetches and uses
\r
13306 profile templates, or</span></span></span></span></p>
\r
13308 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
13309 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
13310 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
13311 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
13313 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span
\r
13314 style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span
\r
13315 style='mso-bookmark:_Toc102494675'><span lang=EN-US><span style='mso-tab-count:
\r
13316 1'> </span><span style='mso-tab-count:1'> </span>t_coffee <your
\r
13317 seq> -mode accurate</span></span></span></span></p>
\r
13321 <p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span
\r
13322 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13323 lang=AF><span style='mso-tab-count:1'> </span>that does everything and
\r
13324 tries to use the best template. Now that you see why it is useful let's see how
\r
13325 to get BLAST up and running, from the easy solution to tailor made ones.</span></span></span></span></p>
\r
13327 <p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span
\r
13328 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13329 lang=AF><o:p> </o:p></span></span></span></span></p>
\r
13331 <h3><span style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span
\r
13332 style='mso-bookmark:_Toc102494675'><a name="_Toc235958475"><span lang=EN-US>Using
\r
13333 the EBI BLAST Client</span></a></span></span></span></h3>
\r
13335 <p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span
\r
13336 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13337 lang=AF>This is by far the easiest (and the default mode). The perl clients are
\r
13338 already incorporated in T-Coffeem and all you need is the SOAP::Lite perl
\r
13339 library. In theory, T-Coffee should have already installed this library during
\r
13340 the standard installation. Yet, this requires having toot access. If you did
\r
13341 not have it at the time of the installation, or if you need your system administrator
\r
13342 to install SOAP::Lite, simply follow the instruction provided on the website:</span></span></span></span></p>
\r
13344 <p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span
\r
13345 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13346 lang=AF><o:p> </o:p></span></span></span></span></p>
\r
13348 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
13349 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
13350 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
13351 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
13353 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span
\r
13354 style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span
\r
13355 style='mso-bookmark:_Toc102494675'><span lang=EN-US><span style='mso-tab-count:
\r
13356 1'> </span>http://search.cpan.org/~byrne/SOAP-Lite-0.60a</span></span></span></span></p>
\r
13360 <p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span
\r
13361 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13362 lang=AF>It really is worth the effort, since the EBI is providing one of the
\r
13363 best webservice available around, and most notably, the only public psiblast
\r
13364 via a web service.</span></span></span></span></p>
\r
13366 <p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span
\r
13367 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13368 lang=AF><span style='mso-spacerun:yes'> </span></span></span></span></span></p>
\r
13370 <p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span
\r
13371 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13372 lang=AF>Another important point is that the EBI requires your E-mail address to
\r
13373 process your queries. Normally, T-Coffee should have asked you to provide this
\r
13374 address. If you have not, or if you have provided a phony address, you should
\r
13375 correct this by directly editing the file</span></span></span></span></p>
\r
13377 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
13378 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
13379 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
13380 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
13382 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span
\r
13383 style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span
\r
13384 style='mso-bookmark:_Toc102494675'><span lang=EN-US><span style='mso-tab-count:
\r
13385 1'> </span>~/.t_coffee/email.txt</span></span></span></span></p>
\r
13389 <p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span
\r
13390 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><b><span
\r
13391 lang=AF>Be Careful! </span></b><span lang=AF>If you provide a fake E-mail, the
\r
13392 EBI may suspend the service for all machines associated with your IP address
\r
13393 (that could mean your entire lab, or entire institute, or even the entire
\r
13394 country or, but I doubt it, the whole universe).</span></span></span></span></p>
\r
13396 <h3><span style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span
\r
13397 style='mso-bookmark:_Toc102494675'><a name="_Toc235958476"><span lang=EN-US>Using
\r
13398 the NCBI BLAST Client</span></a></span></span></span></h3>
\r
13400 <p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span
\r
13401 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13402 lang=AF>The NCBI is the next best alternative. In my hand it was always a bit
\r
13403 slower and most of all, it does not incorporate PSI-BLAST (as a web sevice). A
\r
13404 big miss. The NCBI web blast client is a small executable that you should
\r
13405 install on your system following the instructions given on this link</span></span></span></span></p>
\r
13407 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
13408 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
13409 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
13410 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
13412 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span
\r
13413 style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span
\r
13414 style='mso-bookmark:_Toc102494675'><span lang=EN-US>ftp://ftp.ncbi.nih.gov/blast/executables/LATEST</span></span></span></span></p>
\r
13418 <p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span
\r
13419 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13420 lang=AF>Simply go for <b>netbl,</b> download the executable that corresponds to
\r
13421 your architecture (cygwin users should go for the win executable). Despite all
\r
13422 the files that come along the executable blastcl3 is a stand alone executable
\r
13423 that you can safely move to your $BIN.</span></span></span></span></p>
\r
13425 <p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span
\r
13426 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13427 lang=AF>All you will then need to do is to make sure that T-Coffee uses the
\r
13428 right client, when you run it.</span></span></span></span></p>
\r
13430 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
13431 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
13432 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
13433 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
13435 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span
\r
13436 style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span
\r
13437 style='mso-bookmark:_Toc102494675'><span lang=EN-US>-blast_server=NCBI</span></span></span></span></p>
\r
13441 <p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span
\r
13442 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13443 lang=AF>No need for any E-mail here, but you don't get psiblast, and whenever
\r
13444 T-Coffee wants to use it, blastp will be used instead.</span></span></span></span></p>
\r
13446 <h3><span style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span
\r
13447 style='mso-bookmark:_Toc102494675'><a name="_Toc235958477"><span lang=EN-US>Using
\r
13448 another Client</span></a></span></span></span></h3>
\r
13450 <p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span
\r
13451 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13452 lang=AF>You may have your own client (lucky you). If that is so, all you need
\r
13453 is to make sure that this client is complient with the blast command line. If
\r
13454 your client is named foo.pl, all you need to to is run T-Coffee with</span></span></span></span></p>
\r
13456 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
13457 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
13458 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
13459 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
13461 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span
\r
13462 style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span
\r
13463 style='mso-bookmark:_Toc102494675'><span lang=EN-US>-blast_server=CLIENT_foo.pl</span></span></span></span></p>
\r
13467 <p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span
\r
13468 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13469 lang=AF>Foo will be called as if it were blastpgp, and it is your responsability
\r
13470 to make sure it can handle the following command line:</span></span></span></span></p>
\r
13472 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
13473 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
13474 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
13475 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
13477 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span
\r
13478 style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span
\r
13479 style='mso-bookmark:_Toc102494675'><span lang=EN-US>foo.pl -p <method> -d
\r
13480 <db> -i <infile> -o <outfile> -m 7</span></span></span></span></p>
\r
13484 <p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span
\r
13485 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13486 lang=AF>method can either be blastp or psiblast.</span></span></span></span></p>
\r
13488 <p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span
\r
13489 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13490 lang=AF>infile is a FASTA file</span></span></span></span></p>
\r
13492 <p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span
\r
13493 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13494 lang=AF>-m7 triggers the XML output. T-Coffee is able to parse both the EBI XML
\r
13495 output and the NCBI XML output.</span></span></span></span></p>
\r
13497 <p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span
\r
13498 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13499 lang=AF><o:p> </o:p></span></span></span></span></p>
\r
13501 <p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span
\r
13502 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13503 lang=AF>If foo.pl behaves differently, the easiest will probably be to write a
\r
13504 wrapper around it so that wrapped_foo.pl behaves like blastpgp</span></span></span></span></p>
\r
13506 <p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span
\r
13507 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13508 lang=AF><o:p> </o:p></span></span></span></span></p>
\r
13510 <h3><span style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span
\r
13511 style='mso-bookmark:_Toc102494675'><a name="_Toc235958478"><span lang=EN-US>Using
\r
13512 a BLAST local version on UNIX</span></a></span></span></span></h3>
\r
13514 <p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span
\r
13515 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13516 lang=AF>If you have blastpgp installed, you can run it instead of the remote
\r
13517 clients by using:</span></span></span></span></p>
\r
13519 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
13520 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
13521 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
13522 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
13524 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span
\r
13525 style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span
\r
13526 style='mso-bookmark:_Toc102494675'><span lang=EN-US>-blast_server=LOCAL</span></span></span></span></p>
\r
13530 <p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span
\r
13531 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13532 lang=AF><span style='mso-spacerun:yes'> </span>The documnentation for blastpgp
\r
13533 can be found on:</span></span></span></span></p>
\r
13535 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
13536 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
13537 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
13538 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
13540 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span
\r
13541 style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span
\r
13542 style='mso-bookmark:_Toc102494675'><span lang=EN-US>www.ncbi.nlm.nih.gov/staff/tao/URLAPI/blastpgp.html</span></span></span></span></p>
\r
13546 <p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span
\r
13547 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13548 lang=AF>and the package is part of the standard BLAST distribution</span></span></span></span></p>
\r
13550 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
13551 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
13552 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
13553 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
13555 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span
\r
13556 style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span
\r
13557 style='mso-bookmark:_Toc102494675'><span lang=EN-US>ftp://ftp.ncbi.nih.gov/blast/executables/LATEST</span></span></span></span></p>
\r
13561 <p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span
\r
13562 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13563 lang=AF>Depending on your system, your own skills, your requirements and on
\r
13564 more parameters than I have fingers to count, installing a BLAST server suited
\r
13565 for your needs can range from a 10 minutes job to an achivement spread over
\r
13566 several generations. So at this point, you should roam the NCBI website for
\r
13567 suitable information.</span></span></span></span></p>
\r
13569 <p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span
\r
13570 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13571 lang=AF>If you want to have your own BLAST server to run your own databases,
\r
13572 you should know that it is possible to control both the database and the
\r
13573 program used by BLAST:</span></span></span></span></p>
\r
13575 <p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span
\r
13576 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13577 lang=AF><o:p> </o:p></span></span></span></span></p>
\r
13579 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
\r
13580 mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
\r
13581 background:#E6E6E6'>
\r
13583 <p class=examplefileCxSpFirst><span style='mso-bookmark:_Toc101065206'><span
\r
13584 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13585 lang=EN-US>-prot_db: will specify the database used by all the psi-blast modes</span></span></span></span></p>
\r
13587 <p class=examplefileCxSpLast><span style='mso-bookmark:_Toc101065206'><span
\r
13588 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13589 lang=EN-US>-pdb_db: will specify the database used by the pdb modes</span></span></span></span></p>
\r
13593 <h3><span style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span
\r
13594 style='mso-bookmark:_Toc102494675'><a name="_Toc235958479"><span lang=EN-US>Using
\r
13595 a BLAST local version on Windows/cygwin</span></a></span></span></span></h3>
\r
13597 <p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span
\r
13598 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13599 lang=AF>For those of you using cygwin, be careful. While cygwin behaves like a
\r
13600 UNIX system, the BLAST executable required for cygwin (win32) is expecting
\r
13601 WINDOWS path and not UNIX path. This has three important consequences:</span></span></span></span></p>
\r
13603 <p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span
\r
13604 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13605 lang=AF>1- the ncbi file declaring the Data directory must be:</span></span></span></span></p>
\r
13607 <p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span
\r
13608 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13609 lang=AF><span style='mso-tab-count:1'> </span>C:WINDOWS//ncbi.init<span
\r
13610 style='mso-spacerun:yes'> </span>[at the root of your WINDOWS]</span></span></span></span></p>
\r
13612 <p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span
\r
13613 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13614 lang=AF>2- the address mentionned with this file must be WINDOWS formated, for
\r
13615 instance, on my system:</span></span></span></span></p>
\r
13617 <p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span
\r
13618 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13619 lang=AF>Data=C:\cygwin\home\notredame\blast\data</span></span></span></span></p>
\r
13621 <p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span
\r
13622 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13623 lang=AF>3- When you pass database addresses to BLAST, these must be in Windows
\r
13624 format:</span></span></span></span></p>
\r
13626 <p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span
\r
13627 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13628 lang=AF><span style='mso-tab-count:1'> </span>-protein_db="c:/somewhere/somewhereelse/database"</span></span></span></span></p>
\r
13630 <p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span
\r
13631 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13632 lang=AF>(using the slash (/) or the andtislash (\) does not matter on new
\r
13633 systems but I would reommand against incorporating white spaces.</span></span></span></span></p>
\r
13635 <h2><span style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span
\r
13636 style='mso-bookmark:_Toc102494675'><a name="_Toc235958480"><span lang=EN-US>Installing
\r
13637 Other Companion Packages</span></a></span></span></span></h2>
\r
13639 <p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span
\r
13640 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13641 lang=AF>T-Coffee is meant to interact with as many packages as possible, either
\r
13642 for aligning or using predictions. If you type </span></span></span></span></p>
\r
13644 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
13645 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
13646 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
13647 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
13649 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span
\r
13650 style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span
\r
13651 style='mso-bookmark:_Toc102494675'><span lang=EN-US><span style='mso-tab-count:
\r
13652 1'> </span>t_coffee</span></span></span></span></p>
\r
13656 <p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span
\r
13657 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13658 lang=AF>You will receive a list of supported packages that looks like the next
\r
13659 table. In theory, most of these packages can be installed by T-Coffee</span></span></span></span></p>
\r
13661 <p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span
\r
13662 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13663 lang=AF><o:p> </o:p></span></span></span></span></p>
\r
13665 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
\r
13666 mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
\r
13667 background:#E6E6E6'>
\r
13669 <p class=examplefileCxSpFirst><span style='mso-bookmark:_Toc101065206'><span
\r
13670 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13671 lang=EN-US>****** Pairwise Sequence Alignment Methods:</span></span></span></span></p>
\r
13673 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
13674 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13675 lang=EN-US>--------------------------------------------</span></span></span></span></p>
\r
13677 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
13678 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13679 lang=EN-US>fast_pair <span style='mso-spacerun:yes'> </span>built_in</span></span></span></span></p>
\r
13681 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
13682 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13683 lang=EN-US>exon3_pair<span style='mso-spacerun:yes'> </span>built_in</span></span></span></span></p>
\r
13685 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
13686 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13687 lang=EN-US>exon2_pair<span style='mso-spacerun:yes'> </span>built_in</span></span></span></span></p>
\r
13689 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
13690 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13691 lang=EN-US>exon_pair<span style='mso-spacerun:yes'> </span>built_in</span></span></span></span></p>
\r
13693 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
13694 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13695 lang=EN-US>slow_pair<span style='mso-spacerun:yes'> </span>built_in</span></span></span></span></p>
\r
13697 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
13698 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13699 lang=EN-US>proba_pair<span style='mso-spacerun:yes'> </span>built_in</span></span></span></span></p>
\r
13701 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
13702 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13703 lang=EN-US>lalign_id_pair<span style='mso-spacerun:yes'> </span>built_in</span></span></span></span></p>
\r
13705 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
13706 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13707 lang=EN-US>seq_pair<span style='mso-spacerun:yes'> </span>built_in</span></span></span></span></p>
\r
13709 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
13710 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13711 lang=EN-US>externprofile_pair built_in</span></span></span></span></p>
\r
13713 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
13714 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13715 lang=EN-US>hh_pair<span style='mso-spacerun:yes'> </span><span
\r
13716 style='mso-spacerun:yes'> </span>built_in</span></span></span></span></p>
\r
13718 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
13719 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13720 lang=EN-US>profile_pair<span style='mso-spacerun:yes'> </span>built_in</span></span></span></span></p>
\r
13722 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
13723 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13724 lang=EN-US>cdna_fast_pair<span style='mso-spacerun:yes'> </span>built_in</span></span></span></span></p>
\r
13726 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
13727 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13728 lang=EN-US>cdna_cfast_pair<span style='mso-spacerun:yes'> </span>built_in</span></span></span></span></p>
\r
13730 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
13731 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13732 lang=EN-US>clustalw_pair<span style='mso-spacerun:yes'>
\r
13733 </span>ftp://www.ebi.ac.uk/pub/clustalw</span></span></span></span></p>
\r
13735 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
13736 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13737 lang=EN-US>mafft_pair<span style='mso-spacerun:yes'>
\r
13738 </span>http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft/</span></span></span></span></p>
\r
13740 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
13741 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13742 lang=EN-US>mafftjtt_pair<span style='mso-spacerun:yes'> </span>http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft/</span></span></span></span></p>
\r
13744 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
13745 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13746 lang=EN-US>mafftgins_pair<span style='mso-spacerun:yes'>
\r
13747 </span>http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft/</span></span></span></span></p>
\r
13749 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
13750 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13751 lang=EN-US>dialigntx_pair<span style='mso-spacerun:yes'>
\r
13752 </span>http://dialign-tx.gobics.de/</span></span></span></span></p>
\r
13754 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
13755 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13756 lang=EN-US>dialignt_pair<span style='mso-spacerun:yes'>
\r
13757 </span>http://dialign-t.gobics.de/</span></span></span></span></p>
\r
13759 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
13760 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13761 lang=EN-US>poa_pair<span style='mso-spacerun:yes'> </span>http://www.bioinformatics.ucla.edu/poa/</span></span></span></span></p>
\r
13763 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
13764 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13765 lang=EN-US>probcons_pair<span style='mso-spacerun:yes'>
\r
13766 </span>http://probcons.stanford.edu/</span></span></span></span></p>
\r
13768 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
13769 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13770 lang=EN-US>muscle_pair<span style='mso-spacerun:yes'>
\r
13771 </span>http://www.drive5.com/muscle/</span></span></span></span></p>
\r
13773 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
13774 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13775 lang=EN-US>t_coffee_pair<span style='mso-spacerun:yes'>
\r
13776 </span>http://www.tcoffee.org</span></span></span></span></p>
\r
13778 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
13779 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13780 lang=EN-US>pcma_pair<span style='mso-spacerun:yes'>
\r
13781 </span>ftp://iole.swmed.edu/pub/PCMA/</span></span></span></span></p>
\r
13783 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
13784 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13785 lang=EN-US>kalign_pair<span style='mso-spacerun:yes'>
\r
13786 </span>http://msa.cgb.ki.se</span></span></span></span></p>
\r
13788 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
13789 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13790 lang=EN-US>amap_pair<span style='mso-spacerun:yes'>
\r
13791 </span>http://bio.math.berkeley.edu/amap/</span></span></span></span></p>
\r
13793 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
13794 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13795 lang=EN-US>proda_pair<span style='mso-spacerun:yes'>
\r
13796 </span>http://bio.math.berkeley.edu/proda/</span></span></span></span></p>
\r
13798 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
13799 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13800 lang=EN-US>prank_pair<span style='mso-spacerun:yes'>
\r
13801 </span>http://www.ebi.ac.uk/goldman-srv/prank/</span></span></span></span></p>
\r
13803 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
13804 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13805 lang=EN-US>consan_pair<span style='mso-spacerun:yes'>
\r
13806 </span>http://selab.janelia.org/software/consan/</span></span></span></span></p>
\r
13808 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
13809 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13810 lang=EN-US><o:p> </o:p></span></span></span></span></p>
\r
13812 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
13813 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13814 lang=EN-US>****** Pairwise Structural Alignment Methods:</span></span></span></span></p>
\r
13816 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
13817 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13818 lang=EN-US>--------------------------------------------</span></span></span></span></p>
\r
13820 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
13821 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13822 lang=EN-US>align_pdbpair<span style='mso-spacerun:yes'> </span>built_in</span></span></span></span></p>
\r
13824 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
13825 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13826 lang=EN-US>lalign_pdbpair<span style='mso-spacerun:yes'> </span>built_in</span></span></span></span></p>
\r
13828 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
13829 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13830 lang=EN-US>extern_pdbpair<span style='mso-spacerun:yes'> </span>built_in</span></span></span></span></p>
\r
13832 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
13833 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13834 lang=EN-US>thread_pair<span style='mso-spacerun:yes'> </span>built_in</span></span></span></span></p>
\r
13836 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
13837 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13838 lang=EN-US>fugue_pair<span style='mso-spacerun:yes'>
\r
13839 </span>http://www-cryst.bioc.cam.ac.uk/fugue/download.html</span></span></span></span></p>
\r
13841 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
13842 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13843 lang=EN-US>pdb_pair<span style='mso-spacerun:yes'> </span>built_in</span></span></span></span></p>
\r
13845 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
13846 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13847 lang=EN-US>sap_pair<span style='mso-spacerun:yes'>
\r
13848 </span>http://www-cryst.bioc.cam.ac.uk/fugue/download.html</span></span></span></span></p>
\r
13850 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
13851 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13852 lang=EN-US>mustang_pair<span style='mso-spacerun:yes'>
\r
13853 </span>http://www.cs.mu.oz.au/~arun/mustang/</span></span></span></span></p>
\r
13855 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
13856 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13857 lang=EN-US>tmalign_pair<span style='mso-spacerun:yes'>
\r
13858 </span>http://zhang.bioinformatics.ku.edu/TM-align/</span></span></span></span></p>
\r
13860 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
13861 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13862 lang=EN-US><o:p> </o:p></span></span></span></span></p>
\r
13864 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
13865 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13866 lang=EN-US>****** Multiple Sequence Alignment Methods:</span></span></span></span></p>
\r
13868 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
13869 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13870 lang=EN-US>--------------------------------------------</span></span></span></span></p>
\r
13872 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
13873 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13874 lang=EN-US>clustalw_msa<span style='mso-spacerun:yes'>
\r
13875 </span>ftp://www.ebi.ac.uk/pub/clustalw</span></span></span></span></p>
\r
13877 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
13878 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13879 lang=EN-US>mafft_msa<span style='mso-spacerun:yes'>
\r
13880 </span>http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft/</span></span></span></span></p>
\r
13882 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
13883 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13884 lang=EN-US>mafftjtt_msa<span style='mso-spacerun:yes'>
\r
13885 </span>http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft/</span></span></span></span></p>
\r
13887 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
13888 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13889 lang=EN-US>mafftgins_msa<span style='mso-spacerun:yes'>
\r
13890 </span>http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft/</span></span></span></span></p>
\r
13892 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
13893 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13894 lang=EN-US>dialigntx_msa<span style='mso-spacerun:yes'>
\r
13895 </span>http://dialign-tx.gobics.de/</span></span></span></span></p>
\r
13897 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
13898 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13899 lang=EN-US>dialignt_msa<span style='mso-spacerun:yes'>
\r
13900 </span>http://dialign-t.gobics.de/</span></span></span></span></p>
\r
13902 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
13903 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13904 lang=EN-US>poa_msa<span style='mso-spacerun:yes'>
\r
13905 </span>http://www.bioinformatics.ucla.edu/poa/</span></span></span></span></p>
\r
13907 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
13908 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13909 lang=EN-US>probcons_msa<span style='mso-spacerun:yes'>
\r
13910 </span>http://probcons.stanford.edu/</span></span></span></span></p>
\r
13912 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
13913 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13914 lang=EN-US>muscle_msa<span style='mso-spacerun:yes'>
\r
13915 </span>http://www.drive5.com/muscle/</span></span></span></span></p>
\r
13917 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
13918 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13919 lang=EN-US>t_coffee_msa<span style='mso-spacerun:yes'>
\r
13920 </span>http://www.tcoffee.org</span></span></span></span></p>
\r
13922 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
13923 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13924 lang=EN-US>pcma_msa<span style='mso-spacerun:yes'>
\r
13925 </span>ftp://iole.swmed.edu/pub/PCMA/</span></span></span></span></p>
\r
13927 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
13928 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13929 lang=EN-US>kalign_msa<span style='mso-spacerun:yes'>
\r
13930 </span>http://msa.cgb.ki.se</span></span></span></span></p>
\r
13932 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
13933 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13934 lang=EN-US>amap_msa<span style='mso-spacerun:yes'>
\r
13935 </span>http://bio.math.berkeley.edu/amap/</span></span></span></span></p>
\r
13937 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
13938 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13939 lang=EN-US>proda_msa<span style='mso-spacerun:yes'>
\r
13940 </span>http://bio.math.berkeley.edu/proda/</span></span></span></span></p>
\r
13942 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
13943 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13944 lang=EN-US>prank_msa<span style='mso-spacerun:yes'>
\r
13945 </span>http://www.ebi.ac.uk/goldman-srv/prank/</span></span></span></span></p>
\r
13947 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
13948 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13949 lang=EN-US><o:p> </o:p></span></span></span></span></p>
\r
13951 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
13952 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13953 lang=EN-US>#######<span style='mso-spacerun:yes'> </span>Prediction Methods
\r
13954 available to generate Templates</span></span></span></span></p>
\r
13956 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
13957 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13958 lang=EN-US>-------------------------------------------------------------</span></span></span></span></p>
\r
13960 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
13961 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13962 lang=EN-US>RNAplfold<span style='mso-spacerun:yes'>
\r
13963 </span>http://www.tbi.univie.ac.at/~ivo/RNA/</span></span></span></span></p>
\r
13965 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
13966 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13967 lang=EN-US>HMMtop<span style='mso-spacerun:yes'>
\r
13968 </span>www.enzim.hu/hmmtop/</span></span></span></span></p>
\r
13970 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
13971 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13972 lang=EN-US>GOR4<span style='mso-spacerun:yes'>
\r
13973 </span>http://mig.jouy.inra.fr/logiciels/gorIV/</span></span></span></span></p>
\r
13975 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
13976 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13977 lang=EN-US>wublast_client<span style='mso-spacerun:yes'>
\r
13978 </span>http://www.ebi.ac.uk/Tools/webservices/services/wublast</span></span></span></span></p>
\r
13980 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
13981 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13982 lang=EN-US>blastpgp_client<span style='mso-spacerun:yes'> </span>http://www.ebi.ac.uk/Tools/webservices/services/blastpgp<span
\r
13983 style='mso-spacerun:yes'> </span></span></span></span></span></p>
\r
13985 <p class=examplefileCxSpLast><span style='mso-bookmark:_Toc101065206'><span
\r
13986 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13987 lang=EN-US>==========================================================</span></span></span></span></p>
\r
13991 <p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span
\r
13992 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13993 lang=AF><o:p> </o:p></span></span></span></span></p>
\r
13995 <p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span
\r
13996 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
13997 lang=AF><o:p> </o:p></span></span></span></span></p>
\r
13999 <h2><span style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span
\r
14000 style='mso-bookmark:_Toc102494675'><a name="_Toc235958481"><span lang=EN-US>Installation
\r
14001 of PSI-Coffee and Expresso</span></a></span></span></span></h2>
\r
14003 <p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span
\r
14004 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
14005 lang=AF>PSI-Coffee is a mode of T-Coffee that runs a a Psi-BLAST on each of
\r
14006 your sequences and makes a multiple profile alignment. If you do not have any
\r
14007 structural information, it is by far the most accurate mode of T-Coffee. To use
\r
14008 it, you must have SOAP installed so that the EBI BLAST client can run on your
\r
14009 system.</span></span></span></span></p>
\r
14011 <p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span
\r
14012 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
14013 lang=AF>It is a bit slow, but really worth it if your sequences are hard to
\r
14014 align and if the accuracy of your alignment is important. <span
\r
14015 style='mso-spacerun:yes'> </span></span></span></span></span></p>
\r
14017 <p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span
\r
14018 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
14019 lang=AF>To use this mode, try:</span></span></span></span></p>
\r
14021 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
14022 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
14023 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
14024 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
14026 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span
\r
14027 style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span
\r
14028 style='mso-bookmark:_Toc102494675'><span lang=EN-US><span style='mso-tab-count:
\r
14029 1'> </span>t_coffee <yoursequence> -mode psicoffee</span></span></span></span></p>
\r
14033 <p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span
\r
14034 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
14035 lang=AF>Note that because PSI-BLAST is time consuming, T-Coffee stores the runs
\r
14036 in its cache (./tcoffee/cache) so that it does not need to be re-run. It means
\r
14037 that if you re-align your sequences (or add a few extra sequences), things will
\r
14038 be considerably faster.</span></span></span></span></p>
\r
14040 <p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span
\r
14041 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
14042 lang=AF>If your installation procedure has managed to compile TMalign, and if
\r
14043 T-Coffee has access to the EBI BLAST server (or any other server) you can also
\r
14044 do the following:</span></span></span></span></p>
\r
14046 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
14047 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
14048 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
14049 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
14051 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span
\r
14052 style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span
\r
14053 style='mso-bookmark:_Toc102494675'><span lang=EN-US><span style='mso-tab-count:
\r
14054 1'> </span>t_coffee <yoursequence> -mode expresso</span></span></span></span></p>
\r
14058 <p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span
\r
14059 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
14060 lang=AF>That will look for structural templates. And if both these modes are
\r
14061 running fine, then you are ready for the best, the "crème de la
\r
14062 crème":</span></span></span></span></p>
\r
14064 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
14065 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
14066 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
14067 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
14069 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span
\r
14070 style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span
\r
14071 style='mso-bookmark:_Toc102494675'><span lang=EN-US><span style='mso-tab-count:
\r
14072 1'> </span>t_coffee <yoursequence> -mode accurate</span></span></span></span></p>
\r
14076 <h2><span style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span
\r
14077 style='mso-bookmark:_Toc102494675'><a name="_Toc235958482"><span lang=EN-US>Installation
\r
14078 of M-Coffee</span></a></span></span></span></h2>
\r
14080 <p class=MsoNormal><span style='mso-bookmark:_Toc101065206'><span
\r
14081 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
14082 lang=EN-US><o:p> </o:p></span></span></span></span></p>
\r
14084 <p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span
\r
14085 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
14086 lang=AF>M-Coffee is a special mode of T-Coffee that makes it possible to
\r
14087 combine the output of many multiple sequence alignment packages. </span></span></span></span><span
\r
14088 style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span
\r
14089 style='mso-bookmark:_Toc102494675'><span lang=EN-US style='mso-ansi-language:
\r
14090 EN-US'><o:p></o:p></span></span></span></span></p>
\r
14092 <h3><span style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span
\r
14093 style='mso-bookmark:_Toc102494675'><a name="_Toc235958483"><span lang=EN-US>Automated
\r
14094 Installation</span></a></span></span></span></h3>
\r
14096 <p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span
\r
14097 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
14098 lang=AF>In the T-Coffee distribution, type:</span></span></span></span></p>
\r
14100 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
14101 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
14102 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
14103 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
14105 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span
\r
14106 style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span
\r
14107 style='mso-bookmark:_Toc102494675'><span lang=EN-US>./install mcoffee</span></span></span></span></p>
\r
14111 <p class=MsoNormal><span style='mso-bookmark:_Toc101065206'><span
\r
14112 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
14113 lang=EN-US><o:p> </o:p></span></span></span></span></p>
\r
14115 <p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span
\r
14116 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
14117 lang=AF>In theory, this command should download and install every required
\r
14118 package. If, however, it fails, you should switch to the manual installation
\r
14119 (see next).</span></span></span></span></p>
\r
14121 <p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span
\r
14122 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
14123 lang=AF>By default these packages will be in </span></span></span></span></p>
\r
14125 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
14126 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
14127 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
14128 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
14130 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span
\r
14131 style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span
\r
14132 style='mso-bookmark:_Toc102494675'><span lang=EN-US>$HOME/.t_coffee/plugins</span></span></span></span></p>
\r
14136 <p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span
\r
14137 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
14138 lang=AF>If you want to have these companion packages in a different directory,
\r
14139 you can either set the environement variable </span></span></span></span></p>
\r
14141 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
14142 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
14143 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
14144 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
14146 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span
\r
14147 style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span
\r
14148 style='mso-bookmark:_Toc102494675'><span lang=EN-US>PLUGINS_4_TCOFFEE=<plugins
\r
14149 dir></span></span></span></span></p>
\r
14153 <p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span
\r
14154 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
14155 lang=AF>Or use the command line flag -plugin (over-rides every other setting)</span></span></span></span></p>
\r
14157 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
14158 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
14159 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
14160 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
14162 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span
\r
14163 style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span
\r
14164 style='mso-bookmark:_Toc102494675'><span lang=EN-US>t_coffee ...
\r
14165 -plugins=<plugins dir></span></span></span></span></p>
\r
14169 <p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span
\r
14170 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
14171 lang=AF><o:p> </o:p></span></span></span></span></p>
\r
14173 <p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span
\r
14174 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
14175 lang=AF><o:p> </o:p></span></span></span></span></p>
\r
14177 <h3><span style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span
\r
14178 style='mso-bookmark:_Toc102494675'><a name="_Toc235958484"><span lang=EN-US>Manual
\r
14179 Installation</span></a></span></span></span></h3>
\r
14181 <p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span
\r
14182 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
14183 lang=AF>M-Coffee requires a standard T-Coffee installation (c.f. previous
\r
14184 section) and the following packages to be installed on your system:</span></span></span></span></p>
\r
14186 <p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span
\r
14187 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
14188 lang=AF><span style='mso-tab-count:1'> </span></span></span></span></span></p>
\r
14190 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
\r
14191 mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
\r
14192 background:#E6E6E6'>
\r
14194 <p class=examplefileCxSpFirst><span style='mso-bookmark:_Toc101065206'><span
\r
14195 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
14196 lang=EN-US>Package<span style='mso-tab-count:2'> </span>Where From</span></span></span></span></p>
\r
14198 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
14199 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
14200 lang=EN-US>==========================================================</span></span></span></span></p>
\r
14202 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
14203 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
14204 lang=EN-US>ClustalW<span style='mso-tab-count:2'> </span>can interact
\r
14205 with t_coffee</span></span></span></span></p>
\r
14207 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
14208 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
14209 lang=EN-US>----------------------------------------------------------</span></span></span></span></p>
\r
14211 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
14212 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
14213 lang=EN-US>Poa<span style='mso-tab-count:3'> </span>http://www.bioinformatics.ucla.edu/poa/</span></span></span></span></p>
\r
14215 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
14216 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
14217 lang=EN-US>----------------------------------------------------------</span></span></span></span></p>
\r
14219 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
14220 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
14221 lang=EN-US>Muscle<span style='mso-tab-count:2'> </span>http://www.drive5.com</span></span></span></span></p>
\r
14223 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
14224 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
14225 lang=EN-US><span style='mso-spacerun:yes'> </span>----------------------------------------------------------</span></span></span></span></p>
\r
14227 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
14228 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
14229 lang=EN-US>ProbCons<span style='mso-tab-count:2'> </span>http://probcons.stanford.edu/</span></span></span></span></p>
\r
14231 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
14232 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
14233 lang=EN-US>ProbConsRNA<span style='mso-tab-count:2'> </span>http://probcons.stanford.edu/</span></span></span></span></p>
\r
14235 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
14236 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
14237 lang=EN-US>----------------------------------------------------------</span></span></span></span></p>
\r
14239 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
14240 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
14241 lang=EN-US>MAFFT<span style='mso-tab-count:1'> </span></span></span></span></span><a
\r
14242 href="http://www.biophys.kyoto-/"><span style='mso-bookmark:_Toc101065206'><span
\r
14243 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
14244 lang=EN-US>http://www.biophys.kyoto-</span></span></span></span><span
\r
14245 style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span
\r
14246 style='mso-bookmark:_Toc102494675'></span></span></span></a><span
\r
14247 style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span
\r
14248 style='mso-bookmark:_Toc102494675'><span lang=EN-US>u.ac.jp/~katoh/programs/align/mafft/</span></span></span></span></p>
\r
14250 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
14251 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
14252 lang=EN-US>----------------------------------------------------------</span></span></span></span></p>
\r
14254 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
14255 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
14256 lang=EN-US>Dialign-T<span style='mso-tab-count:2'> </span></span></span></span></span><a
\r
14257 href="http://dialign-t.gobics.de/"><span style='mso-bookmark:_Toc101065206'><span
\r
14258 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
14259 lang=EN-US>http://dialign-t.gobics.de/</span></span></span></span><span
\r
14260 style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span
\r
14261 style='mso-bookmark:_Toc102494675'></span></span></span></a><span
\r
14262 style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span
\r
14263 style='mso-bookmark:_Toc102494675'></span></span></span></p>
\r
14265 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
14266 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
14267 lang=EN-US>Dialign-TX<span style='mso-tab-count:2'> </span></span></span></span></span><a
\r
14268 href="http://dialign-t.gobics.de/"><span style='mso-bookmark:_Toc101065206'><span
\r
14269 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
14270 lang=EN-US>http://dialign-tx.gobics.de/</span></span></span></span><span
\r
14271 style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span
\r
14272 style='mso-bookmark:_Toc102494675'></span></span></span></a><span
\r
14273 style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span
\r
14274 style='mso-bookmark:_Toc102494675'></span></span></span></p>
\r
14276 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
14277 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
14278 lang=EN-US>----------------------------------------------------------</span></span></span></span></p>
\r
14280 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
14281 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
14282 lang=EN-US>PCMA<span style='mso-tab-count:3'> </span></span></span></span></span><a
\r
14283 href="ftp://iole.swmed.edu/pub/PCMA/"><span style='mso-bookmark:_Toc101065206'><span
\r
14284 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
14285 lang=EN-US>ftp://iole.swmed.edu/pub/PCMA/</span></span></span></span><span
\r
14286 style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span
\r
14287 style='mso-bookmark:_Toc102494675'></span></span></span></a><span
\r
14288 style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span
\r
14289 style='mso-bookmark:_Toc102494675'></span></span></span></p>
\r
14291 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
14292 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
14293 lang=EN-US>----------------------------------------------------------</span></span></span></span></p>
\r
14295 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
14296 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
14297 lang=EN-US>kalign<span style='mso-spacerun:yes'>
\r
14298 </span>http://msa.cgb.ki.se</span></span></span></span></p>
\r
14300 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
14301 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
14302 lang=EN-US>----------------------------------------------------------</span></span></span></span></p>
\r
14304 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
14305 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
14306 lang=EN-US>amap<span style='mso-spacerun:yes'>
\r
14307 </span>http://bio.math.berkeley.edu/amap/</span></span></span></span></p>
\r
14309 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
14310 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
14311 lang=EN-US>-----------------------------------------------------------</span></span></span></span></p>
\r
14313 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
14314 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
14315 lang=EN-US>proda_msa<span style='mso-spacerun:yes'>
\r
14316 </span>http://bio.math.berkeley.edu/proda/</span></span></span></span></p>
\r
14318 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
14319 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
14320 lang=EN-US>-----------------------------------------------------------</span></span></span></span></p>
\r
14322 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
14323 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
14324 lang=EN-US>prank_msa<span style='mso-spacerun:yes'> </span>http://www.ebi.ac.uk/goldman-srv/prank/</span></span></span></span></p>
\r
14326 <p class=examplefileCxSpLast><span style='mso-bookmark:_Toc101065206'><span
\r
14327 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
14328 lang=EN-US><o:p> </o:p></span></span></span></span></p>
\r
14332 <p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span
\r
14333 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
14334 lang=AF><o:p> </o:p></span></span></span></span></p>
\r
14336 <p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span
\r
14337 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
14338 lang=AF>In our hands all these packages where very straightforward to compile
\r
14339 and install on a standard cygwin or Linux configuration. Just make sure you
\r
14340 have gcc, the C compiler, properly installed.</span></span></span></span></p>
\r
14342 <p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span
\r
14343 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
14344 lang=AF>Once the package is compiled and ready to use, make sure that the
\r
14345 executable is on your path, so that t_coffee can find it automatically. Our
\r
14346 favorite procedure is to create a bin directory in the home. If you do so, make
\r
14347 sure this bin is in your path and fill it with all your executables (this is a
\r
14348 standard Unix practice).</span></span></span></span></p>
\r
14350 <p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span
\r
14351 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
14352 lang=AF>If for some reason, you do not want this directory to be on your path,
\r
14353 or you want to specify a precise directory containing the executables, you can
\r
14354 use:</span></span></span></span></p>
\r
14356 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
14357 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
14358 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
14359 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
14361 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span
\r
14362 style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span
\r
14363 style='mso-bookmark:_Toc102494675'><span lang=EN-US><span style='mso-tab-count:
\r
14364 1'> </span>export PLUGINS_4_TCOFFEE=<dir></span></span></span></span></p>
\r
14368 <p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span
\r
14369 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
14370 lang=AF>By default this directory is set to $HOME/.t_coffee/plugins/$OS, but
\r
14371 you can over-ride it with the environement variable or using the flag:</span></span></span></span></p>
\r
14373 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
14374 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
14375 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
14376 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
14378 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span
\r
14379 style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span
\r
14380 style='mso-bookmark:_Toc102494675'><span lang=EN-US><span style='mso-tab-count:
\r
14381 1'> </span>t_coffee ...-plugins=<dir></span></span></span></span></p>
\r
14385 <p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span
\r
14386 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
14387 lang=AF><o:p> </o:p></span></span></span></span></p>
\r
14389 <p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span
\r
14390 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
14391 lang=AF>If you cannot, or do not want to use a single bin directory, you can
\r
14392 set the following environment variables to the absolute path values of the
\r
14393 executable you want to use. Whenever they are set, these variables will supersede
\r
14394 any other declaration. This is a convenient way to experiment with multiple
\r
14395 package versions.</span></span></span></span></p>
\r
14397 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
14398 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
14399 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
14400 background:#FFFFCC;margin-left:70.2pt;margin-right:0mm'>
\r
14402 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span
\r
14403 style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span
\r
14404 style='mso-bookmark:_Toc102494675'><span lang=EN-US>POA_4_TCOOFFEE<br>
\r
14405 CLUSTALW_4_TCOFFEE<br>
\r
14406 POA_4_TCOFFEE<br>
\r
14407 TCOFFEE_4_TCOFFEE<br>
\r
14408 MAFFT_4_TCOFFEE<br>
\r
14409 MUSCLE_4_TCOFFEE<br>
\r
14410 DIALIGNT_4_TCOFFEE<br>
\r
14411 PRANK_4_TCOFFEE<br>
\r
14412 DIALIGNTX_4_TCOFFEE<br>
\r
14413 <span style='mso-spacerun:yes'> </span></span></span></span></span></p>
\r
14417 <p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span
\r
14418 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
14419 lang=AF>For three of these packages, you will need to copy some of the files in
\r
14420 a special T-Coffee directory.</span></span></span></span></p>
\r
14422 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
14423 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
14424 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
14425 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
14427 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span
\r
14428 style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span
\r
14429 style='mso-bookmark:_Toc102494675'><span lang=EN-US><span style='mso-tab-count:
\r
14430 1'> </span>cp POA_DIR/* ~/.t_coffee/mcoffee/</span></span></span></span></p>
\r
14432 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span
\r
14433 style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span
\r
14434 style='mso-bookmark:_Toc102494675'><span lang=EN-US><span style='mso-tab-count:
\r
14435 1'> </span>cp DIALIGN-T/conf/*<span style='mso-spacerun:yes'> </span>~/.t_coffee/mcoffee</span></span></span></span></p>
\r
14437 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span
\r
14438 style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span
\r
14439 style='mso-bookmark:_Toc102494675'><span lang=EN-US><span style='mso-tab-count:
\r
14440 1'> </span>cp DIALIGN-TX/conf/*<span style='mso-spacerun:yes'>
\r
14441 </span>~/.t_coffee/mcoffee</span></span></span></span></p>
\r
14445 <p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span
\r
14446 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
14447 lang=AF>Note that the following files are enough for default usage:</span></span></span></span></p>
\r
14449 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
14450 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
14451 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
14452 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
14454 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span
\r
14455 style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span
\r
14456 style='mso-bookmark:_Toc102494675'><span lang=EN-US>BLOSUM.diag_prob_t10<span
\r
14457 style='mso-spacerun:yes'> </span>BLOSUM75.scr<span style='mso-spacerun:yes'>
\r
14458 </span>blosum80_trunc.mat<span style='mso-spacerun:yes'> </span></span></span></span></span></p>
\r
14460 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span
\r
14461 style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span
\r
14462 style='mso-bookmark:_Toc102494675'><span lang=EN-US>dna_diag_prob_100_exp_330000<span
\r
14463 style='mso-spacerun:yes'> </span>dna_diag_prob_200_exp_110000</span></span></span></span></p>
\r
14465 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span
\r
14466 style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span
\r
14467 style='mso-bookmark:_Toc102494675'><span lang=EN-US>BLOSUM.scr<span
\r
14468 style='mso-spacerun:yes'> </span>BLOSUM90.scr<span
\r
14469 style='mso-spacerun:yes'> </span>dna_diag_prob_100_exp_110000</span></span></span></span></p>
\r
14471 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span
\r
14472 style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span
\r
14473 style='mso-bookmark:_Toc102494675'><span lang=EN-US>dna_diag_prob_100_exp_550000<span
\r
14474 style='mso-spacerun:yes'> </span>dna_diag_prob_250_exp_110000</span></span></span></span></p>
\r
14476 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span
\r
14477 style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span
\r
14478 style='mso-bookmark:_Toc102494675'><span lang=EN-US>BLOSUM75.diag_prob_t2<span
\r
14479 style='mso-spacerun:yes'> </span>blosum80.mat<span style='mso-spacerun:yes'>
\r
14480 </span>dna_diag_prob_100_exp_220000<span style='mso-spacerun:yes'> </span></span></span></span></span></p>
\r
14482 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span
\r
14483 style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span
\r
14484 style='mso-bookmark:_Toc102494675'><span lang=EN-US>dna_diag_prob_150_exp_110000<span
\r
14485 style='mso-spacerun:yes'> </span>dna_matrix.scr</span></span></span></span></p>
\r
14489 <p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span
\r
14490 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
14491 lang=AF><o:p> </o:p></span></span></span></span></p>
\r
14493 <p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span
\r
14494 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
14495 lang=AF>If you would rather have the mcoffee directory in some other location,
\r
14496 set the MCOFFEE_4_TCOFFEE environement variable to the propoer directory:</span></span></span></span></p>
\r
14498 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
14499 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
14500 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
14501 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
14503 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span
\r
14504 style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span
\r
14505 style='mso-bookmark:_Toc102494675'><span lang=EN-US><span style='mso-tab-count:
\r
14506 1'> </span>setenv MCOFFEE_4_TCOFFEE <directory containing mcoffee
\r
14507 files></span></span></span></span></p>
\r
14511 <h2><span style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span
\r
14512 style='mso-bookmark:_Toc102494675'><a name="_Toc235958485"><span lang=EN-US>Installation
\r
14513 of APDB and iRMSD</span></a></span></span></span></h2>
\r
14515 <p class=MsoBodyText><span style='mso-bookmark:_Toc101065206'><span
\r
14516 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
14517 lang=EN-US>APDB and iRMSD are incorporated in T-Coffee. Once t_coffee is
\r
14518 installed, you can invoque these programs by typing:</span></span></span></span></p>
\r
14520 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
14521 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
14522 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
14523 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
14525 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span
\r
14526 style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span
\r
14527 style='mso-bookmark:_Toc102494675'><span lang=EN-US><span style='mso-tab-count:
\r
14528 1'> </span>t_coffee
\96other_pg apdb<br>
\r
14529 <span style='mso-tab-count:1'> </span>t_coffee
\96other_pg irmsd</span></span></span></span></p>
\r
14533 <h2><span style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span
\r
14534 style='mso-bookmark:_Toc102494675'><a name="_Toc235958486"><span lang=EN-US>Installation
\r
14535 of tRMSD</span></a></span></span></span></h2>
\r
14537 <p class=MsoBodyText><span style='mso-bookmark:_Toc101065206'><span
\r
14538 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
14539 lang=EN-US>tRMSD comes along with t_coffee but it also requires the package
\r
14540 phylip in order to be functional. Phylip can be obtained from:</span></span></span></span></p>
\r
14542 <p class=MyNormal><span style='mso-bookmark:_Toc101065206'><span
\r
14543 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
14544 lang=AF><span style='mso-tab-count:1'> </span></span></span></span></span></p>
\r
14546 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
\r
14547 mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
\r
14548 background:#E6E6E6'>
\r
14550 <p class=examplefileCxSpFirst><span style='mso-bookmark:_Toc101065206'><span
\r
14551 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
14552 lang=EN-US>Package<span style='mso-tab-count:2'> </span>Function</span></span></span></span></p>
\r
14554 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
14555 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
14556 lang=EN-US>===================================================</span></span></span></span></p>
\r
14558 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
14559 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
14560 lang=EN-US>---------------------------------------------------</span></span></span></span></p>
\r
14562 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
14563 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
14564 lang=EN-US>Phylip<span style='mso-tab-count:2'> </span>Phylogenetic
\r
14565 tree computation</span></span></span></span></p>
\r
14567 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065206'><span
\r
14568 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
14569 lang=EN-US><span style='mso-tab-count:3'> </span>evolution.genetics.washington.edu/phylip.html</span></span></span></span></p>
\r
14571 <p class=examplefileCxSpLast><span style='mso-bookmark:_Toc101065206'><span
\r
14572 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
14573 lang=EN-US>---------------------------------------------------</span></span></span></span></p>
\r
14577 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
14578 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
14579 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
14580 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
14582 <p class=MyExample style='margin-left:0mm;text-indent:14.1pt;background:#FFFFCC'><span
\r
14583 style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span
\r
14584 style='mso-bookmark:_Toc102494675'><span lang=EN-US>t_coffee
\96other_pg trmsd</span></span></span></span></p>
\r
14588 <h2><span style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span
\r
14589 style='mso-bookmark:_Toc102494675'><span lang=EN-US><o:p> </o:p></span></span></span></span></h2>
\r
14591 <h2><span style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span
\r
14592 style='mso-bookmark:_Toc102494675'><a name="_Toc235958487"><span lang=EN-US>Installation
\r
14593 of seq_reformat</span></a></span></span></span></h2>
\r
14595 <p class=MsoBodyText><span style='mso-bookmark:_Toc101065206'><span
\r
14596 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
14597 lang=EN-US>Seq_reformat is a reformatting package that is part of t_coffee. To
\r
14598 use it (and see the available options), type:</span></span></span></span></p>
\r
14600 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
14601 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
14602 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
14603 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
14605 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span
\r
14606 style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span
\r
14607 style='mso-bookmark:_Toc102494675'><span lang=EN-US><span style='mso-tab-count:
\r
14608 1'> </span>t_coffee
\96other_pg seq_reformat</span></span></span></span></p>
\r
14612 <h2><span style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span
\r
14613 style='mso-bookmark:_Toc102494675'><a name="_Toc235958488"><span lang=EN-US>Installation
\r
14614 of extract_from_pdb</span></a></span></span></span></h2>
\r
14616 <p class=MsoBodyText><span style='mso-bookmark:_Toc101065206'><span
\r
14617 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
14618 lang=EN-US>Extract_from_pdb is a PDB reformatting package that is part of
\r
14619 t_coffee. To use it (and see the available options), type.</span></span></span></span></p>
\r
14621 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
14622 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
14623 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
14624 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
14626 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span
\r
14627 style='mso-bookmark:_Toc101065206'><span style='mso-bookmark:_Toc102494295'><span
\r
14628 style='mso-bookmark:_Toc102494675'><span lang=EN-US><span style='mso-tab-count:
\r
14629 1'> </span>t_coffee
\96other_pg apdb
\96h</span></span></span></span></p>
\r
14633 <p class=MsoBodyText><span style='mso-bookmark:_Toc101065206'><span
\r
14634 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
14635 lang=EN-US>Extract_from_pdb requires wget in order to automatically fetch PDB
\r
14636 structures.</span></span></span></span></p>
\r
14638 <p class=MsoBodyText><span style='mso-bookmark:_Toc101065206'><span
\r
14639 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc102494675'><span
\r
14640 lang=EN-US><o:p> </o:p></span></span></span></span></p>
\r
14642 <span style='mso-bookmark:_Toc102494675'></span><span style='mso-bookmark:_Toc102494295'></span><span
\r
14643 style='mso-bookmark:_Toc101065206'></span>
\r
14645 <h2><a name="_Toc235958489"><span lang=EN-US>Installation of 3D-Coffee/Expresso</span></a></h2>
\r
14647 <p class=MyNormal><span lang=AF>3D-Coffee/Expresso is a special mode of
\r
14648 T-Coffee that makes it possible to combine sequences and structures. The main
\r
14649 difference between Expresso and 3D-Coffee is that Expresso fetches the
\r
14650 structures itself. </span><span lang=EN-US style='mso-ansi-language:EN-US'><o:p></o:p></span></p>
\r
14652 <h3><a name="_Toc235958490"><span lang=EN-US>Automated Installation</span></a></h3>
\r
14654 <p class=MyNormal><span lang=AF>In the T-Coffee distribution, type:</span></p>
\r
14656 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
14657 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
14658 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
14659 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
14661 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>./install
\r
14662 expresso</span></p>
\r
14664 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>OR</span></p>
\r
14666 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>./install
\r
14667 3dcoffee</span></p>
\r
14671 <p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p>
\r
14673 <p class=MyNormal><span lang=AF>In theory, this command should download and
\r
14674 install every required package (<b>except fugue</b>). If, however, it fails,
\r
14675 you should switch to the manual installation (see next).</span></p>
\r
14677 <h3><a name="_Toc235958491"><span lang=EN-US>Manual Installation</span></a></h3>
\r
14679 <p class=MyNormal><span lang=AF>In order to make the most out of T-Coffee, you
\r
14680 will need to install the following packages (make sure the executable is named
\r
14681 as indicated below):</span></p>
\r
14683 <p class=MyNormal><span lang=AF><span style='mso-tab-count:1'> </span></span></p>
\r
14685 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
\r
14686 mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
\r
14687 background:#E6E6E6'>
\r
14689 <p class=examplefileCxSpFirst><span lang=EN-US>Package<span style='mso-tab-count:
\r
14690 2'> </span>Function</span></p>
\r
14692 <p class=examplefileCxSpMiddle><span lang=EN-US>===================================================</span></p>
\r
14694 <p class=examplefileCxSpMiddle><span lang=EN-US>---------------------------------------------------</span></p>
\r
14696 <p class=examplefileCxSpMiddle><span lang=EN-US>wget<span style='mso-tab-count:
\r
14697 2'> </span><span style='mso-tab-count:1'> </span>3DCoffee </span></p>
\r
14699 <p class=examplefileCxSpMiddle><span lang=EN-US><span style='mso-tab-count:
\r
14700 3'> </span>Automatic Downloading of Structures</span></p>
\r
14702 <p class=examplefileCxSpMiddle><span lang=EN-US>---------------------------------------------------</span></p>
\r
14704 <p class=examplefileCxSpMiddle><span lang=EN-US>sap<span style='mso-tab-count:
\r
14705 1'> </span><span style='mso-tab-count:1'> </span><span style='mso-tab-count:
\r
14706 1'> </span>structure/structure comparisons </span></p>
\r
14708 <p class=examplefileCxSpMiddle><span lang=EN-US>(obtain it from <st1:place
\r
14709 w:st="on">W. Taylor</st1:place>, NIMR-MRC).</span></p>
\r
14711 <p class=examplefileCxSpMiddle><span lang=EN-US>---------------------------------------------------</span></p>
\r
14713 <p class=examplefileCxSpMiddle><span lang=EN-US>TMalign<span style='mso-tab-count:
\r
14714 2'> </span>zhang.bioinformatics.ku.edu/TM-align/</span></p>
\r
14716 <p class=examplefileCxSpMiddle><span lang=EN-US>---------------------------------------------------</span></p>
\r
14718 <p class=examplefileCxSpMiddle><span lang=EN-US>mustang<span style='mso-tab-count:
\r
14719 2'> </span>www.cs.mu.oz.au/~arun/mustang/</span></p>
\r
14721 <p class=examplefileCxSpMiddle><span lang=EN-US>---------------------------------------------------</span></p>
\r
14723 <p class=examplefileCxSpMiddle><span lang=EN-US>wublastclient<span
\r
14724 style='mso-spacerun:yes'> </span>www.ebi.ac.uk/Tools/webservices/clients/wublast</span></p>
\r
14726 <p class=examplefileCxSpMiddle><span lang=EN-US>---------------------------------------------------</span></p>
\r
14728 <p class=examplefileCxSpMiddle><span lang=EN-US>Blast<span style='mso-tab-count:
\r
14729 2'> </span><span style='mso-tab-count:1'> </span><a
\r
14730 href="http://www.ncbi.nih.nlm.gov/">www.ncbi.nih.nlm.gov</a></span></p>
\r
14732 <p class=examplefileCxSpMiddle><span lang=EN-US>---------------------------------------------------</span></p>
\r
14734 <p class=examplefileCxSpMiddle><span lang=EN-US>Fugue*<span style='mso-tab-count:
\r
14735 2'> </span>protein to structure alignment program</span></p>
\r
14737 <p class=examplefileCxSpMiddle><span lang=EN-US><span style='mso-tab-count:
\r
14738 3'> </span>http://www-cryst.bioc.cam.ac.uk/fugue/download.html</span></p>
\r
14740 <p class=examplefileCxSpLast><span lang=EN-US><span style='mso-tab-count:3'> </span>***NOT
\r
14741 COMPULSORY***</span></p>
\r
14745 <p class=MyNormal><span lang=AF><o:p> </o:p></span></p>
\r
14747 <p class=MyNormal><span lang=AF>Once the package is installed, make sure make
\r
14748 sure that the executable is on your path, so that t_coffee can find it
\r
14749 automatically.</span></p>
\r
14751 <p class=MyNormal><span lang=AF><o:p> </o:p></span></p>
\r
14753 <p class=MyNormal><span lang=AF>The wublast client makes it possible to run
\r
14754 BLAST at the EBI without having to install any database locally. It is an ideal
\r
14755 solution if you are only using expresso occasionally.</span></p>
\r
14757 <p class=MyNormal><span lang=AF><o:p> </o:p></span></p>
\r
14759 <h3><a name="_Toc235958492"><span lang=EN-US>Installing Fugue for T-Coffee</span></a></h3>
\r
14761 <p class=MyNormal><span lang=AF>Uses a standard fugue installation. You only
\r
14762 need to install the following packages:</span></p>
\r
14764 <p class=MyNormal><span lang=AF><span style='mso-spacerun:yes'> </span>joy,
\r
14765 melody, fugueali, sstruc, hbond</span></p>
\r
14767 <p class=MyNormal><span lang=AF>If you have root privileges, you can install
\r
14768 the common data in: </span></p>
\r
14770 <p class=MyNormal><span lang=AF>cp fugue/classdef.dat<span style='mso-tab-count:
\r
14771 1'> </span>/data/fugue/SUBST/classdef.dat</span></p>
\r
14773 <p class=MyNormal><span lang=AF>otherwise</span></p>
\r
14775 <p class=MyNormal><span lang=AF>Setenv MELODY_CLASSDEF=<location></span></p>
\r
14777 <p class=MyNormal><span lang=AF>Setenv MELODY_SUBST=fugue/allmat.dat</span></p>
\r
14779 <p class=MyNormal><span lang=AF><span style='mso-spacerun:yes'> </span></span></p>
\r
14781 <p class=MyNormal><span lang=AF>All the other configuration files must be in
\r
14782 the right location. </span></p>
\r
14784 <h2><a name="_Toc235958493"><span lang=EN-US>Installation of R-Coffee</span></a></h2>
\r
14786 <p class=MyNormal><span lang=AF>R-Coffee is a special mode able to align RNA
\r
14787 sequences while taking into account their secondary structure.</span><span
\r
14788 lang=EN-US style='mso-ansi-language:EN-US'><o:p></o:p></span></p>
\r
14790 <h3><a name="_Toc235958494"><span lang=EN-US>Automated Installation</span></a></h3>
\r
14792 <p class=MyNormal><span lang=AF>In the T-Coffee distribution, type:</span></p>
\r
14794 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
14795 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
14796 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
14797 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
14799 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>./install
\r
14800 rcoffee</span></p>
\r
14804 <p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p>
\r
14806 <p class=MyNormal><span lang=AF>In theory, this command should download and
\r
14807 install every required package (except <b>consan</b>). If, however, it fails,
\r
14808 you should switch to the manual installation (see next).</span></p>
\r
14810 <h3><a name="_Toc235958495"><span lang=EN-US>Manual Installation</span></a></h3>
\r
14812 <p class=MyNormal><span lang=AF>R-Coffee only requires the package <st1:place
\r
14813 w:st="on"><st1:City w:st="on">Vienna</st1:City></st1:place> to be installed, in
\r
14814 order to compute multiple sequence alignments. To make the best out of it, you
\r
14815 should also have all the packages required by M-Coffee</span></p>
\r
14817 <p class=MyNormal><span lang=AF><span style='mso-tab-count:1'> </span></span></p>
\r
14819 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
\r
14820 mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
\r
14821 background:#E6E6E6'>
\r
14823 <p class=examplefileCxSpFirst><span lang=EN-US>Package<span style='mso-tab-count:
\r
14824 2'> </span>Function</span></p>
\r
14826 <p class=examplefileCxSpMiddle><span lang=EN-US>===================================================</span></p>
\r
14828 <p class=examplefileCxSpMiddle><span lang=EN-US>---------------------------------------------------</span></p>
\r
14830 <p class=examplefileCxSpMiddle><span lang=EN-US>consan<span style='mso-tab-count:
\r
14831 2'> </span>R-Coffee </span></p>
\r
14833 <p class=examplefileCxSpMiddle><span lang=EN-US><span style='mso-tab-count:
\r
14834 3'> </span>Computes highly accurate pairwise Alignments</span></p>
\r
14836 <p class=examplefileCxSpMiddle><span lang=EN-US><span style='mso-tab-count:
\r
14837 3'> </span>***NOT COMPULSORY***</span></p>
\r
14839 <p class=examplefileCxSpMiddle><span lang=EN-US><span style='mso-tab-count:
\r
14840 3'> </span>selab.janelia.org/software/consan/</span></p>
\r
14842 <p class=examplefileCxSpMiddle><span lang=EN-US>---------------------------------------------------</span></p>
\r
14844 <p class=examplefileCxSpMiddle><span lang=EN-US>RNAplfold<span
\r
14845 style='mso-tab-count:2'> </span>Computes RNA secondary Structures </span></p>
\r
14847 <p class=examplefileCxSpMiddle><span lang=EN-US><span style='mso-tab-count:
\r
14848 3'> </span>www.tbi.univie.ac.at/~ivo/RNA/</span></p>
\r
14850 <p class=examplefileCxSpMiddle><span lang=EN-US>---------------------------------------------------</span></p>
\r
14852 <p class=examplefileCxSpMiddle><span lang=EN-US>probconsRNA<span
\r
14853 style='mso-tab-count:2'> </span>probcons.stanford.edu/</span></p>
\r
14855 <p class=examplefileCxSpMiddle><span lang=EN-US><span
\r
14856 style='mso-spacerun:yes'> </span></span></p>
\r
14858 <p class=examplefileCxSpMiddle><span lang=EN-US>---------------------------------------------------</span></p>
\r
14860 <p class=examplefileCxSpMiddle><span lang=EN-US>M-Coffee<span style='mso-tab-count:
\r
14861 2'> </span>T-Coffee and the most common MSA Packages</span></p>
\r
14863 <p class=examplefileCxSpLast><span lang=EN-US><span style='mso-tab-count:3'> </span>(cf
\r
14864 M-Coffee in this installation guide)</span></p>
\r
14868 <h3><a name="_Toc235958496"><span lang=EN-US>Installing ProbbonsRNA for R-Coffee</span></a></h3>
\r
14870 <p class=MyNormal><span lang=AF>Follow the installation procedure, but make
\r
14871 sure you rename the probcons executable into probconsRNA.</span></p>
\r
14873 <h3><a name="_Toc235958497"><span lang=EN-US>Installing Consan for R-Coffee</span></a></h3>
\r
14875 <p class=MyNormal><span lang=AF>In order to insure a proper interface beween
\r
14876 consan and R-Coffee, you must make sure that the file mix80.mod is in the
\r
14877 directory ~/.t_coffee/mcoffee or in the mcoffee directory otherwise declared.</span></p>
\r
14879 <p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p>
\r
14881 <div style='mso-element:para-border-div;border:solid windowtext 3.0pt;
\r
14882 padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#CCCCCC;margin-left:0mm;margin-right:
\r
14885 <p class=ChapterTitle><a name="_Toc235958498"></a><a name="_Toc102494676"></a><a
\r
14886 name="_Toc101065207"><span style='mso-bookmark:_Toc102494676'><span
\r
14887 style='mso-bookmark:_Toc235958498'><span lang=EN-US>Q</span></span></span></a><span
\r
14888 style='mso-bookmark:_Toc235958498'><span lang=EN-US>uick Start</span></span></p>
\r
14892 <p class=MsoBodyText><span lang=EN-US>We only give you the very basics here.
\r
14893 Please use the Tutorial for more detailed information on how to use our tools.</span></p>
\r
14895 <div style='mso-element:para-border-div;border:solid windowtext 1.5pt;
\r
14896 padding:0mm 0mm 0mm 0mm;background:#F7CBB7'>
\r
14898 <p class=Warning><a name="_Toc102494677"></a><a name="_Toc102494296"></a><a
\r
14899 name="_Toc101065208"><span style='mso-bookmark:_Toc102494296'><span
\r
14900 style='mso-bookmark:_Toc102494677'><span lang=EN-US>IMPORTANT: All the files
\r
14901 mentionned here (sampe_seq...) can be found in the example directory of the
\r
14902 distribution.</span></span></span></a></p>
\r
14906 <h2><span style='mso-bookmark:_Toc101065208'><span style='mso-bookmark:_Toc102494296'><span
\r
14907 style='mso-bookmark:_Toc102494677'><a name="_Toc235958499"><span lang=EN-US>T-COFFEE</span></a></span></span></span></h2>
\r
14909 <p class=MyNormal><span lang=AF>Write your sequences in the same file
\r
14910 (Swiss-prot, Fasta or Pir) and type. </span></p>
\r
14912 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
14913 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
14914 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
14915 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
14917 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:
\r
14918 t_coffee sample_seq1.fasta<span style='mso-spacerun:yes'> </span></span></p>
\r
14922 <p class=MyNormal><span lang=AF>This will output two files:</span></p>
\r
14924 <p class=example2CxSpFirst><span lang=EN-US>sample_seq1.aln: your Multiple
\r
14925 Sequence Alignment</span></p>
\r
14927 <p class=example2CxSpLast><span lang=EN-US>sample_seq1.dnd: The Guide tree
\r
14928 (newick Format)</span></p>
\r
14930 <div style='mso-element:para-border-div;border:solid windowtext 1.5pt;
\r
14931 padding:0mm 0mm 0mm 0mm;background:#F7CBB7'>
\r
14933 <p class=Warning><span lang=EN-US>IMPORTANT: </span></p>
\r
14935 <p class=Warning><span lang=EN-US>In theory nucleic acids should be
\r
14936 automatically detected and the default methods should be adapted appropriately.
\r
14937 However, sometimes this may fail, either because the sequences are too short or
\r
14938 contain too many ambiguity codes. </span></p>
\r
14940 <p class=Warning><span lang=EN-US>When this happens, you are advised to
\r
14941 explicitly set the type of your sequences</span></p>
\r
14943 <p class=Warning><span lang=EN-US>NOTE: the
\96mode=dna is not needed or
\r
14944 supported anymore</span></p>
\r
14948 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
14949 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
14950 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
14951 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
14953 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:
\r
14954 t_coffee sample_dnaseq1.fasta
\96type=dna</span></p>
\r
14958 <h2><a name="_Toc102494678"></a><a name="_Toc102494297"></a><a
\r
14959 name="_Toc101065209"></a><a name="_Toc235958500"><span style='mso-bookmark:
\r
14960 _Toc101065209'><span style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:
\r
14961 _Toc102494678'><span lang=EN-US>M-Coffee</span></span></span></span></a><span
\r
14962 style='mso-bookmark:_Toc101065209'><span style='mso-bookmark:_Toc102494297'><span
\r
14963 style='mso-bookmark:_Toc102494678'></span></span></span></h2>
\r
14965 <p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span
\r
14966 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span
\r
14967 lang=AF>M-Coffee is a <st1:place w:st="on">Meta</st1:place> version of T-Coffee
\r
14968 that makes it possible to combine the output of at least eight packages
\r
14969 (Muscle, probcons, poa, dialignT, mafft, clustalw, PCMA and T-Coffee).</span></span></span></span></p>
\r
14971 <p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span
\r
14972 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span
\r
14973 lang=AF>If all these packages are already installed on your machine. You must:</span></span></span></span></p>
\r
14975 <p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span
\r
14976 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span
\r
14977 lang=AF><o:p> </o:p></span></span></span></span></p>
\r
14979 <p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span
\r
14980 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span
\r
14981 lang=AF>1-set the following environment variables</span></span></span></span></p>
\r
14983 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
14984 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
14985 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
14986 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
14988 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span
\r
14989 style='mso-bookmark:_Toc101065209'><span style='mso-bookmark:_Toc102494297'><span
\r
14990 style='mso-bookmark:_Toc102494678'><span lang=EN-US><span style='mso-tab-count:
\r
14991 1'> </span>export POA_DIR=[absolute path of the POA installation dir]</span></span></span></span></p>
\r
14993 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span
\r
14994 style='mso-bookmark:_Toc101065209'><span style='mso-bookmark:_Toc102494297'><span
\r
14995 style='mso-bookmark:_Toc102494678'><span lang=EN-US><span style='mso-tab-count:
\r
14996 1'> </span>export DIALIGNT_DIR=[Absolute path of the DIALIGN-T/conf</span></span></span></span></p>
\r
15000 <p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span
\r
15001 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span
\r
15002 lang=AF>Once this is done, write your sequences in a file and run: same file
\r
15003 (Swiss-prot, Fasta or Pir) and type. </span></span></span></span></p>
\r
15005 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
15006 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
15007 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
15008 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
15010 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span
\r
15011 style='mso-bookmark:_Toc101065209'><span style='mso-bookmark:_Toc102494297'><span
\r
15012 style='mso-bookmark:_Toc102494678'><span lang=EN-US>PROMPT: t_coffee
\r
15013 sample_seq1.fasta
\96mode mcoffee </span></span></span></span></p>
\r
15017 <p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span
\r
15018 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span
\r
15019 lang=AF>If the program starts complaining one package or the other is missing,
\r
15020 this means you will have to go the hard way and install all these packages
\r
15021 yourself... Proceed to the M-Coffee section for more detailed instructions.</span></span></span></span></p>
\r
15023 <h2><span style='mso-bookmark:_Toc101065209'><span style='mso-bookmark:_Toc102494297'><span
\r
15024 style='mso-bookmark:_Toc102494678'><a name="_Toc235958501"><span lang=EN-US>Expresso</span></a></span></span></span></h2>
\r
15026 <p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span
\r
15027 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span
\r
15028 lang=AF>If you have installed the EBI wublast.pl client, Expresso will BLAST
\r
15029 your sequences against PDB, identify the best targets and use these to align
\r
15030 your proteins.</span></span></span></span></p>
\r
15032 <p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span
\r
15033 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span
\r
15034 lang=AF><o:p> </o:p></span></span></span></span></p>
\r
15036 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
15037 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
15038 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
15039 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
15041 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span
\r
15042 style='mso-bookmark:_Toc101065209'><span style='mso-bookmark:_Toc102494297'><span
\r
15043 style='mso-bookmark:_Toc102494678'><span lang=EN-US>PROMPT: t_coffee
\r
15044 sample_seq1.fasta
\96mode expresso</span></span></span></span></p>
\r
15048 <p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span
\r
15049 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span
\r
15050 lang=AF>If you did not manage to install all the required structural packages
\r
15051 for Expresso, like Fugue or Sap, you can still run expresso by selecting
\r
15052 yourself the structural packages you want to use. For instance, if you'd rather
\r
15053 use TM-Align than sap, try: </span></span></span></span></p>
\r
15055 <p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span
\r
15056 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span
\r
15057 lang=AF><span style='mso-tab-count:1'> </span></span></span></span></span></p>
\r
15059 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
15060 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
15061 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
15062 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
15064 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span
\r
15065 style='mso-bookmark:_Toc101065209'><span style='mso-bookmark:_Toc102494297'><span
\r
15066 style='mso-bookmark:_Toc102494678'><span lang=EN-US>PROMPT: t_coffee
\r
15067 sample_seq1.fasta
\96template_file EXPRESSO -method TMalign_pair</span></span></span></span></p>
\r
15071 <p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span
\r
15072 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span
\r
15073 lang=AF><o:p> </o:p></span></span></span></span></p>
\r
15075 <h2><span style='mso-bookmark:_Toc101065209'><span style='mso-bookmark:_Toc102494297'><span
\r
15076 style='mso-bookmark:_Toc102494678'><a name="_Toc235958502"><span lang=EN-US>R-Coffee</span></a></span></span></span></h2>
\r
15078 <p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span
\r
15079 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span
\r
15080 lang=AF>R-Coffee can be used to align RNA sequences, using their RNApfold
\r
15081 predicted secondary structures. The best results are obtained by using the
\r
15082 consan pairwise method. If you have consan installed:</span></span></span></span></p>
\r
15084 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
15085 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
15086 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
15087 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
15089 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span
\r
15090 style='mso-bookmark:_Toc101065209'><span style='mso-bookmark:_Toc102494297'><span
\r
15091 style='mso-bookmark:_Toc102494678'><span lang=EN-US>t_coffee
\r
15092 sample_rnaseq1.fasta
\96special_mode rcoffee_consan </span></span></span></span></p>
\r
15096 <p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span
\r
15097 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span
\r
15098 lang=AF>This will only work if your sequences are short enough (less than 200
\r
15099 nucleotides). A good alternative is the rmcoffee mode that will run Muscle,
\r
15100 Probcons4RNA and MAfft and then use the secondary structures predicted by
\r
15101 RNApfold. </span></span></span></span></p>
\r
15103 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
15104 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
15105 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
15106 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
15108 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span
\r
15109 style='mso-bookmark:_Toc101065209'><span style='mso-bookmark:_Toc102494297'><span
\r
15110 style='mso-bookmark:_Toc102494678'><span lang=EN-US>PROMPT: t_coffee
\r
15111 sample_rnaseq1.fasta
\96mode mrcoffee </span></span></span></span></p>
\r
15115 <p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span
\r
15116 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span
\r
15117 lang=AF><o:p> </o:p></span></span></span></span></p>
\r
15119 <p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span
\r
15120 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span
\r
15121 lang=AF>If you want to decide yourself which methods should be combined by
\r
15122 R-Coffee, run:</span></span></span></span></p>
\r
15124 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
15125 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
15126 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
15127 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
15129 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span
\r
15130 style='mso-bookmark:_Toc101065209'><span style='mso-bookmark:_Toc102494297'><span
\r
15131 style='mso-bookmark:_Toc102494678'><span lang=EN-US>PROMPT: t_coffee
\r
15132 sample_rnaseq1.fasta
\96mode rcoffee -method lalign_id_pair slow_pair </span></span></span></span></p>
\r
15136 <p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span
\r
15137 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span
\r
15138 lang=AF><o:p> </o:p></span></span></span></span></p>
\r
15140 <p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span
\r
15141 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span
\r
15142 lang=AF><o:p> </o:p></span></span></span></span></p>
\r
15144 <h2><span style='mso-bookmark:_Toc101065209'><span style='mso-bookmark:_Toc102494297'><span
\r
15145 style='mso-bookmark:_Toc102494678'><span lang=EN-US><br>
\r
15146 <a name="_Toc235958503">iRMSD and APDB</a></span></span></span></span></h2>
\r
15148 <p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span
\r
15149 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span
\r
15150 lang=AF>All you need is a file containing the alignment of sequences with a
\r
15151 known structure. These sequences must be named according to their PDB ID,
\r
15152 followed by the chain index ( 1aabA for instance). All the sequences do not
\r
15153 need to have a known structure, but at least two need to have it.</span></span></span></span></p>
\r
15155 <p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span
\r
15156 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span
\r
15157 lang=AF>Given the alignment:</span></span></span></span></p>
\r
15159 <p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span
\r
15160 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span
\r
15161 lang=AF><o:p> </o:p></span></span></span></span></p>
\r
15163 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
15164 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
15165 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
15166 background:#FFFFCC;margin-left:42.55pt;margin-right:0mm'>
\r
15168 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span
\r
15169 style='mso-bookmark:_Toc101065209'><span style='mso-bookmark:_Toc102494297'><span
\r
15170 style='mso-bookmark:_Toc102494678'><span lang=EN-US>PROMPT: t_coffee
\96other_pg
\r
15171 irmsd -aln 3d_sample4.aln </span></span></span></span></p>
\r
15175 <h2><span style='mso-bookmark:_Toc101065209'><span style='mso-bookmark:_Toc102494297'><span
\r
15176 style='mso-bookmark:_Toc102494678'><a name="_Toc235958504"><span lang=EN-US>tRMSD</span></a></span></span></span></h2>
\r
15178 <p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span
\r
15179 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span
\r
15180 lang=AF>tRMSD is a structure based clustering method using the iRMSD to drive
\r
15181 the clustering. The T-RMSD supports all the parameters supported by iRMSD or
\r
15182 APDB.</span></span></span></span></p>
\r
15184 <p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span
\r
15185 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span
\r
15186 lang=AF><o:p> </o:p></span></span></span></span></p>
\r
15188 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
15189 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
15190 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
15191 background:#FFFFCC;margin-left:42.55pt;margin-right:0mm'>
\r
15193 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span
\r
15194 style='mso-bookmark:_Toc101065209'><span style='mso-bookmark:_Toc102494297'><span
\r
15195 style='mso-bookmark:_Toc102494678'><span lang=EN-US>PROMPT: t_coffee
\96other_pg
\r
15196 trmsd -aln 3d_sample5.aln -template_file 3d_sample5.template_list </span></span></span></span></p>
\r
15200 <p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span
\r
15201 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span
\r
15202 lang=EN-US style='mso-ansi-language:EN-US'>3d_sample5.aln is a multiple
\r
15203 alignment in which each sequence has a known structure. The file </span><span
\r
15204 lang=AF>3d_sample5.template_list is a fasta like file declaring the structure
\r
15205 associated with each sequence, in the form: </span></span></span></span></p>
\r
15207 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
\r
15208 mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
\r
15209 background:#E6E6E6;margin-left:0mm;margin-right:10.0mm'>
\r
15211 <p class=examplefilesmall><span style='mso-bookmark:_Toc101065209'><span
\r
15212 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span
\r
15213 lang=EN-US>> <seq_name> _P_ <PDB structure file or name> </span></span></span></span></p>
\r
15217 <p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span
\r
15218 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span
\r
15219 lang=AF><o:p> </o:p></span></span></span></span></p>
\r
15221 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
\r
15222 mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
\r
15223 background:#E6E6E6'>
\r
15225 <p class=examplefileCxSpFirst><span style='mso-bookmark:_Toc101065209'><span
\r
15226 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span
\r
15227 lang=EN-US>******* 3d_sample5.template_list ********<span style='mso-tab-count:
\r
15228 1'> </span></span></span></span></span></p>
\r
15230 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065209'><span
\r
15231 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span
\r
15232 lang=EN-US>>2UWI-3A _P_ 2UWI-3.pdb</span></span></span></span></p>
\r
15234 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065209'><span
\r
15235 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span
\r
15236 lang=EN-US>>2UWI-2A _P_ 2UWI-2.pdb</span></span></span></span></p>
\r
15238 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065209'><span
\r
15239 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span
\r
15240 lang=EN-US>>2UWI-1A _P_ 2UWI-1.pdb</span></span></span></span></p>
\r
15242 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065209'><span
\r
15243 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span
\r
15244 lang=EN-US>>2HEY-4R _P_ 2HEY-4.pdb</span></span></span></span></p>
\r
15246 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065209'><span
\r
15247 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span
\r
15248 lang=EN-US>...</span></span></span></span></p>
\r
15250 <p class=examplefileCxSpLast><span style='mso-bookmark:_Toc101065209'><span
\r
15251 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span
\r
15252 lang=EN-US>**************************************</span></span></span></span></p>
\r
15256 <p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span
\r
15257 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span
\r
15258 lang=AF><o:p> </o:p></span></span></span></span></p>
\r
15260 <p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span
\r
15261 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span
\r
15262 lang=AF>The program then outputs a series of files</span></span></span></span></p>
\r
15264 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
\r
15265 mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
\r
15266 background:#E6E6E6'>
\r
15268 <p class=examplefileCxSpFirst><span style='mso-bookmark:_Toc101065209'><span
\r
15269 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span
\r
15270 lang=EN-US style='font-size:8.0pt'>Template Type: [3d_sample5.template_list]
\r
15271 Mode Or File: [3d_sample5.template_list] [Start]<o:p></o:p></span></span></span></span></p>
\r
15273 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065209'><span
\r
15274 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span
\r
15275 lang=EN-US style='font-size:8.0pt'><span style='mso-spacerun:yes'>
\r
15276 </span>[Sample Columns][TOT=<span style='mso-spacerun:yes'> </span>51][100
\r
15277 %][ELAPSED TIME:<span style='mso-spacerun:yes'> </span>0 sec.]<o:p></o:p></span></span></span></span></p>
\r
15279 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065209'><span
\r
15280 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span
\r
15281 lang=EN-US style='font-size:8.0pt'><span style='mso-spacerun:yes'> </span><span
\r
15282 style='mso-spacerun:yes'> </span>[Tree Cmp][TOT=<span
\r
15283 style='mso-spacerun:yes'> </span>13][ 92 %][ELAPSED TIME:<span
\r
15284 style='mso-spacerun:yes'> </span>0 sec.]<o:p></o:p></span></span></span></span></p>
\r
15286 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065209'><span
\r
15287 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span
\r
15288 lang=EN-US style='font-size:8.0pt'><span style='mso-spacerun:yes'> </span>####
\r
15289 File Type=<span style='mso-spacerun:yes'> </span>TreeList Format=<span
\r
15290 style='mso-spacerun:yes'> </span>newick Name= 3d_sample5.tot_pos_list<o:p></o:p></span></span></span></span></p>
\r
15292 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065209'><span
\r
15293 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span
\r
15294 lang=EN-US style='font-size:8.0pt'><span style='mso-spacerun:yes'> </span>####
\r
15295 File Type=<span style='mso-spacerun:yes'> </span>Tree Format=<span
\r
15296 style='mso-spacerun:yes'> </span>newick Name= 3d_sample5.struc_tree10<o:p></o:p></span></span></span></span></p>
\r
15298 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065209'><span
\r
15299 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span
\r
15300 lang=EN-US style='font-size:8.0pt'><span style='mso-spacerun:yes'> </span>####
\r
15301 File Type=<span style='mso-spacerun:yes'> </span>Tree Format=<span
\r
15302 style='mso-spacerun:yes'> </span>newick Name= 3d_sample5.struc_tree50<o:p></o:p></span></span></span></span></p>
\r
15304 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065209'><span
\r
15305 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span
\r
15306 lang=EN-US style='font-size:8.0pt'><span style='mso-spacerun:yes'> </span>####
\r
15307 File Type=<span style='mso-spacerun:yes'> </span>Tree Format=<span
\r
15308 style='mso-spacerun:yes'> </span>newick Name= 3d_sample5.struc_tree100<o:p></o:p></span></span></span></span></p>
\r
15310 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065209'><span
\r
15311 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span
\r
15312 lang=EN-US style='font-size:8.0pt'><span style='mso-spacerun:yes'> </span>####
\r
15313 File Type= Colored MSA Format= score_html Name= 3d_sample5.struc_tree.html<o:p></o:p></span></span></span></span></p>
\r
15315 <p class=examplefileCxSpLast><span style='mso-bookmark:_Toc101065209'><span
\r
15316 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span
\r
15317 lang=EN-US><o:p> </o:p></span></span></span></span></p>
\r
15321 <p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span
\r
15322 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span
\r
15323 lang=AF><o:p> </o:p></span></span></span></span></p>
\r
15325 <p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span
\r
15326 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span
\r
15327 lang=AF>3d_sample5.tot_pos_list <span style='mso-tab-count:1'> </span>is a
\r
15328 list of the tRMSD tree associated with every position. </span></span></span></span></p>
\r
15330 <p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span
\r
15331 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span
\r
15332 lang=AF>3d_sample5.struc_tree100<span style='mso-tab-count:1'> </span>is a
\r
15333 consensus tree (phylip/consense) of the trees contained in the previous file. <b>This
\r
15334 file is the default output<o:p></o:p></b></span></span></span></span></p>
\r
15336 <p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span
\r
15337 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span
\r
15338 lang=AF>3d_sample5.struc_tree10<span style='mso-tab-count:1'> </span>is a
\r
15339 consensus tree (phylip/consense) of the 10% trees having the higest average
\r
15340 agreement with the rest</span></span></span></span></p>
\r
15342 <p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span
\r
15343 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span
\r
15344 lang=AF>3d_sample5.struc_tree10<span style='mso-tab-count:1'> </span>is a
\r
15345 consensus tree (phylip/consense) of the 50% trees having the higest average
\r
15346 agreement with the rest</span></span></span></span></p>
\r
15348 <p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span
\r
15349 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span
\r
15350 lang=AF>3d_sample5.html<span style='mso-tab-count:1'> </span>is a colored
\r
15351 version of the output showing in red the positions that give the highest
\r
15352 support to 3d_sample5.struc_tree100</span></span></span></span></p>
\r
15354 <p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span
\r
15355 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span
\r
15356 lang=AF><o:p> </o:p></span></span></span></span></p>
\r
15358 <p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span
\r
15359 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span
\r
15360 lang=AF><o:p> </o:p></span></span></span></span></p>
\r
15362 <p class=MyNormal><span style='mso-bookmark:_Toc101065209'><span
\r
15363 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc102494678'><span
\r
15364 lang=AF><o:p> </o:p></span></span></span></span></p>
\r
15366 <h2><span style='mso-bookmark:_Toc101065209'><span style='mso-bookmark:_Toc102494297'><span
\r
15367 style='mso-bookmark:_Toc102494678'><a name="_Toc235958505"><span lang=EN-US>MOCCA</span></a></span></span></span></h2>
\r
15369 <p class=MyNormal><span lang=AF>Write your sequences in the same file
\r
15370 (Swiss-prot, Fasta or Pir) and type. </span></p>
\r
15372 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
15373 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
15374 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
15375 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
15377 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:
\r
15378 t_coffee
\96other_pg mocca sample_seq1.fasta </span></p>
\r
15382 <p class=MyNormal><span lang=AF>This command output one files (<your
\r
15383 sequences>.mocca_lib) and starts an interactive menu. </span></p>
\r
15385 <div style='mso-element:para-border-div;border:solid windowtext 3.0pt;
\r
15386 padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#CCCCCC;margin-left:0mm;margin-right:
\r
15389 <p class=ChapterTitle><a name="_Toc235958506"></a><a name="_Toc102494679"></a><a
\r
15390 name="_Toc101065210"><span style='mso-bookmark:_Toc102494679'><span
\r
15391 style='mso-bookmark:_Toc235958506'><span lang=EN-US>Recent M</span></span></span></a><span
\r
15392 style='mso-bookmark:_Toc235958506'><span lang=EN-US>odifications</span></span></p>
\r
15396 <p class=MyNormal><span lang=AF>Warning: This log of recent modifications is
\r
15397 not as thorough and accurate as it should be.</span></p>
\r
15399 <p class=MyNormal><span lang=AF>-5.80 Novel assembly algorithm
\r
15400 (linked_pair_wise) and the primary library is now made of probcons style
\r
15401 pairwise alignments (proba_pair)</span></p>
\r
15403 <p class=MyNormal><span lang=AF>-4.30 and upward: the FAQ has moved into a new
\r
15404 tutorial document</span></p>
\r
15406 <p class=MyNormal><span lang=AF>-4.30 and upward: -in has will be deprecated
\r
15407 and replaced by the flags: -profile,-method,-aln,-seq,-pdb</span></p>
\r
15409 <p class=MyNormal><span lang=AF>-4.02: -mode=dna is still available but not any
\r
15410 more needed or supported. Use type=protein or dna if you need to force things</span></p>
\r
15412 <p class=MyNormal><b style='mso-bidi-font-weight:normal'><span lang=AF>-</span></b><span
\r
15413 lang=AF>3.28: corrected a bug that prevents short sequences from being
\r
15414 correctly aligned</span></p>
\r
15416 <p class=MyNormal><span lang=AF>-Use of @ as a separator when specifying
\r
15417 methods parameters</span></p>
\r
15419 <p class=MyNormal><span lang=AF>-The most notable modifications have to do with
\r
15420 the structure of the input. From version 2.20, all files must be tagged to
\r
15421 indicate their nature (A: alignment, S: Sequence, L: Library
\85). We are becoming
\r
15422 stricter, but that
\92s for your own good
\85 </span></p>
\r
15424 <p class=MyNormal><span lang=AF>Another important modification has to do with
\r
15425 the flag -matrix: it now controls the matrix being used for the computation </span></p>
\r
15427 <span lang=AF style='font-size:11.0pt;font-family:"Times New Roman";mso-fareast-font-family:
\r
15428 "Times New Roman";mso-bidi-font-family:"Courier New";mso-ansi-language:AF;
\r
15429 mso-fareast-language:EN-US;mso-bidi-language:AR-SA'><br clear=all
\r
15430 style='page-break-before:always'>
\r
15433 <div style='mso-element:para-border-div;border:solid windowtext 3.0pt;
\r
15434 padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#CCCCCC;margin-left:0mm;margin-right:
\r
15437 <p class=ChapterTitle><a name="_Toc235958507"><span lang=EN-US>Reference Manual</span></a></p>
\r
15441 <p class=MyNormal><span lang=AF><o:p> </o:p></span></p>
\r
15443 <p class=MyNormal><span lang=AF>This reference manual gives a list of all the
\r
15444 flags that can be used to modify the behavior of T-Coffee. For your
\r
15445 convenience, we have grouped them according to their nature. To display a list
\r
15446 of all the flags used in the version of T-Coffee you are using (along with
\r
15447 their default value), type:</span></p>
\r
15449 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
15450 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
15451 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
15452 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
15454 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:
\r
15455 t_coffee </span></p>
\r
15459 <p class=MyNormal><span lang=AF>Or</span></p>
\r
15461 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
15462 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
15463 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
15464 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
15466 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:
\r
15467 t_coffee
\96help </span></p>
\r
15471 <p class=MyNormal><span lang=AF>Or</span></p>
\r
15473 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
15474 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
15475 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
15476 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
15478 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:
\r
15479 t_coffee
\96help
\96in</span><span class=MyNormalChar><span lang=EN-US
\r
15480 style='font-size:11.0pt;mso-ansi-language:EN-US'><o:p></o:p></span></span></p>
\r
15484 <p class=MyNormal><span lang=AF>Or any other parameter</span></p>
\r
15486 <h2><a name="_Toc102494743"></a><a name="_Toc102494358"></a><a
\r
15487 name="_Toc101065212"><span style='mso-bookmark:_Toc102494358'><span
\r
15488 style='mso-bookmark:_Toc102494743'><span lang=EN-US><o:p> </o:p></span></span></span></a></h2>
\r
15490 <h2><span style='mso-bookmark:_Toc101065212'><span style='mso-bookmark:_Toc102494358'><span
\r
15491 style='mso-bookmark:_Toc102494743'><a name="_Toc235958508"><span lang=EN-US>Environment
\r
15492 Variables</span></a></span></span></span></h2>
\r
15494 <p class=MsoBodyText><span style='mso-bookmark:_Toc101065212'><span
\r
15495 style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc102494743'><span
\r
15496 lang=EN-US>It is possible to modify T-Coffee
\92s behavior by setting any of the
\r
15497 following environement variables. On the bash shell, use export VAR=
\94value
\94. On
\r
15498 the cshell, use set $VAR=
\94xxx
\94</span></span></span></span></p>
\r
15500 <h3><span style='mso-bookmark:_Toc101065212'><span style='mso-bookmark:_Toc102494358'><span
\r
15501 style='mso-bookmark:_Toc102494743'><a name="_Toc235958509"><span lang=EN-US>http_proxy_4_TCOFFEE</span></a></span></span></span></h3>
\r
15503 <p class=MyNormal><span style='mso-bookmark:_Toc101065212'><span
\r
15504 style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc102494743'><span
\r
15505 lang=AF>Sets the http_proxy and HTTP_proxy values used by T-Coffee. </span></span></span></span></p>
\r
15507 <p class=MyNormal><span style='mso-bookmark:_Toc101065212'><span
\r
15508 style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc102494743'><span
\r
15509 lang=AF>These values get supersede http_proxy and HTTP_proxy.
\r
15510 http_proxy_4_TCOFFEE gets superseded by the command line values (-proxy and
\r
15511 -email)</span></span></span></span></p>
\r
15513 <p class=MyNormal><span style='mso-bookmark:_Toc101065212'><span
\r
15514 style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc102494743'><span
\r
15515 lang=AF>If you have no proxy, just set this value to an empty string.</span></span></span></span></p>
\r
15517 <h3><span style='mso-bookmark:_Toc101065212'><span style='mso-bookmark:_Toc102494358'><span
\r
15518 style='mso-bookmark:_Toc102494743'><a name="_Toc235958510"><span lang=EN-US>email_4_TCOFFEE</span></a></span></span></span></h3>
\r
15520 <p class=MyNormal><span style='mso-bookmark:_Toc101065212'><span
\r
15521 style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc102494743'><span
\r
15522 lang=AF>Set the E-mail values provided to web services called upon by T-Coffee.
\r
15523 Can be over-riden by the flag <i>-email.<o:p></o:p></i></span></span></span></span></p>
\r
15525 <h3><span style='mso-bookmark:_Toc101065212'><span style='mso-bookmark:_Toc102494358'><span
\r
15526 style='mso-bookmark:_Toc102494743'><a name="_Toc235958511"><span lang=EN-US>DIR_4_TCOFFEE</span></a></span></span></span></h3>
\r
15528 <p class=MyNormal><span style='mso-bookmark:_Toc101065212'><span
\r
15529 style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc102494743'><span
\r
15530 lang=AF>By default this variable is set to $HOME/.t_coffee. This is where
\r
15531 T-Coffee expects to find its cache, tmp dir and possibly any temporary data
\r
15532 stored by the program.</span></span></span></span></p>
\r
15534 <h3><span style='mso-bookmark:_Toc101065212'><span style='mso-bookmark:_Toc102494358'><span
\r
15535 style='mso-bookmark:_Toc102494743'><a name="_Toc235958512"><span lang=EN-US>TMP_4_TCOFFEE</span></a></span></span></span></h3>
\r
15537 <p class=MyNormal><span style='mso-bookmark:_Toc101065212'><span
\r
15538 style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc102494743'><span
\r
15539 lang=AF>By default this variable is set to $HOME/.t_coffee/tmp. This is where
\r
15540 T-Coffee stores temporary files.</span></span></span></span></p>
\r
15542 <h3><span style='mso-bookmark:_Toc101065212'><span style='mso-bookmark:_Toc102494358'><span
\r
15543 style='mso-bookmark:_Toc102494743'><a name="_Toc235958513"><span lang=EN-US>CACHE_4_TCOFFEE</span></a></span></span></span></h3>
\r
15545 <p class=MyNormal><span style='mso-bookmark:_Toc101065212'><span
\r
15546 style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc102494743'><span
\r
15547 lang=AF>By default this variable is set to $HOME/.t_coffee/cache. This is where
\r
15548 T-Coffee stores any data expensive to obtain: pdb files, sap alignments....</span></span></span></span></p>
\r
15550 <h3><span style='mso-bookmark:_Toc101065212'><span style='mso-bookmark:_Toc102494358'><span
\r
15551 style='mso-bookmark:_Toc102494743'><span lang=EN-US>PLUGINS_4_TCOFFEE</span></span></span></span></h3>
\r
15553 <p class=MyNormal><span style='mso-bookmark:_Toc101065212'><span
\r
15554 style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc102494743'><span
\r
15555 lang=AF>By default all the companion packages are searched in the directory
\r
15556 DIR_4_TCOFFEE/plugins/<OS>. This variable overrides the default. This
\r
15557 variable can also be overriden by the <i>-plugins</i> T-Coffee flag</span></span></span></span></p>
\r
15559 <h3><span style='mso-bookmark:_Toc101065212'><span style='mso-bookmark:_Toc102494358'><span
\r
15560 style='mso-bookmark:_Toc102494743'><a name="_Toc235958514"><span lang=EN-US>NO_ERROR_REPORT_4_TCOFFEE</span></a></span></span></span></h3>
\r
15562 <p class=MyNormal><span style='mso-bookmark:_Toc101065212'><span
\r
15563 style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc102494743'><span
\r
15564 lang=AF>By default this variable is no set. Set it if you do not want the
\r
15565 program to generate a verbose error output file (useful for running a server).</span></span></span></span></p>
\r
15567 <h3><span style='mso-bookmark:_Toc101065212'><span style='mso-bookmark:_Toc102494358'><span
\r
15568 style='mso-bookmark:_Toc102494743'><a name="_Toc235958515"><span lang=EN-US>PDB_DIR</span></a></span></span></span></h3>
\r
15570 <p class=MyNormal><span style='mso-bookmark:_Toc101065212'><span
\r
15571 style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc102494743'><span
\r
15572 lang=AF>Indicate the location of your local PDB installation.</span></span></span></span></p>
\r
15574 <h3><span style='mso-bookmark:_Toc101065212'><span style='mso-bookmark:_Toc102494358'><span
\r
15575 style='mso-bookmark:_Toc102494743'><a name="_Toc235958516"><span lang=EN-US>NO_WARNING_4_TCOFFEE</span></a></span></span></span></h3>
\r
15577 <p class=MyNormal><span style='mso-bookmark:_Toc101065212'><span
\r
15578 style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc102494743'><span
\r
15579 lang=AF>Suppresses all the warnings.</span></span></span></span></p>
\r
15581 <p class=MyNormal><span style='mso-bookmark:_Toc101065212'><span
\r
15582 style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc102494743'><span
\r
15583 lang=AF><o:p> </o:p></span></span></span></span></p>
\r
15585 <h2><span style='mso-bookmark:_Toc101065212'><span style='mso-bookmark:_Toc102494358'><span
\r
15586 style='mso-bookmark:_Toc102494743'><a name="_Toc235958517"><span lang=EN-US>Setting
\r
15587 up the T-Coffee environment variables</span></a></span></span></span></h2>
\r
15589 <p class=MsoBodyText><span style='mso-bookmark:_Toc101065212'><span
\r
15590 style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc102494743'><span
\r
15591 lang=EN-US>T-Coffee can have its own environment file. This environment is kept
\r
15592 in a file named $HOME/.t_coffee/t_coffee_env and can be edited. The value of
\r
15593 any legal variable can be modified through that file. For instance, here is an
\r
15594 example of a configuration file when not requiring a proxy.</span></span></span></span></p>
\r
15596 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
\r
15597 mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
\r
15598 background:#E6E6E6'>
\r
15600 <p class=examplefileCxSpFirst><span style='mso-bookmark:_Toc101065212'><span
\r
15601 style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc102494743'><span
\r
15602 lang=EN-US>http_proxy_4_TCOFFEE=</span></span></span></span></p>
\r
15604 <p class=examplefileCxSpLast><span style='mso-bookmark:_Toc101065212'><span
\r
15605 style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc102494743'><span
\r
15606 lang=EN-US>EMAIL_4_TCOFFEE=cedric.notredame@europe.com</span></span></span></span></p>
\r
15610 <div style='mso-element:para-border-div;border:solid windowtext 1.5pt;
\r
15611 padding:0mm 0mm 0mm 0mm;background:#F7CBB7'>
\r
15613 <p class=Warning><span style='mso-bookmark:_Toc101065212'><span
\r
15614 style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc102494743'><span
\r
15615 lang=EN-US>IMPORTANT: </span></span></span></span></p>
\r
15617 <p class=Warning style='text-align:justify;text-indent:35.4pt;background:#F7CBB7'><span
\r
15618 style='mso-bookmark:_Toc101065212'><span style='mso-bookmark:_Toc102494358'><span
\r
15619 style='mso-bookmark:_Toc102494743'><span lang=EN-US>-proxy, -email >>
\r
15620 t_coffee_env >> env</span></span></span></span></p>
\r
15622 <p class=Warning style='text-align:justify;background:#F7CBB7'><span
\r
15623 style='mso-bookmark:_Toc101065212'><span style='mso-bookmark:_Toc102494358'><span
\r
15624 style='mso-bookmark:_Toc102494743'><span lang=EN-US><o:p> </o:p></span></span></span></span></p>
\r
15628 <p class=MsoBodyText><span style='mso-bookmark:_Toc101065212'><span
\r
15629 style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc102494743'><span
\r
15630 lang=EN-US><o:p> </o:p></span></span></span></span></p>
\r
15632 <p class=MsoBodyText><span style='mso-bookmark:_Toc101065212'><span
\r
15633 style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc102494743'><span
\r
15634 lang=EN-US><o:p> </o:p></span></span></span></span></p>
\r
15636 <h2><span style='mso-bookmark:_Toc101065212'><span style='mso-bookmark:_Toc102494358'><span
\r
15637 style='mso-bookmark:_Toc102494743'><a name="_Toc235958518"><span lang=EN-US>Well
\r
15638 Behaved Parameters</span></a></span></span></span></h2>
\r
15640 <h3><a name="_Toc235958519"></a><a name="_Toc102494744"></a><a
\r
15641 name="_Toc102494359"></a><a name="_Toc101065213"><span style='mso-bookmark:
\r
15642 _Toc102494359'><span style='mso-bookmark:_Toc102494744'><span style='mso-bookmark:
\r
15643 _Toc235958519'><span lang=EN-US>Separation</span></span></span></span></a></h3>
\r
15645 <p class=MyNormal><span lang=AF>You can use any kind of separator you want
\r
15646 (i.e. ,; <space>=). The syntax used in this document is meant to be
\r
15647 consistent with that of ClustalW. However, in order to take advantage of the
\r
15648 automatic filename compleation provided by many shells, you can replace
\93=
\94 and
\r
15649 \93,
\94 with a space.</span></p>
\r
15651 <h3><a name="_Toc235958520"></a><a name="_Toc102494745"></a><a
\r
15652 name="_Toc102494360"></a><a name="_Toc101065214"><span style='mso-bookmark:
\r
15653 _Toc102494360'><span style='mso-bookmark:_Toc102494745'><span style='mso-bookmark:
\r
15654 _Toc235958520'><span lang=EN-US>Posix</span></span></span></span></a></h3>
\r
15656 <p class=MyNormal><span lang=AF>T-Coffee is not POSIX compliant.</span></p>
\r
15658 <h3><a name="_Toc235958521"></a><a name="_Toc102494746"></a><a
\r
15659 name="_Toc102494361"></a><a name="_Toc101065215"><span style='mso-bookmark:
\r
15660 _Toc102494361'><span style='mso-bookmark:_Toc102494746'><span style='mso-bookmark:
\r
15661 _Toc235958521'><span lang=EN-US>Entering the right parameters</span></span></span></span></a></h3>
\r
15663 <p class=MyNormal><span lang=AF>There are many ways to enter parameters in
\r
15664 T-Coffee, see the -parameter flag in </span></p>
\r
15666 <p class=Noteboxtitle><span lang=EN-US><o:p> </o:p></span></p>
\r
15668 <div style='mso-element:para-border-div;border:solid windowtext 1.5pt;
\r
15669 padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#FFFF89'>
\r
15671 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut align=center
\r
15672 style='text-align:center;background:#FFFF89'><span lang=EN-US style='font-size:
\r
15673 20.0pt;mso-bidi-font-size:10.0pt'>Parameters Priority<o:p></o:p></span></p>
\r
15675 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span lang=EN-US><o:p> </o:p></span></p>
\r
15677 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span lang=EN-US>In
\r
15678 general you will not need to use these complicated parameters. Yet, if you find
\r
15679 yourself typing long command lines on a regular basis, it may be worth reading
\r
15680 this section.</span></p>
\r
15682 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span lang=EN-US><o:p> </o:p></span></p>
\r
15684 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span lang=EN-US>One
\r
15685 may easily feel confused with the various manners in which the parameters can
\r
15686 be passed to t_coffee. The reason for these many mechanisms is that they allow
\r
15687 several levels of intervention. For instance, you may install t_coffee for all
\r
15688 the users and decide that the defaults we provide are not the proper ones
\85 In
\r
15689 this case, you will need to make your own t_coffee_default file.</span></p>
\r
15691 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span lang=EN-US><o:p> </o:p></span></p>
\r
15693 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span lang=EN-US>Later
\r
15694 on, a user may find that he/she needs to keep re-using a specific set of
\r
15695 parameters, different from those in t_coffee_default, hence the possibility to
\r
15696 write an extra parameter file: parameters. In summary:</span></p>
\r
15698 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span lang=EN-US><o:p> </o:p></span></p>
\r
15700 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span lang=EN-US>-parameters
\r
15701 > prompt parameters > -t_coffee_defaults > -mode</span></p>
\r
15703 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span lang=EN-US><o:p> </o:p></span></p>
\r
15705 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span lang=EN-US>This
\r
15706 means that -<i>parameters</i> supersede all the others, while parameters
\r
15707 provided via -<i>special mode</i> are the weakest.</span></p>
\r
15711 <p class=MyNormal><span lang=AF><o:p> </o:p></span></p>
\r
15713 <p class=MyNormal><span lang=AF><o:p> </o:p></span></p>
\r
15715 <h2><a name="_Toc235958522"></a><a name="_Toc102494747"></a><a
\r
15716 name="_Toc102494362"></a><a name="_Toc101065216"><span style='mso-bookmark:
\r
15717 _Toc102494362'><span style='mso-bookmark:_Toc102494747'><span style='mso-bookmark:
\r
15718 _Toc235958522'><span lang=EN-US>Parameters Syntax</span></span></span></span></a></h2>
\r
15720 <p class=flag><a name="_Toc235958523"></a><a name="_Toc102494748"></a><a
\r
15721 name="_Toc101065218"><span style='mso-bookmark:_Toc102494748'><span
\r
15722 style='mso-bookmark:_Toc235958523'><span lang=AF>No Flag</span></span></span></a></p>
\r
15724 <p class=flagdescription><span lang=EN-US>If no flag is used<b
\r
15725 style='mso-bidi-font-weight:normal'> </b><i style='mso-bidi-font-style:normal'><your
\r
15726 sequence> </i>must be the first argument. See format for further
\r
15727 information.</span></p>
\r
15729 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
15730 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
15731 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
15732 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
15734 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:
\r
15735 t_coffee sample_seq1.fasta </span></p>
\r
15739 <p class=flagdescription><span lang=EN-US>Which is equivalent to</span></p>
\r
15741 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
15742 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
15743 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
15744 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
15746 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:
\r
15747 t_coffee Ssample_seq1.fasta </span></p>
\r
15751 <p class=flagdescription><span lang=EN-US>When you do so, <b style='mso-bidi-font-weight:
\r
15752 normal'>sample_seq1</b> is used as a name prefix for every file the program
\r
15753 outputs.</span></p>
\r
15755 <p class=flag><a name="_Toc235958524"></a><a name="_Toc102494749"></a><a
\r
15756 name="_Toc101065219"><span style='mso-bookmark:_Toc102494749'><span
\r
15757 style='mso-bookmark:_Toc235958524'><span lang=AF>-parameters</span></span></span></a><span
\r
15758 lang=AF style='background:gray;mso-highlight:gray'><o:p></o:p></span></p>
\r
15760 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:
\r
15761 -parameters=parameters_file<o:p></o:p></span></p>
\r
15763 <p class=instruction><span lang=EN-US>Default: no parameters file</span></p>
\r
15765 <p class=flagdescription><span lang=EN-US>Indicates a file containing extra parameters.
\r
15766 Parameters read this way behave as if they had been added on the right end of
\r
15767 the command line that they either supersede(one value parameter) or complete
\r
15768 (list of values). For instance, the following file (parameter.file) could be
\r
15771 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
\r
15772 mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
\r
15773 background:#E6E6E6'>
\r
15775 <p class=examplefileCxSpFirst><span lang=EN-US>*******sample_param_file.param********<span
\r
15776 style='mso-tab-count:1'> </span></span></p>
\r
15778 <p class=examplefileCxSpMiddle><span lang=EN-US><span style='mso-tab-count:
\r
15779 1'> </span>-in=Ssample_seq1.fasta,Mfast_pair</span></p>
\r
15781 <p class=examplefileCxSpMiddle><span lang=EN-US><span style='mso-tab-count:
\r
15782 1'> </span>-output=msf_aln</span></p>
\r
15784 <p class=examplefileCxSpLast><span lang=EN-US>**************************************</span></p>
\r
15788 <p class=Note><span lang=EN-US style='mso-ansi-language:EN-US'>Note: This is
\r
15789 one of the exceptions (with
\96infile) where the identifier tag (S,A,L,M
\85) can be
\r
15790 omitted. Any dataset provided this way will be assumed to be a sequence (S).
\r
15791 These exceptions have been designed to keep the program compatible with
\r
15792 ClustalW.<o:p></o:p></span></p>
\r
15794 <p class=Note><span lang=EN-US style='mso-ansi-language:EN-US'>Note: This
\r
15795 parameter file can ONLY contain valid parameters. Comments are not allowed.
\r
15796 Parameters passed this way will be checked like normal parameters.<o:p></o:p></span></p>
\r
15798 <p class=flagdescription><span lang=EN-US>Used with:</span></p>
\r
15800 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
15801 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
15802 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
15803 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
15805 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:
\r
15806 t_coffee -parameters=sample_param_file.param</span></p>
\r
15810 <p class=flagdescription><span lang=EN-US>Will cause t_coffee to apply the
\r
15811 fast_pair method onto to the sequences contained in sample_seq.fasta. If you
\r
15812 wish, you can also pipe these arguments into t_coffee, by naming the parameter
\r
15813 file "stdin" (as a rule, any file named stdin is expected to receive
\r
15814 its content via the stdin)</span></p>
\r
15816 <p class=example2><span lang=EN-US>cat sample_param_file.param<span
\r
15817 style='mso-spacerun:yes'> </span>| t_coffee -parameters=stdin <a
\r
15818 name="_Toc101065220"></a></span></p>
\r
15820 <p class=flag><span style='mso-bookmark:_Toc101065220'><a name="_Toc235958525"></a><a
\r
15821 name="_Toc102494750"><span style='mso-bookmark:_Toc235958525'><span lang=AF>-t_coffee_defaults</span></span></a></span></p>
\r
15823 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:
\r
15824 -t_coffee_defaults=<file_name><o:p></o:p></span></p>
\r
15826 <p class=instruction><span lang=EN-US>Default: not used.</span></p>
\r
15828 <p class=flagdescription><span lang=EN-US>This flag tells the program to use
\r
15829 some default parameter file for t_coffee. The format of that file is the same
\r
15830 as the one used with -parameters. The file used is either:</span></p>
\r
15832 <p class=flagdescription><span lang=EN-US><span style='mso-tab-count:1'> </span>1.
\r
15833 <file name> if a name has been specified</span></p>
\r
15835 <p class=flagdescription><span lang=EN-US><span style='mso-tab-count:1'> </span>2.<span
\r
15836 style='mso-spacerun:yes'> </span><b>~/.t_coffee_defaults </b>if no file was
\r
15837 specified</span></p>
\r
15839 <p class=flagdescription><span lang=EN-US><span style='mso-tab-count:1'> </span>3.
\r
15840 The file indicated by the environment variable <b>TCOFFEE_DEFAULTS</b></span></p>
\r
15842 <p class=flag><a name="_Toc235958526"><span lang=AF>-mode</span></a></p>
\r
15844 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage: -mode=
\r
15845 hard coded mode<o:p></o:p></span></p>
\r
15847 <p class=instruction><span lang=EN-US>Default: not used.</span></p>
\r
15849 <p class=flagdescription><span lang=EN-US>It indicates that t_coffee will use
\r
15850 some hard coded parameters. These include:</span></p>
\r
15852 <p class=flagdescription><span lang=EN-US><span style='mso-tab-count:1'> </span><b
\r
15853 style='mso-bidi-font-weight:normal'>quickaln</b>: very fast approximate
\r
15854 alignment</span></p>
\r
15856 <p class=flagdescription><span lang=EN-US><span style='mso-tab-count:1'> </span><b
\r
15857 style='mso-bidi-font-weight:normal'>dali</b>: a mode used to combine dali
\r
15858 pairwise alignments</span></p>
\r
15860 <p class=flagdescription><span lang=EN-US><span style='mso-tab-count:1'> </span><b
\r
15861 style='mso-bidi-font-weight:normal'>evaluate</b>: defaults for evaluating an
\r
15862 alignment</span></p>
\r
15864 <p class=flagdescription><span lang=EN-US><span style='mso-tab-count:1'> </span><b
\r
15865 style='mso-bidi-font-weight:normal'>3dcoffee</b>: runs t_coffee with the
\r
15866 3dcoffee parameterization</span></p>
\r
15868 <p class=flagdescription><span lang=EN-US><o:p> </o:p></span></p>
\r
15870 <p class=flagdescription><span lang=EN-US>Other modes exist that are not yet
\r
15871 fully supported<span style='mso-tab-count:1'> </span></span></p>
\r
15873 <p class=flag><a name="_Toc235958527"></a><a name="_Toc102494752"></a><a
\r
15874 name="_Toc101065222"><span style='mso-bookmark:_Toc102494752'><span
\r
15875 style='mso-bookmark:_Toc235958527'><span lang=AF>-score</span></span></span></a><span
\r
15876 style='mso-bookmark:_Toc102494752'><span style='mso-bookmark:_Toc235958527'><span
\r
15877 lang=AF> [Deprecated]</span></span></span></p>
\r
15879 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:
\r
15880 -score<o:p></o:p></span></p>
\r
15882 <p class=instruction><span lang=EN-US>Default: not used</span></p>
\r
15884 <p class=flagdescription><span lang=EN-US>Toggles on the evaluate mode and
\r
15885 causes t_coffee to evaluates a precomputed alignment provided via <b>-infile=<alignment></b>.
\r
15886 The flag <b>-output</b> must be set to an appropriate format (i.e.
\r
15887 -output=score_ascii, score_html or score_pdf). A better default parameterization
\r
15888 is obtained when using the flag <b>-mode=evaluate.</b></span></p>
\r
15890 <p class=flag><a name="_Toc235958528"></a><a name="_Toc102494753"><span
\r
15891 style='mso-bookmark:_Toc235958528'><span lang=AF>-evaluate</span></span></a></p>
\r
15893 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:
\r
15894 -evaluate<o:p></o:p></span></p>
\r
15896 <p class=instruction><span lang=EN-US>Default: not used</span></p>
\r
15898 <p class=flagdescription><span lang=EN-US>Replaces
\96score. This flag toggles on
\r
15899 the evaluate mode and causes t_coffee to evaluates a pre-computed alignment
\r
15900 provided via <b>-infile=<alignment></b>. The flag <b>-output</b> must be
\r
15901 set to an appropriate format (i.e. -output=score_ascii, score_html or
\r
15902 score_pdf). </span></p>
\r
15904 <p class=flagdescription><span lang=EN-US><o:p> </o:p></span></p>
\r
15906 <p class=flagdescription><span lang=EN-US>The main purpose of
\96evaluate is to
\r
15907 let you control every aspect of the evaluation. Yet it is advisable to use
\r
15908 pre-defined parameterization: <b>mode=evaluate.</b></span></p>
\r
15910 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
15911 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
15912 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
15913 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
15915 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:
\r
15916 t_coffee
\96infile=sample_aln1.aln -mode=evaluate </span></p>
\r
15918 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:
\r
15919 t_coffee
\96infile=sample_seq1.aln
\96in<span style='mso-spacerun:yes'>
\r
15920 </span>Lsample_lib1.tc_lib
\96mode=evaluate </span></p>
\r
15924 <p class=flag><a name="_Toc235958529"></a><a name="_Toc102494754"></a><a
\r
15925 name="_Toc101065223"><span style='mso-bookmark:_Toc102494754'><span
\r
15926 style='mso-bookmark:_Toc235958529'><span lang=AF>-convert [cw]</span></span></span></a></p>
\r
15928 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:
\r
15929 -convert<o:p></o:p></span></p>
\r
15931 <p class=instruction><span lang=EN-US>Default: turned off</span></p>
\r
15933 <p class=flagdescription><span lang=EN-US>Toggles on the conversion mode and
\r
15934 causes T-Coffee to convert the sequences, alignments, libraries or structures
\r
15935 provided via the <b>-infile</b> and <b>-in</b> flags. The output format must be
\r
15936 set via the <b>-output</b> flag. This flag can also be used if you simply want
\r
15937 to compute a library (i.e. you have an alignment and you want to turn it into a
\r
15938 library).</span></p>
\r
15940 <p class=flagdescription><span lang=EN-US>This flag is ClustalW compliant.</span></p>
\r
15942 <p class=flag><a name="_Toc235958530"></a><a name="_Toc102494755"></a><a
\r
15943 name="_Toc101065224"><span style='mso-bookmark:_Toc102494755'><span
\r
15944 style='mso-bookmark:_Toc235958530'><span lang=AF>-do_align [cw]</span></span></span></a></p>
\r
15946 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span
\r
15947 style='mso-spacerun:yes'> </span>-do_align<o:p></o:p></span></p>
\r
15949 <p class=instruction><span lang=EN-US>Default: turned on</span></p>
\r
15951 <h2><a name="_Toc235958531"></a><a name="_Toc102494756"></a><a
\r
15952 name="_Toc102494363"></a><a name="_Toc101065225"><span style='mso-bookmark:
\r
15953 _Toc102494363'><span style='mso-bookmark:_Toc102494756'><span style='mso-bookmark:
\r
15954 _Toc235958531'><span lang=EN-US>Special Parameters</span></span></span></span></a></h2>
\r
15956 <p class=flag><a name="_Toc235958532"></a><a name="_Toc102494757"></a><a
\r
15957 name="_Toc101065226"><span style='mso-bookmark:_Toc102494757'><span
\r
15958 style='mso-bookmark:_Toc235958532'><span lang=AF>-version</span></span></span></a></p>
\r
15960 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:
\r
15961 -version<o:p></o:p></span></p>
\r
15963 <p class=instruction><span lang=EN-US>Default: not used</span></p>
\r
15965 <p class=flagdescription><span lang=EN-US>Returns the current version number</span></p>
\r
15967 <p class=flag><a name="_Toc102494758"></a><a name="_Toc101065227"></a><a
\r
15968 name="_Toc235958533"><span style='mso-bookmark:_Toc101065227'><span
\r
15969 style='mso-bookmark:_Toc102494758'><span lang=AF>-proxy</span></span></span></a><span
\r
15970 style='mso-bookmark:_Toc101065227'><span style='mso-bookmark:_Toc102494758'></span></span></p>
\r
15972 <p class=flagusage><span style='mso-bookmark:_Toc101065227'><span
\r
15973 style='mso-bookmark:_Toc102494758'><span lang=EN-US style='mso-ansi-language:
\r
15974 EN-US'>Usage: -proxy=<proxy><o:p></o:p></span></span></span></p>
\r
15976 <p class=instruction><span style='mso-bookmark:_Toc101065227'><span
\r
15977 style='mso-bookmark:_Toc102494758'><span lang=EN-US>Default: not used</span></span></span></p>
\r
15979 <p class=flagdescription><span style='mso-bookmark:_Toc101065227'><span
\r
15980 style='mso-bookmark:_Toc102494758'><span lang=EN-US>Sets the proxy used by
\r
15981 HTTP_proxy AND http_proxy. Setting with the propmpt supersedes ANY other
\r
15982 setting.</span></span></span></p>
\r
15984 <p class=flagdescription><span style='mso-bookmark:_Toc101065227'><span
\r
15985 style='mso-bookmark:_Toc102494758'><span lang=EN-US>Note that if you use no
\r
15986 proxy, you should set</span></span></span></p>
\r
15988 <p class=flagdescription><span style='mso-bookmark:_Toc101065227'><span
\r
15989 style='mso-bookmark:_Toc102494758'><span lang=EN-US><span style='mso-tab-count:
\r
15990 1'> </span>-proxy</span></span></span></p>
\r
15992 <p class=flag><span style='mso-bookmark:_Toc101065227'><span style='mso-bookmark:
\r
15993 _Toc102494758'><a name="_Toc235958534"><span lang=AF>-email</span></a></span></span></p>
\r
15995 <p class=flagusage><span style='mso-bookmark:_Toc101065227'><span
\r
15996 style='mso-bookmark:_Toc102494758'><span lang=EN-US style='mso-ansi-language:
\r
15997 EN-US'>Usage: -email=<email><o:p></o:p></span></span></span></p>
\r
15999 <p class=instruction><span style='mso-bookmark:_Toc101065227'><span
\r
16000 style='mso-bookmark:_Toc102494758'><span lang=EN-US>Default: not used</span></span></span></p>
\r
16002 <p class=flagdescription><span style='mso-bookmark:_Toc101065227'><span
\r
16003 style='mso-bookmark:_Toc102494758'><span lang=EN-US>Sets your email value as
\r
16004 provided to web services</span></span></span></p>
\r
16006 <p class=flag><span style='mso-bookmark:_Toc101065227'><span style='mso-bookmark:
\r
16007 _Toc102494758'><a name="_Toc235958535"><span lang=AF>-check_configuration</span></a></span></span></p>
\r
16009 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:
\r
16010 -check_configuration<o:p></o:p></span></p>
\r
16012 <p class=instruction><span lang=EN-US>Default: not used</span></p>
\r
16014 <p class=flagdescription><span lang=EN-US>Checks your system to determine
\r
16015 whether all the programs T-Coffee can interact with are installed.</span></p>
\r
16017 <p class=flag><a name="_Toc235958536"></a><a name="_Toc102494759"></a><a
\r
16018 name="_Toc101065228"><span style='mso-bookmark:_Toc102494759'><span
\r
16019 style='mso-bookmark:_Toc235958536'><span lang=AF>-cache</span></span></span></a></p>
\r
16021 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:
\r
16022 -cache=<use, update, ignore, <filename>><o:p></o:p></span></p>
\r
16024 <p class=instruction><span lang=EN-US>Default: -cache=use</span></p>
\r
16026 <p class=flagdescription><span lang=EN-US>By default, t_coffee stores in a
\r
16027 cache directory, the results of computationally expensive (structural
\r
16028 alignment) or network intensive (BLAST search) operations.<a
\r
16029 name="_Toc101065229"></a></span></p>
\r
16031 <p class=flag><span style='mso-bookmark:_Toc101065229'><a name="_Toc235958537"></a><a
\r
16032 name="_Toc102494760"><span style='mso-bookmark:_Toc235958537'><span lang=AF>-update</span></span></a></span></p>
\r
16034 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:
\r
16035 -update<o:p></o:p></span></p>
\r
16037 <p class=instruction><span lang=EN-US>Default: turned off</span></p>
\r
16039 <p class=flagdescription><span lang=EN-US>Causes a <span
\r
16040 class=StyleflagdescriptionBoldItalicChar>wget</span> access that checks whether
\r
16041 the t_coffee version you are using needs updating.<a name="_Toc101065230"></a></span></p>
\r
16043 <p class=flag><span style='mso-bookmark:_Toc101065230'><a name="_Toc235958538"></a><a
\r
16044 name="_Toc102494761"><span style='mso-bookmark:_Toc235958538'><span lang=AF>-full_log</span></span></a></span></p>
\r
16046 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:
\r
16047 -full_log=<filename><o:p></o:p></span></p>
\r
16049 <p class=instruction><span lang=EN-US>Default: turned off</span></p>
\r
16051 <p class=flagdescription><span lang=EN-US>Causes t_coffee to output a full log
\r
16052 file that contains all the input/output files.<a name="_Toc101065231"></a></span></p>
\r
16054 <p class=flag><span style='mso-bookmark:_Toc101065231'><a name="_Toc235958539"></a><a
\r
16055 name="_Toc102494762"><span style='mso-bookmark:_Toc235958539'><span lang=AF>-plugins</span></span></a></span></p>
\r
16057 <p class=flagusage><span style='mso-bookmark:_Toc101065231'><span
\r
16058 style='mso-bookmark:_Toc102494762'><span style='mso-bookmark:_Toc235958539'><span
\r
16059 lang=EN-US style='mso-ansi-language:EN-US'>Usage: -plugins=<dir><o:p></o:p></span></span></span></span></p>
\r
16061 <p class=instruction><span style='mso-bookmark:_Toc101065231'><span
\r
16062 style='mso-bookmark:_Toc102494762'><span style='mso-bookmark:_Toc235958539'><span
\r
16063 lang=EN-US>Default: default</span></span></span></span></p>
\r
16065 <p class=flagdescription><span style='mso-bookmark:_Toc101065231'><span
\r
16066 style='mso-bookmark:_Toc102494762'><span style='mso-bookmark:_Toc235958539'><span
\r
16067 lang=EN-US>Specifies the directory in which the companion packages (other
\r
16068 multiple aligners used by M-Coffee, structural aligners, etc
\85) are kept as an
\r
16069 alternative, you can also set the environment variable PLUGINS_4_TCOFFEE</span></span></span></span></p>
\r
16071 <p class=flagdescription><span style='mso-bookmark:_Toc101065231'><span
\r
16072 style='mso-bookmark:_Toc102494762'><span style='mso-bookmark:_Toc235958539'><span
\r
16073 lang=EN-US>The default is ~/.t_coffee/plugins/</span></span></span></span></p>
\r
16075 <p class=flag><span style='mso-bookmark:_Toc101065231'><span style='mso-bookmark:
\r
16076 _Toc102494762'><span style='mso-bookmark:_Toc235958539'><span lang=AF>-other_pg</span></span></span></span></p>
\r
16078 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:
\r
16079 -other_pg=<filename><o:p></o:p></span></p>
\r
16081 <p class=instruction><span lang=EN-US>Default: turned off</span></p>
\r
16083 <p class=flagdescription><span lang=EN-US>Some rumours claim that Tetris is
\r
16084 embedded within T-Coffee and could be ran using some special set of commands.
\r
16085 We wish to deny these rumours, although we may admit that several interesting
\r
16086 reformatting programs are now embedded in t_coffee and can be ran through the
\r
16087 \96other_pg flag.</span></p>
\r
16089 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
16090 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
16091 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
16092 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
16094 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:
\r
16095 t_coffee
\96other_pg=seq_reformat </span></p>
\r
16097 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:
\r
16098 t_coffee
\96other_pg=unpack_all </span></p>
\r
16100 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:
\r
16101 t_coffee
\96other_pg=unpack_extract_from_pdb </span></p>
\r
16105 <h2><a name="_Toc235958540"></a><a name="_Toc102494763"></a><a
\r
16106 name="_Toc102494364"></a><a name="_Toc101065232"><span style='mso-bookmark:
\r
16107 _Toc102494364'><span style='mso-bookmark:_Toc102494763'><span style='mso-bookmark:
\r
16108 _Toc235958540'><span lang=EN-US>Input</span></span></span></span></a><span
\r
16109 lang=EN-US> </span></h2>
\r
16111 <h3><a name="_Toc235958541"></a><a name="_Toc102494764"></a><a
\r
16112 name="_Toc102494365"></a><a name="_Toc101065233"><span style='mso-bookmark:
\r
16113 _Toc102494365'><span style='mso-bookmark:_Toc102494764'><span style='mso-bookmark:
\r
16114 _Toc235958541'><span lang=EN-US>Sequence Input</span></span></span></span></a></h3>
\r
16116 <p class=flag><a name="_Toc235958542"></a><a name="_Toc102494765"></a><a
\r
16117 name="_Toc101065234"><span style='mso-bookmark:_Toc102494765'><span
\r
16118 style='mso-bookmark:_Toc235958542'><span lang=AF>-infile [cw]</span></span></span></a></p>
\r
16120 <p class=flagdescription><span lang=EN-US>To remain compatible with ClustalW,
\r
16121 it is possible to indicate the sequences with this flag</span></p>
\r
16123 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
16124 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
16125 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
16126 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
16128 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:
\r
16129 t_coffee -infile=sample_seq1.fasta </span></p>
\r
16133 <p class=Note><span lang=EN-US style='mso-ansi-language:EN-US'>Note: Common
\r
16134 multiple sequence alignments format constitute a valid input format.<o:p></o:p></span></p>
\r
16136 <p class=Note><span lang=EN-US style='mso-ansi-language:EN-US'>Note: T-Coffee
\r
16137 automatically removes the gaps </span><i><span lang=EN-US style='mso-ansi-language:
\r
16138 EN-US;mso-bidi-font-weight:bold'>before</span></i><span lang=EN-US
\r
16139 style='mso-ansi-language:EN-US'> doing the alignment. This behaviour is different
\r
16140 from that of ClustalW where the gaps are kept.<o:p></o:p></span></p>
\r
16142 <p class=flag><a name="_Toc235958543"></a><a name="_Toc102494766"></a><a
\r
16143 name="_Toc101065235"><span style='mso-bookmark:_Toc102494766'><span
\r
16144 style='mso-bookmark:_Toc235958543'><span lang=AF>-in</span></span></span></a><span
\r
16145 style='mso-bookmark:_Toc102494766'><span style='mso-bookmark:_Toc235958543'><span
\r
16146 lang=AF> (Cf
\96in from the Method and Library Input section)</span></span></span></p>
\r
16148 <p class=flag><a name="_Toc235958544"></a><a name="_Toc102494767"></a><a
\r
16149 name="_Toc101065236"><span style='mso-bookmark:_Toc102494767'><span
\r
16150 style='mso-bookmark:_Toc235958544'><span lang=AF>-get_type</span></span></span></a></p>
\r
16152 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:
\r
16153 -get_type<o:p></o:p></span></p>
\r
16155 <p class=instruction><span lang=EN-US>Default: turned off</span></p>
\r
16157 <p class=flagdescription><span lang=EN-US>Forces t_coffee to identify the
\r
16158 sequences type (PROTEIN, DNA).</span></p>
\r
16160 <p class=flag><a name="_Toc235958545"></a><a name="_Toc102494768"></a><a
\r
16161 name="_Toc101065237"><span style='mso-bookmark:_Toc102494768'><span
\r
16162 style='mso-bookmark:_Toc235958545'><span lang=AF>-type [cw]</span></span></span></a></p>
\r
16164 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:
\r
16165 -type=DNA ¦ PROTEIN¦ DNA_PROTEIN<o:p></o:p></span></p>
\r
16167 <p class=instruction><span lang=EN-US>Default: -type=<automatically set></span></p>
\r
16169 <p class=flagdescription><span lang=EN-US>This flag sets the type of the
\r
16170 sequences. If omitted, the type is guessed automatically. This flag is
\r
16171 compatible with ClustalW.</span></p>
\r
16173 <div style='mso-element:para-border-div;border:solid windowtext 1.5pt;
\r
16174 padding:0mm 0mm 0mm 0mm;background:#F7CBB7'>
\r
16176 <p class=Warning><span lang=EN-US>Warning:<span style='mso-spacerun:yes'>
\r
16177 </span>In case of low complexity or short sequences, it is recommended to set
\r
16178 the type manually.<a name="_Toc101065238"></a></span></p>
\r
16182 <p class=flag><span style='mso-bookmark:_Toc101065238'><a name="_Toc235958546"></a><a
\r
16183 name="_Toc102494769"><span style='mso-bookmark:_Toc235958546'><span lang=AF>-seq</span></span></a></span></p>
\r
16185 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:
\r
16186 -seq=[<P,S><name>,]<o:p></o:p></span></p>
\r
16188 <p class=instruction><span lang=EN-US>Default: none</span></p>
\r
16190 <p class=MyNormal><span lang=AF>-seq is now the recommended flag to provide
\r
16191 your sequences. It behaves mostly like the -in flag.</span></p>
\r
16193 <p class=flag><a name="_Toc235958547"></a><a name="_Toc102494770"></a><a
\r
16194 name="_Toc101065239"><span style='mso-bookmark:_Toc102494770'><span
\r
16195 style='mso-bookmark:_Toc235958547'><span lang=AF>-seq_source</span></span></span></a></p>
\r
16197 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:
\r
16198 -seq_source=<ANY or<span style='mso-spacerun:yes'> </span>_LS or LS ><o:p></o:p></span></p>
\r
16200 <p class=instruction><span lang=EN-US>Default: ANY.</span></p>
\r
16202 <p class=flagdescription><span lang=EN-US>You may not want to combine all the
\r
16203 provided sequences into a single sequence list. You can do by specifying that
\r
16204 you do not want to treat all the
\96in files as potential sequence sources.</span></p>
\r
16206 <p class=flagdescription><span lang=EN-US>-seq_source=_LA indicates that
\r
16207 neither sequences provided via the A (Alignment) flag or via the L (Library
\r
16208 flag) should be added to the sequence list.</span></p>
\r
16210 <p class=flagdescription><span lang=EN-US>-seq_source=S means that only
\r
16211 sequences provided via the S tag will be considered. All the other sequences
\r
16212 will be ignored.</span></p>
\r
16214 <p class=Note><span lang=EN-US style='mso-ansi-language:EN-US'>Note:<span
\r
16215 style='mso-spacerun:yes'> </span>This flag is mostly designed for interactions
\r
16216 between T-Coffee and T-CoffeeDPA (the large scale version of T-Coffee).</span><span
\r
16217 lang=EN-US style='mso-ansi-language:EN-US;mso-bidi-font-weight:bold'><o:p></o:p></span></p>
\r
16219 <h3><a name="_Toc235958548"></a><a name="_Toc102494771"></a><a
\r
16220 name="_Toc102494366"></a><a name="_Toc101065241"><span style='mso-bookmark:
\r
16221 _Toc102494366'><span style='mso-bookmark:_Toc102494771'><span style='mso-bookmark:
\r
16222 _Toc235958548'><span lang=EN-US>Structure Input</span></span></span></span></a></h3>
\r
16224 <p class=flag><a name="_Toc235958549"></a><a name="_Toc102494772"></a><a
\r
16225 name="_Toc101065242"><span style='mso-bookmark:_Toc102494772'><span
\r
16226 style='mso-bookmark:_Toc235958549'><span lang=AF>-pdb</span></span></span></a></p>
\r
16228 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span
\r
16229 style='mso-spacerun:yes'> </span>-pdb=<pdbid1>,<pdbid2>
\85[Max 200]<o:p></o:p></span></p>
\r
16231 <p class=instruction><span lang=EN-US>Default: None</span></p>
\r
16233 <p class=flagdescription><span lang=EN-US>Reads or fetch a pdb file. It is
\r
16234 possible to specify a chain or even a sub-chain:</span></p>
\r
16236 <p class=example2><span lang=EN-US>PDBID(PDB_CHAIN)[opt] (FIRST,LAST)[opt]<a
\r
16237 name="_Toc101065243"></a></span></p>
\r
16239 <p class=flagdescription><span style='mso-bookmark:_Toc101065243'><span
\r
16240 lang=EN-US>It is also possible to input structures via the
\96in flag. In that
\r
16241 case, you will need to use the TAG identifier:</span></span></p>
\r
16243 <p class=example2><span style='mso-bookmark:_Toc101065243'><span lang=EN-US>-in
\r
16244 Ppdb1 Ppdb2
\85 </span></span></p>
\r
16246 <h3><span style='mso-bookmark:_Toc101065243'><a name="_Toc235958550"></a><a
\r
16247 name="_Toc102494773"></a><a name="_Toc102494367"><span style='mso-bookmark:
\r
16248 _Toc102494773'><span style='mso-bookmark:_Toc235958550'><span lang=EN-US>Tree
\r
16249 Input</span></span></span></a></span></h3>
\r
16251 <p class=flag><a name="_Toc235958551"></a><a name="_Toc102494774"></a><a
\r
16252 name="_Toc101065244"><span style='mso-bookmark:_Toc102494774'><span
\r
16253 style='mso-bookmark:_Toc235958551'><span lang=AF>-usetree</span></span></span></a></p>
\r
16255 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:
\r
16256 -usetree=<tree file><o:p></o:p></span></p>
\r
16258 <p class=instruction><span lang=EN-US>Default: No file specified</span></p>
\r
16260 <p class=instruction><span lang=EN-US>Format: newick tree format (ClustalW
\r
16261 Style)</span></p>
\r
16263 <p class=flagdescription><span lang=EN-US>This flag indicates that rather than
\r
16264 computing a new dendrogram, t_coffee must use a pre-computed one. The tree
\r
16265 files are in phylips format and compatible with ClustalW. In most cases, using
\r
16266 a pre-computed tree will halve the computation time required by t_coffee. It is
\r
16267 also possible to use trees output by ClustalW, Phylips and any other program.</span></p>
\r
16269 <h3><a name="_Toc235958552"></a><a name="_Toc102494775"></a><a
\r
16270 name="_Toc102494368"></a><a name="_Toc101065245"><span style='mso-bookmark:
\r
16271 _Toc102494368'><span style='mso-bookmark:_Toc102494775'><span style='mso-bookmark:
\r
16272 _Toc235958552'><span lang=EN-US>Structures, Sequences Methods and Library Input</span></span></span></span></a><span
\r
16273 style='mso-bookmark:_Toc235958552'><span lang=EN-US> via the </span></span><span
\r
16274 style='mso-bookmark:_Toc235958552'><span lang=EN-US style='font-family:Symbol;
\r
16275 mso-ascii-font-family:"Arial Black"'>–</span><span lang=EN-US>in Flag</span></span></h3>
\r
16277 <div style='mso-element:para-border-div;border:solid windowtext 1.5pt;
\r
16278 padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#FFFF89'>
\r
16280 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut align=center
\r
16281 style='text-align:center;background:#FFFF89'><a name="_Toc101065246"><span
\r
16282 lang=EN-US style='font-size:20.0pt;mso-bidi-font-size:10.0pt'>The -in Flag and
\r
16283 its Identifier TAGS<o:p></o:p></span></a></p>
\r
16285 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span
\r
16286 style='mso-bookmark:_Toc101065246'><span lang=EN-US><o:p> </o:p></span></span></p>
\r
16288 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span
\r
16289 style='mso-bookmark:_Toc101065246'><span lang=EN-US><-in> is the real
\r
16290 grinder of T-Coffee. Sequences, methods and alignments all pass through so that
\r
16291 T-Coffee can turn it all into a single list of constraints (the library).
\r
16292 Everything is done automatically with T-Coffee going through each file to
\r
16293 extract the sequences it contains. The methods are then applied to the
\r
16294 sequences. Pre-compiled constraint list can also be provided. Each file
\r
16295 provided via this flag must be preceded with a symbol (Identifier TAG) that
\r
16296 indicates its nature to T-Coffee. The TAGs currently supported are the
\r
16297 following:</span></span></p>
\r
16299 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span
\r
16300 style='mso-bookmark:_Toc101065246'><span lang=EN-US><o:p> </o:p></span></span></p>
\r
16302 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span
\r
16303 style='mso-bookmark:_Toc101065246'><span lang=EN-US>P<span style='mso-tab-count:
\r
16304 1'> </span>PDB structure</span></span></p>
\r
16306 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span
\r
16307 style='mso-bookmark:_Toc101065246'><span lang=EN-US>S <span style='mso-tab-count:
\r
16308 1'> </span>for sequences (use it as well to treat an MSA as unaligned
\r
16309 sequences)</span></span></p>
\r
16311 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span
\r
16312 style='mso-bookmark:_Toc101065246'><span lang=EN-US><o:p> </o:p></span></span></p>
\r
16314 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span
\r
16315 style='mso-bookmark:_Toc101065246'><span lang=EN-US>M <span style='mso-tab-count:
\r
16316 1'> </span>Methods used to build the library</span></span></p>
\r
16318 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span
\r
16319 style='mso-bookmark:_Toc101065246'><span lang=EN-US>L <span style='mso-tab-count:
\r
16320 1'> </span>Pre-computed T-Coffee library</span></span></p>
\r
16322 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span
\r
16323 style='mso-bookmark:_Toc101065246'><span lang=EN-US>A <span style='mso-tab-count:
\r
16324 1'> </span>Multiple Alignments that must be turned into a Library</span></span></p>
\r
16326 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span
\r
16327 style='mso-bookmark:_Toc101065246'><span lang=EN-US><o:p> </o:p></span></span></p>
\r
16329 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span
\r
16330 style='mso-bookmark:_Toc101065246'><span lang=EN-US>X <span style='mso-tab-count:
\r
16331 1'> </span>Substitution matrices.</span></span></p>
\r
16333 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut style='margin-left:
\r
16334 35.25pt;text-indent:-35.25pt;background:#FFFF89'><span style='mso-bookmark:
\r
16335 _Toc101065246'><span lang=EN-US>R <span style='mso-tab-count:1'> </span><span
\r
16336 style='mso-tab-count:1'> </span>Profiles. This is a legal multiple
\r
16337 alignments that will be treated as single sequences (the sequences it contains
\r
16338 will not be realigned). </span></span></p>
\r
16340 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut style='margin-left:
\r
16341 35.25pt;text-indent:-35.25pt;background:#FFFF89'><span style='mso-bookmark:
\r
16342 _Toc101065246'><span lang=EN-US><o:p> </o:p></span></span></p>
\r
16344 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut style='margin-left:
\r
16345 35.25pt;text-indent:-35.25pt;background:#FFFF89'><span style='mso-bookmark:
\r
16346 _Toc101065246'><span lang=EN-US>If you do not want to use the TAGS, you will
\r
16347 need to use the following flags in replacement of -in. Do not use the TAGS when
\r
16348 using these flags:</span></span></p>
\r
16350 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut style='margin-left:
\r
16351 35.25pt;text-indent:-35.25pt;background:#FFFF89'><span style='mso-bookmark:
\r
16352 _Toc101065246'><span lang=EN-US><o:p> </o:p></span></span></p>
\r
16354 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut style='margin-left:
\r
16355 35.25pt;text-indent:-35.25pt;background:#FFFF89'><span style='mso-bookmark:
\r
16356 _Toc101065246'><span lang=EN-US>-aln <span style='mso-tab-count:3'> </span>Alignments
\r
16357 <span style='mso-tab-count:1'> </span>(A)</span></span></p>
\r
16359 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut style='margin-left:
\r
16360 35.25pt;text-indent:-35.25pt;background:#FFFF89'><span style='mso-bookmark:
\r
16361 _Toc101065246'><span lang=EN-US>-profile<span style='mso-tab-count:1'> </span>Profiles
\r
16362 <span style='mso-tab-count:1'> </span>(R)</span></span></p>
\r
16364 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut style='margin-left:
\r
16365 35.25pt;text-indent:-35.25pt;background:#FFFF89'><span style='mso-bookmark:
\r
16366 _Toc101065246'><span lang=EN-US>-method<span style='mso-tab-count:1'> </span>Method
\r
16367 <span style='mso-tab-count:1'> </span>(M)</span></span></p>
\r
16369 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut style='margin-left:
\r
16370 35.25pt;text-indent:-35.25pt;background:#FFFF89'><span style='mso-bookmark:
\r
16371 _Toc101065246'><span lang=EN-US>-seq<span style='mso-tab-count:3'> </span>Sequences
\r
16372 <span style='mso-tab-count:1'> </span>(S)</span></span></p>
\r
16374 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut style='margin-left:
\r
16375 35.25pt;text-indent:-35.25pt;background:#FFFF89'><span style='mso-bookmark:
\r
16376 _Toc101065246'><span lang=EN-US>-lib<span style='mso-tab-count:3'> </span>Libraries<span
\r
16377 style='mso-tab-count:1'> </span>(L)<a name="_Toc102494776"></a></span></span></p>
\r
16381 <p class=flag><span style='mso-bookmark:_Toc101065246'><span style='mso-bookmark:
\r
16382 _Toc102494776'><a name="_Toc235958553"><span lang=AF>-in</span></a></span></span></p>
\r
16384 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:
\r
16385 -in=[<P,S,A,L,M,X><name>,]<o:p></o:p></span></p>
\r
16387 <p class=instruction><span lang=EN-US>Default:
\r
16388 -in=Mlalign_id_pair,Mclustalw_pair</span></p>
\r
16390 <div style='mso-element:para-border-div;border:solid windowtext 1.5pt;
\r
16391 padding:0mm 0mm 0mm 0mm;background:#F7CBB7'>
\r
16393 <p class=Warning><span lang=EN-US>Note: -in can be replaced with the combined
\r
16394 usage of -aln, iprofile, .pdb, .lib, -method.</span></p>
\r
16398 <p class=flagdescription><span lang=EN-US>See the box for an explanation of the
\r
16399 -in flag. The following argument passed via -in</span></p>
\r
16401 <p class=flagdescription><span lang=EN-US><o:p> </o:p></span></p>
\r
16403 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
16404 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
16405 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
16406 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
16408 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:
\r
16410 -in=Ssample_seq1.fasta,Asample_aln1.aln,Asample_aln2.msf,Mlalign_id_pair,Lsample_lib1.tc_lib
\r
16411 \96outfile=outaln</span></p>
\r
16415 <p class=flagdescription><span lang=EN-US><o:p> </o:p></span></p>
\r
16417 <p class=flagdescription><span lang=EN-US>This command will trigger the following
\r
16418 chain of events:</span></p>
\r
16420 <p class=flagdescription><span lang=EN-US><o:p> </o:p></span></p>
\r
16422 <p class=flagdescription><span lang=EN-US>1-Gather all the sequences</span></p>
\r
16424 <p class=flagdescription><span lang=EN-US>Sequences within all the provided
\r
16425 files are pooled together. Format recognition is automatic. Duplicates are
\r
16426 removed (if they have the same name). Duplicates in a single file are only
\r
16427 tolerated in FASTA format file, although they will cause sequences to be
\r
16428 renamed.</span></p>
\r
16430 <p class=flagdescription><span lang=EN-US>In the above case, the total set of
\r
16431 sequences will be made of sequences contained in sequences1.seq,
\r
16432 alignment1.aln, alignment2.msf and library.lib, plus the sequences initially
\r
16433 gathered<span style='mso-spacerun:yes'> </span>by -infile.</span></p>
\r
16435 <p class=flagdescription><span lang=EN-US>2-Turn alignments into libraries</span></p>
\r
16437 <p class=flagdescription><span lang=EN-US>alignment1.aln and alignment2.msf
\r
16438 will be read and turned into libraries. Another library will be produced by
\r
16439 applying the method lalign_id_pair to the set of sequences previously obtained
\r
16440 (1). The final library used for the alignment will be the combination of all
\r
16441 this information. </span></p>
\r
16443 <p class=flagdescription><span lang=EN-US>Note as well the following rules: </span></p>
\r
16445 <p class=flagdescription><span lang=EN-US><o:p> </o:p></span></p>
\r
16447 <p class=flagdescription><b style='mso-bidi-font-weight:normal'><span
\r
16448 lang=EN-US>1-Order</span></b><span lang=EN-US style='mso-bidi-font-weight:bold'>:</span><span
\r
16449 lang=EN-US> The order in which sequences, methods, alignments and libraries are
\r
16450 fed in is irrelevant.</span></p>
\r
16452 <p class=flagdescription><b style='mso-bidi-font-weight:normal'><span
\r
16453 lang=EN-US>2-Heterogeneity</span></b><span lang=EN-US style='mso-bidi-font-weight:
\r
16454 bold'>:</span><span lang=EN-US> There is no need for each element (A, S, L) to
\r
16455 contain the same sequences.</span></p>
\r
16457 <p class=flagdescription><b style='mso-bidi-font-weight:normal'><span
\r
16458 lang=EN-US>3-No Duplicate</span></b><span lang=EN-US style='mso-bidi-font-weight:
\r
16459 bold'>:</span><span lang=EN-US> Each file should contain only one copy of each
\r
16460 sequence. Duplicates are only allowed in FASTA files but will cause the
\r
16461 sequences to be renamed.</span></p>
\r
16463 <p class=flagdescription><b style='mso-bidi-font-weight:normal'><span
\r
16464 lang=EN-US>4-Reconciliation</span></b><span lang=EN-US style='mso-bidi-font-weight:
\r
16465 bold'>:</span><span lang=EN-US> If two files (for instance two alignments)
\r
16466 contain different versions of the same sequence due to an indel, a new sequence
\r
16467 will be reconstructed and used instead:</span></p>
\r
16469 <p class=example2CxSpFirst><span lang=EN-US>aln 1:hgab1 <span style='mso-tab-count:
\r
16470 1'> </span>AAAAABAAAAA</span></p>
\r
16472 <p class=example2CxSpLast><span lang=EN-US>aln 2:hgab1<span style='mso-tab-count:
\r
16473 1'> </span>AAAAAAAAAACCC</span></p>
\r
16475 <p class=flagdescription><span lang=EN-US>will cause the program to reconstruct
\r
16476 and use the following sequence </span></p>
\r
16478 <p class=example2><span lang=EN-US>hgab1<span style='mso-tab-count:1'> </span>AAAAABAAAAACCC
\r
16481 <p class=flagdescription><span lang=EN-US>This can be useful if you are trying
\r
16482 to combine several runs of blast, or structural information where residues may
\r
16483 have been deleted. However substitutions are forbidden. If two sequences with
\r
16484 the same name cannot be merged, they will cause the program to exit with an
\r
16485 information message.</span></p>
\r
16487 <p class=flagdescription><b style='mso-bidi-font-weight:normal'><span
\r
16488 lang=EN-US>5-Methods</span></b><span lang=EN-US style='mso-bidi-font-weight:
\r
16489 bold'>:</span><span lang=EN-US> The method describer can either be built in
\r
16490 (See ### for a list of all the available methods) or be a file describing the
\r
16491 method to be used. The exact syntax is provided in part 4 of this manual.</span></p>
\r
16493 <p class=flagdescription><b style='mso-bidi-font-weight:normal'><span
\r
16494 lang=EN-US>6-Substitution Matrices</span></b><span lang=EN-US style='mso-bidi-font-weight:
\r
16495 bold'>: </span><span lang=EN-US>If the method is a substitution matrix (X) then
\r
16496 no other type of information should be provided. For instance:</span></p>
\r
16498 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
16499 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
16500 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
16501 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
16503 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:
\r
16504 t_coffee sample_seq1.fasta -in=Xpam250mt<span style='mso-spacerun:yes'>
\r
16505 </span>-gapopen=-10<span style='mso-spacerun:yes'> </span>-gapext=-1 </span></p>
\r
16509 <p class=flagdescription><span lang=EN-US>This command results in a progressive
\r
16510 alignment carried out on the sequences in seqfile. The procedure does not use
\r
16511 any more the T-Coffee concistency based algorithm, but switches to a standard
\r
16512 progressive alignment algorithm (like ClustalW or Pileup) much less accurate.
\r
16513 In this context, appropriate gap penalties should be provided. The matrices are
\r
16514 in the file source/matrices.h. Add-Hoc matrices can also be provided by the
\r
16515 user (see the matrices format section at the end of this manual).</span></p>
\r
16517 <div style='mso-element:para-border-div;border:solid windowtext 1.5pt;
\r
16518 padding:0mm 0mm 0mm 0mm;background:#F7CBB7'>
\r
16520 <p class=Warning><span lang=EN-US>Warning: Xmatrix does not have the same
\r
16521 effect as using the -matrix flag.<span style='mso-spacerun:yes'> </span>The
\r
16522 -matrix defines the matrix that will be used while compiling the library while
\r
16523 the Xmatrix defines the matrix used when assembling the final alignment.</span></p>
\r
16527 <h3><a name="_Toc235958554"></a><a name="_Toc102494777"></a><a
\r
16528 name="_Toc102494369"></a><a name="_Toc101065247"><span style='mso-bookmark:
\r
16529 _Toc102494369'><span style='mso-bookmark:_Toc102494777'><span style='mso-bookmark:
\r
16530 _Toc235958554'><span lang=EN-US>Profile Input</span></span></span></span></a></h3>
\r
16532 <p class=flag><a name="_Toc235958555"></a><a name="_Toc102494778"></a><a
\r
16533 name="_Toc101065248"><span style='mso-bookmark:_Toc102494778'><span
\r
16534 style='mso-bookmark:_Toc235958555'><span lang=AF>-profile</span></span></span></a></p>
\r
16536 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:
\r
16537 -profile=[<name>,] maximum of 200 profiles.<o:p></o:p></span></p>
\r
16539 <p class=instruction><span lang=EN-US>Default: no default</span></p>
\r
16541 <p class=flagdescription><span lang=EN-US>This flag causes T-Coffee to treat
\r
16542 multiple alignments as a single sequences, thus making it possible to make
\r
16543 multiple profile alignments. The profile-profile alignment is controlled by <span
\r
16544 style='mso-bidi-font-weight:bold'>-profile_mode</span> and <span
\r
16545 style='mso-bidi-font-weight:bold'>-profile_comparison</span>. When provided
\r
16546 with the <b style='mso-bidi-font-weight:normal'>-in</b> flag, profiles must be
\r
16547 preceded with the letter R.</span></p>
\r
16549 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
16550 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
16551 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
16552 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
16554 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:
\r
16555 t_coffee
\96profile sample_aln1.aln,sample_aln2.aln
\96outfile=profile_aln</span></p>
\r
16557 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:
\r
16558 t_coffee
\96in Rsample_aln1.aln,Rsample_aln2.aln,Mslow_pair,Mlalign_id_pair
\r
16559 \96outfile=profile_aln</span></p>
\r
16563 <p class=flagdescription><span lang=EN-US>Note that when using
\96template_file,
\r
16564 the program will also look for the templates associated with the profiles, even
\r
16565 if the profiles have been provided as templates themselves (however it will not
\r
16566 look for the template of the profile templates of the profile templates
\85)</span></p>
\r
16568 <p class=flag><a name="_Toc235958556"></a><a name="_Toc102494779"></a><a
\r
16569 name="_Toc101065249"><span style='mso-bookmark:_Toc102494779'><span
\r
16570 style='mso-bookmark:_Toc235958556'><span lang=AF>-profile1 [cw]</span></span></span></a></p>
\r
16572 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:
\r
16573 -profile1=[<name>], one name only<o:p></o:p></span></p>
\r
16575 <p class=instruction><span lang=EN-US>Default: no default</span></p>
\r
16577 <p class=flagdescription><span lang=EN-US>Similar to the previous one and was
\r
16578 provided for compatibility with ClustalW.</span></p>
\r
16580 <p class=flag><a name="_Toc235958557"></a><a name="_Toc102494780"></a><a
\r
16581 name="_Toc101065250"><span style='mso-bookmark:_Toc102494780'><span
\r
16582 style='mso-bookmark:_Toc235958557'><span lang=AF>-profile2 [cw]</span></span></span></a></p>
\r
16584 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:
\r
16585 -profile1=[<name>], one name only<o:p></o:p></span></p>
\r
16587 <p class=instruction><span lang=EN-US>Default: no default</span></p>
\r
16589 <p class=flagdescription><span lang=EN-US>Similar to the previous one and was
\r
16590 provided for compatibility with ClustalW.</span></p>
\r
16592 <h2><a name="_Toc235958558"></a><a name="_Toc102494781"></a><a
\r
16593 name="_Toc102494370"></a><a name="_Toc101065251"><span style='mso-bookmark:
\r
16594 _Toc102494370'><span style='mso-bookmark:_Toc102494781'><span style='mso-bookmark:
\r
16595 _Toc235958558'><span lang=EN-US>Alignment Computation</span></span></span></span></a></h2>
\r
16597 <h3><a name="_Toc235958559"></a><a name="_Toc102494782"></a><a
\r
16598 name="_Toc102494371"></a><a name="_Toc101065252"><span style='mso-bookmark:
\r
16599 _Toc102494371'><span style='mso-bookmark:_Toc102494782'><span style='mso-bookmark:
\r
16600 _Toc235958559'><span lang=EN-US>Library Computation: Methods</span></span></span></span></a></h3>
\r
16602 <p class=flag><a name="_Toc235958560"></a><a name="_Toc102494783"><span
\r
16603 style='mso-bookmark:_Toc235958560'><span lang=AF>-lalign_n_top</span></span></a></p>
\r
16605 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:
\r
16606 -lalign_n_top=<Integer><o:p></o:p></span></p>
\r
16608 <p class=instruction><span lang=EN-US>Default: -lalign_n_top=10</span></p>
\r
16610 <p class=flagdescription><span lang=EN-US>Number of alignment reported by the
\r
16611 local method (lalign).</span></p>
\r
16613 <p class=flag><a name="_Toc235958561"></a><a name="_Toc102494784"><span
\r
16614 style='mso-bookmark:_Toc235958561'><span lang=AF>-align_pdb_param_file</span></span></a></p>
\r
16616 <p class=flagdescription><span lang=EN-US>Unsuported</span></p>
\r
16618 <p class=flag><a name="_Toc235958562"></a><a name="_Toc102494785"><span
\r
16619 style='mso-bookmark:_Toc235958562'><span lang=AF>-align_pdb_hasch_mode</span></span></a></p>
\r
16621 <p class=flagdescription><span lang=EN-US>Unsuported<a name="_Toc101065253"></a></span></p>
\r
16623 <h3><span style='mso-bookmark:_Toc101065253'><a name="_Toc235958563"></a><a
\r
16624 name="_Toc102494786"></a><a name="_Toc102494372"><span style='mso-bookmark:
\r
16625 _Toc102494786'><span style='mso-bookmark:_Toc235958563'><span lang=EN-US>Library
\r
16626 Computation: Extension</span></span></span></a></span></h3>
\r
16628 <p class=flag><a name="_Toc101065255"></a><a name="_Toc235958564"></a><a
\r
16629 name="_Toc102494787"></a><a name="_Toc101065254"><span style='mso-bookmark:
\r
16630 _Toc102494787'><span style='mso-bookmark:_Toc235958564'><span style='mso-bookmark:
\r
16631 _Toc101065255'><span lang=AF>-</span></span></span></span></a><span
\r
16632 style='mso-bookmark:_Toc102494787'><span style='mso-bookmark:_Toc235958564'><span
\r
16633 style='mso-bookmark:_Toc101065255'><span lang=AF>lib_list [Unsupported]</span></span></span></span><span
\r
16634 style='mso-bookmark:_Toc101065255'></span></p>
\r
16636 <p class=flagusage><span style='mso-bookmark:_Toc101065255'><span lang=EN-US
\r
16637 style='mso-ansi-language:EN-US'>Usage:<span style='mso-spacerun:yes'>
\r
16638 </span>-lib_list=<filename> <o:p></o:p></span></span></p>
\r
16640 <p class=instruction><span style='mso-bookmark:_Toc101065255'><span lang=EN-US>Default:unset</span></span></p>
\r
16642 <p class=flagdescription><span style='mso-bookmark:_Toc101065255'><span
\r
16643 lang=EN-US>Use this flag if you do not want the library computation to take
\r
16644 into account all the possible pairs in your dataset. For instance</span></span></p>
\r
16646 <p class=flagdescription><span style='mso-bookmark:_Toc101065255'><span
\r
16647 lang=EN-US>Format:</span></span></p>
\r
16649 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
\r
16650 mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
\r
16651 background:#E6E6E6'>
\r
16653 <p class=examplefileCxSpFirst><span style='mso-bookmark:_Toc101065255'><span
\r
16654 lang=EN-US><span style='mso-tab-count:1'> </span>2 Name1 name2 </span></span></p>
\r
16656 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065255'><span
\r
16657 lang=EN-US><span style='mso-tab-count:1'> </span>2 Name1 name4</span></span></p>
\r
16659 <p class=examplefileCxSpLast><span style='mso-bookmark:_Toc101065255'><span
\r
16660 lang=EN-US><span style='mso-tab-count:1'> </span>3 Name1 Name2 Name3
\85</span></span></p>
\r
16664 <p class=flagdescription><span style='mso-bookmark:_Toc101065255'><span
\r
16665 lang=EN-US><span style='mso-tab-count:1'> </span>(the line 3 would
\r
16666 be used by a multiple alignment method).</span></span></p>
\r
16668 <p class=flag><span style='mso-bookmark:_Toc101065255'><a name="_Toc235958565"></a><a
\r
16669 name="_Toc102494788"><span style='mso-bookmark:_Toc235958565'><span lang=AF>-do_normalise</span></span></a></span></p>
\r
16671 <p class=flagusage><span style='mso-bookmark:_Toc101065255'><span lang=EN-US
\r
16672 style='mso-ansi-language:EN-US'>Usage:<span style='mso-spacerun:yes'>
\r
16673 </span>-do_normalise=<0 or a positive value> <o:p></o:p></span></span></p>
\r
16675 <p class=instruction><span style='mso-bookmark:_Toc101065255'><span lang=EN-US>Default:-do_normalise=1000</span></span></p>
\r
16677 <p class=instruction><span style='mso-bookmark:_Toc101065255'><span lang=EN-US>Development
\r
16678 Only</span></span></p>
\r
16680 <p class=flagdescription><span style='mso-bookmark:_Toc101065255'><span
\r
16681 lang=EN-US>When using a value different from 0, this flag sets the score of the
\r
16682 highest scoring pair to 1000. </span></span></p>
\r
16684 <p class=flag><span style='mso-bookmark:_Toc101065255'><a name="_Toc235958566"></a><a
\r
16685 name="_Toc102494789"><span style='mso-bookmark:_Toc235958566'><span lang=AF>-extend</span></span></a></span></p>
\r
16687 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span
\r
16688 style='mso-spacerun:yes'> </span>-extend=<0,1 or a positive value> <o:p></o:p></span></p>
\r
16690 <p class=instruction><span lang=EN-US>Default:-extend=1</span></p>
\r
16692 <p class=instruction><span lang=EN-US>Development Only</span></p>
\r
16694 <p class=flagdescription><span lang=EN-US>When turned on, this flag indicates
\r
16695 that the library extension should be carried out when performing the multiple
\r
16696 alignment. If <b>-extend =0</b>, the extension is not made, if it is set to 1,
\r
16697 the extension is made on all the pairs in the library. If the extension is set
\r
16698 to another positive value, the extension is only carried out on pairs having a weight
\r
16699 value superior to the specified limit.<a name="_Toc101065256"></a></span></p>
\r
16701 <p class=flag><span style='mso-bookmark:_Toc101065256'><a name="_Toc235958567"></a><a
\r
16702 name="_Toc102494790"><span style='mso-bookmark:_Toc235958567'><span lang=AF>-extend_mode</span></span></a></span></p>
\r
16704 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span
\r
16705 style='mso-spacerun:yes'> </span>-extend=<string><o:p></o:p></span></p>
\r
16707 <p class=instruction><span lang=EN-US>Default:-extend=very_fast_triplet</span></p>
\r
16709 <p class=instruction><span lang=EN-US>Warning: Development Only</span></p>
\r
16711 <p class=flagdescription><span lang=EN-US>Controls the algorithm for matrix
\r
16712 extension. Available modes include:</span></p>
\r
16714 <p class=flagdescription><span lang=EN-US>relative_triplet<span
\r
16715 style='mso-tab-count:2'> </span>Unsupported</span></p>
\r
16717 <p class=flagdescription><span lang=EN-US>g_coffee<span style='mso-tab-count:
\r
16718 3'> </span>Unsupported</span></p>
\r
16720 <p class=flagdescription><span lang=EN-US>g_coffee_quadruplets<span
\r
16721 style='mso-tab-count:1'> </span>Unsupported</span></p>
\r
16723 <p class=flagdescription><span lang=EN-US>fast_triplet<span style='mso-tab-count:
\r
16724 2'> </span>Fast triplet extension</span></p>
\r
16726 <p class=flagdescription><span lang=EN-US>very_fast_triplet<span
\r
16727 style='mso-tab-count:2'> </span>slow triplet
\r
16728 extension, limited to the <b>-max_n_pair</b> best sequence pairs when aligning
\r
16729 two profiles</span></p>
\r
16731 <p class=flagdescription><span lang=EN-US>slow_triplet<span style='mso-tab-count:
\r
16732 2'> </span>Exhaustive use of all the triplets</span></p>
\r
16734 <p class=flagdescription><span lang=EN-US>mixt<span style='mso-tab-count:3'> </span>Unsupported</span></p>
\r
16736 <p class=flagdescription><span lang=EN-US>quadruplet<span style='mso-tab-count:
\r
16737 2'> </span>Unsupported</span></p>
\r
16739 <p class=flagdescription><span lang=EN-US>test<span style='mso-tab-count:3'> </span>Unsupported</span></p>
\r
16741 <p class=flagdescription><span lang=EN-US>matrix<span style='mso-tab-count:
\r
16742 3'> </span>Use of the matrix <b>-matrix<o:p></o:p></b></span></p>
\r
16744 <p class=flagdescription><span lang=EN-US>fast_matrix<span style='mso-tab-count:
\r
16745 2'> </span>Use of the matrix <b>-matrix</b>. Profiles are
\r
16746 turned into consensus</span></p>
\r
16748 <p class=flag><a name="_Toc235958568"></a><a name="_Toc102494791"></a><a
\r
16749 name="_Toc101065257"><span style='mso-bookmark:_Toc102494791'><span
\r
16750 style='mso-bookmark:_Toc235958568'><span lang=AF>-max_n_pair</span></span></span></a></p>
\r
16752 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span
\r
16753 style='mso-spacerun:yes'> </span>-max_n_pair=<integer><o:p></o:p></span></p>
\r
16755 <p class=instruction><span lang=EN-US>Default:-extend=10</span></p>
\r
16757 <p class=instruction><span lang=EN-US>Development Only</span></p>
\r
16759 <p class=flagdescription><span lang=EN-US>Controls the number of pairs
\r
16760 considered by the <b>-extend_mode</b>=very_fast_triplet. Setting it to 0 forces
\r
16761 all the pairs to be considered (equivalent to <b>-extend_mode</b>=slow_triplet).</span></p>
\r
16763 <p class=flag><a name="_Toc235958569"></a><a name="_Toc102494792"></a><a
\r
16764 name="_Toc101065258"><span style='mso-bookmark:_Toc102494792'><span
\r
16765 style='mso-bookmark:_Toc235958569'><span lang=AF>-seq_name_for_quadruplet</span></span></span></a></p>
\r
16767 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span
\r
16768 style='mso-spacerun:yes'> </span>Unsupported<o:p></o:p></span></p>
\r
16770 <p class=flag><a name="_Toc235958570"></a><a name="_Toc102494793"></a><a
\r
16771 name="_Toc101065259"><span style='mso-bookmark:_Toc102494793'><span
\r
16772 style='mso-bookmark:_Toc235958570'><span lang=AF>-compact</span></span></span></a></p>
\r
16774 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span
\r
16775 style='mso-spacerun:yes'> </span>Unsupported<o:p></o:p></span></p>
\r
16777 <p class=flag><a name="_Toc235958571"></a><a name="_Toc102494794"></a><a
\r
16778 name="_Toc101065260"><span style='mso-bookmark:_Toc102494794'><span
\r
16779 style='mso-bookmark:_Toc235958571'><span lang=AF>-clean</span></span></span></a></p>
\r
16781 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span
\r
16782 style='mso-spacerun:yes'> </span>Unsupported<o:p></o:p></span></p>
\r
16784 <p class=flag><a name="_Toc235958572"></a><a name="_Toc102494795"></a><a
\r
16785 name="_Toc101065261"><span style='mso-bookmark:_Toc102494795'><span
\r
16786 style='mso-bookmark:_Toc235958572'><span lang=AF>-maximise</span></span></span></a></p>
\r
16788 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span
\r
16789 style='mso-spacerun:yes'> </span>Unsupported<o:p></o:p></span></p>
\r
16791 <p class=flag><a name="_Toc235958573"></a><a name="_Toc102494796"></a><a
\r
16792 name="_Toc101065262"><span style='mso-bookmark:_Toc102494796'><span
\r
16793 style='mso-bookmark:_Toc235958573'><span lang=AF>-do_self</span></span></span></a></p>
\r
16795 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span
\r
16796 style='mso-spacerun:yes'> </span>Flag -do_self<o:p></o:p></span></p>
\r
16798 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Default: No<o:p></o:p></span></p>
\r
16800 <p class=flagdescription><span lang=EN-US>This flag causes the extension to
\r
16801 carried out within the sequences (as opposed to between sequences). This is
\r
16802 necessary when looking for internal repeats with Mocca.</span></p>
\r
16804 <p class=flag><a name="_Toc235958574"></a><a name="_Toc102494797"></a><a
\r
16805 name="_Toc101065263"><span style='mso-bookmark:_Toc102494797'><span
\r
16806 style='mso-bookmark:_Toc235958574'><span lang=AF>-seq_name_for_quadruplet</span></span></span></a></p>
\r
16808 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span
\r
16809 style='mso-spacerun:yes'> </span>Unsupported<o:p></o:p></span></p>
\r
16811 <p class=flag><a name="_Toc235958575"></a><a name="_Toc102494798"></a><a
\r
16812 name="_Toc101065264"><span style='mso-bookmark:_Toc102494798'><span
\r
16813 style='mso-bookmark:_Toc235958575'><span lang=AF>-weight</span></span></span></a></p>
\r
16815 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span
\r
16816 style='mso-spacerun:yes'> </span>-weight=<winsimN, sim or
\r
16817 sim_<matrix_name or matrix_file> or <integer value><o:p></o:p></span></p>
\r
16819 <p class=instruction><span lang=EN-US>Default: -weight=sim</span></p>
\r
16821 <p class=flagdescription><span lang=EN-US>Weight defines the way alignments are
\r
16822 weighted when turned into a library. <span
\r
16823 style='mso-spacerun:yes'> </span>Overweighting can be obtained with the
\r
16824 OW<X> weight mode.</span></p>
\r
16826 <p class=flagdescription><span class=StyleflagdescriptionBoldItalicChar><span
\r
16827 lang=EN-US><o:p> </o:p></span></span></p>
\r
16829 <p class=flagdescription><span class=StyleflagdescriptionBoldItalicChar><span
\r
16830 lang=EN-US>winsimN </span></span><span lang=EN-US>indicates that the weight
\r
16831 assigned to a given pair will be equal to the percent identity within a window
\r
16832 of 2N+1 length centered on that pair. For instance winsim10 defines a window of
\r
16833 10 residues around the pair being considered. This gives its own weight to each
\r
16834 residue in the output library. In our hands, this type of weighting scheme has
\r
16835 not provided any significant improvement over the standard sim value.</span></p>
\r
16837 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
16838 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
16839 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
16840 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
16842 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:
\r
16843 t_coffee sample_seq1.fasta -weight=winsim10
\96out_lib=test.tc_lib </span></p>
\r
16847 <p class=flagdescription><span class=StyleflagdescriptionBoldItalicChar><span
\r
16848 lang=EN-US>sim</span></span><span lang=EN-US> indicates that the weight equals
\r
16849 the average identity within the sequences containing the matched residues.</span></p>
\r
16851 <p class=flagdescription><span class=StyleflagdescriptionBoldItalicChar><span
\r
16852 lang=EN-US>OW<X></span></span><span
\r
16853 class=StyleflagdescriptionBoldItalicChar><span lang=EN-US style='font-style:
\r
16854 normal;mso-bidi-font-style:italic'> </span></span><span
\r
16855 class=StyleflagdescriptionBoldItalicChar><span lang=EN-US style='font-weight:
\r
16856 normal;mso-bidi-font-weight:bold;font-style:normal;mso-bidi-font-style:italic'>Will
\r
16857 cause the sim weight to be multiplied by X<o:p></o:p></span></span></p>
\r
16859 <p class=flagdescription><span class=StyleflagdescriptionBoldItalicChar><span
\r
16860 lang=EN-US>sim_matrix_name</span></span><span lang=EN-US> indicates the average
\r
16861 identity with two residues regarded as identical when their substitution value
\r
16862 is positive. The valid matrices names are in <i style='mso-bidi-font-style:
\r
16863 normal'>matrices.h (pam250mt) .</i>Matrices not found in this header are
\r
16864 considered to be filenames. See the format section for matrices. For instance, <i
\r
16865 style='mso-bidi-font-style:normal'>-weight=sim_pam250mt</i> indicates that the
\r
16866 grouping used for similarity will be the set of classes with positive
\r
16867 substitutions. </span></p>
\r
16869 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
16870 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
16871 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
16872 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
16874 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:
\r
16875 t_coffee sample_seq1.fasta -weight=winsim10
\96out_lib=test.tc_lib </span></p>
\r
16879 <p class=flagdescription><span lang=EN-US>Other groups include </span></p>
\r
16881 <p class=flagdescription><span class=StyleflagdescriptionBoldItalicChar><span
\r
16882 lang=EN-US>sim_clustalw_col</span></span><i style='mso-bidi-font-style:normal'><span
\r
16883 lang=EN-US> </span></i><span lang=EN-US>( categories of clustalw marked with :)</span></p>
\r
16885 <p class=flagdescription><span class=StyleflagdescriptionBoldItalicChar><span
\r
16886 lang=EN-US>sim_clustalw_dot</span></span><span lang=EN-US> ( categories of
\r
16887 clustalw marked with .)</span></p>
\r
16889 <p class=flagdescription><span class=StyleflagdescriptionBoldItalicChar><span
\r
16890 lang=EN-US>Value</span></span><i style='mso-bidi-font-style:normal'><span
\r
16891 lang=EN-US> </span></i><span lang=EN-US>indicates that all the pairs found in
\r
16892 the alignments must be given the same weight equal to value. This is useful
\r
16893 when the alignment one wishes to turn into a library must be given a
\r
16894 pre-specified score (for instance if they come from a structure
\r
16895 super-imposition program). Value is an integer:</span></p>
\r
16897 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
16898 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
16899 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
16900 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
16902 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:
\r
16903 t_coffee sample_seq1.fasta -weight=1000
\96out_lib=test.tc_lib </span></p>
\r
16907 <h3><a name="_Toc235958576"></a><a name="_Toc102494799"></a><a
\r
16908 name="_Toc102494373"></a><a name="_Toc101065265"><span style='mso-bookmark:
\r
16909 _Toc102494373'><span style='mso-bookmark:_Toc102494799'><span style='mso-bookmark:
\r
16910 _Toc235958576'><span lang=EN-US>Tree Computation</span></span></span></span></a></h3>
\r
16912 <p class=flag><a name="_Toc235958577"></a><a name="_Toc102494800"></a><a
\r
16913 name="_Toc101065266"><span style='mso-bookmark:_Toc102494800'><span
\r
16914 style='mso-bookmark:_Toc235958577'><span lang=AF>-</span></span></span></a><span
\r
16915 style='mso-bookmark:_Toc235958577'><span lang=AF>distance_matrix_mode</span></span></p>
\r
16917 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:
\r
16918 -distance_matrix_mode=<slow, fast, very_fast><o:p></o:p></span></p>
\r
16920 <p class=instruction><span lang=EN-US>Default: very_fast</span></p>
\r
16922 <p class=flagdescription><span lang=EN-US>This flag indicates the method used
\r
16923 for computing the distance matrix (distance between every pair of sequences)
\r
16924 required for the computation of the dendrogram. </span></p>
\r
16926 <p class=flagdescription><b style='mso-bidi-font-weight:normal'><span
\r
16927 lang=EN-US>Slow</span></b><span lang=EN-US> <span style='mso-tab-count:1'> </span>The
\r
16928 chosen dp_mode using the extended library, </span></p>
\r
16930 <p class=flagdescription><b style='mso-bidi-font-weight:normal'><span
\r
16931 lang=EN-US>fast</span></b><span lang=EN-US>:<span style='mso-spacerun:yes'>
\r
16932 </span><span style='mso-tab-count:1'> </span>The fasta dp_mode using the
\r
16933 extended library.</span></p>
\r
16935 <p class=flagdescription><b style='mso-bidi-font-weight:normal'><span
\r
16936 lang=EN-US>very_fast</span></b><span lang=EN-US><span style='mso-tab-count:
\r
16937 1'> </span>The fasta dp_mode using blosum62mt.</span></p>
\r
16939 <p class=flagdescription><b style='mso-bidi-font-weight:normal'><span
\r
16940 lang=EN-US>ktup<span style='mso-tab-count:1'> </span></span></b><span
\r
16941 lang=EN-US>Ktup matching (Muscle kind) </span></p>
\r
16943 <p class=flagdescription><b style='mso-bidi-font-weight:normal'><span
\r
16944 lang=EN-US>aln<span style='mso-tab-count:2'> </span></span></b><span
\r
16945 lang=EN-US>Read the distances on a precomputed MSA</span></p>
\r
16947 <p class=flag><a name="_Toc235958578"></a><a name="_Toc102494801"></a><a
\r
16948 name="_Toc101065267"><span style='mso-bookmark:_Toc102494801'><span
\r
16949 style='mso-bookmark:_Toc235958578'><span lang=AF>-quicktree [CW]</span></span></span></a></p>
\r
16951 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:
\r
16952 -quicktree<o:p></o:p></span></p>
\r
16954 <p class=instruction><span lang=EN-US>Description: Causes T-Coffee to compute a
\r
16955 fast approximate guide tree</span></p>
\r
16957 <p class=MyNormal><span lang=AF>This flag is kept for compatibility with
\r
16958 ClustalW. It indicates that:</span></p>
\r
16960 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
16961 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
16962 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
16963 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
16965 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:
\r
16966 t_coffee sample_seq1.fasta
\96distance_matrix_mode=very_fast </span></p>
\r
16968 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:
\r
16969 t_coffee sample_seq1.fasta
\96quicktree </span></p>
\r
16973 <h3><a name="_Toc235958579"></a><a name="_Toc102494802"></a><a
\r
16974 name="_Toc102494374"></a><a name="_Toc101065268"><span style='mso-bookmark:
\r
16975 _Toc102494374'><span style='mso-bookmark:_Toc102494802'><span style='mso-bookmark:
\r
16976 _Toc235958579'><span lang=EN-US>Pair-wise Alignment Computation</span></span></span></span></a></h3>
\r
16978 <p class=Noteboxtitle><span lang=EN-US><o:p> </o:p></span></p>
\r
16980 <div style='mso-element:para-border-div;border:solid windowtext 1.5pt;
\r
16981 padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#FFFF89'>
\r
16983 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut align=center
\r
16984 style='text-align:center;background:#FFFF89'><span lang=EN-US style='font-size:
\r
16985 20.0pt'>Controlling Alignment Computation<o:p></o:p></span></p>
\r
16987 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span lang=EN-US><o:p> </o:p></span></p>
\r
16989 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span lang=EN-US>Most
\r
16990 parameters in this section refer to the alignment mode fasta_pair_wise and
\r
16991 cfatsa_pair_wise. When using these alignment modes, things proceed as follow:</span></p>
\r
16993 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span lang=EN-US>1-Sequences
\r
16994 are recoded using a degenerated alphabet provided with <-sim_matrix> </span></p>
\r
16996 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span lang=EN-US>2-Recoded
\r
16997 sequences are then hashed into ktuples of size <u><-ktup></u></span></p>
\r
16999 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span lang=EN-US>3-Dynamic
\r
17000 programming runs on the <u><-ndiag></u> best diagonals whose score is
\r
17001 higher than <u><-diag_threshold></u>, the way diagonals are scored is
\r
17002 controlled via <u><-diag_mode></u> .</span></p>
\r
17004 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span lang=EN-US>4-The
\r
17005 Dynamic computation is made to optimize either the library scoring scheme (as
\r
17006 defined by the <u>-in</u> flag) or a substitution matrix as provided via the <u>-matrix</u>
\r
17007 flag. The penalty scheme is defined by <u>-gapopen</u> and <u>-gapext</u>. If <u>-gapopen</u>
\r
17008 is undefined, the value defined in <u>-cosmetic_penalty</u> is used instead.</span></p>
\r
17010 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span lang=EN-US>5-Terminal
\r
17011 gaps are scored according to <u>-tg_mode</u></span></p>
\r
17015 <p class=noteboxbody><span lang=EN-US><o:p> </o:p></span></p>
\r
17017 <p class=MyNormal><span lang=AF><o:p> </o:p></span></p>
\r
17019 <p class=flag><a name="_Toc235958580"></a><a name="_Toc102494803"></a><a
\r
17020 name="_Toc101065269"><span style='mso-bookmark:_Toc102494803'><span
\r
17021 style='mso-bookmark:_Toc235958580'><span lang=AF>-dp_mode</span></span></span></a></p>
\r
17023 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span
\r
17024 style='mso-spacerun:yes'> </span>-dp_mode=<string><o:p></o:p></span></p>
\r
17026 <p class=instruction><span lang=EN-US>Default: -dp_mode=cfasta_fair_wise</span></p>
\r
17028 <p class=flagdescription><span lang=EN-US>This flag indicates the type of
\r
17029 dynamic programming used by the program:</span></p>
\r
17031 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
17032 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
17033 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
17034 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
17036 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:
\r
17037 t_coffee sample_seq1.fasta
\96dp_mode myers_miller_pair_wise </span></p>
\r
17041 <p class=flagdescription><span class=StyleflagdescriptionBoldItalicChar><span
\r
17042 lang=EN-US>gotoh_pair_wise</span></span><span lang=EN-US>: implementation of
\r
17043 the gotoh algorithm (quadratic in memory and time)</span></p>
\r
17045 <p class=flagdescription><span class=StyleflagdescriptionBoldItalicChar><span
\r
17046 lang=EN-US>myers_miller_pair_wise</span></span><span lang=EN-US>:
\r
17047 implementation of the Myers and Miller dynamic programming algorithm (
\r
17048 quadratic in time and linear in space). This algorithm is recommended for very
\r
17049 long sequences. It is about 2 times slower than gotoh and only accepts <i
\r
17050 style='mso-bidi-font-style:normal'>tg_mode=1or 2 (i.e. gaps penalized for
\r
17051 opening).<o:p></o:p></i></span></p>
\r
17053 <p class=flagdescription><span class=StyleflagdescriptionBoldItalicChar><span
\r
17054 lang=EN-US>fasta_pair_wise</span></span><i style='mso-bidi-font-style:normal'><span
\r
17055 lang=EN-US>: </span></i><span lang=EN-US>implementation of the fasta algorithm.
\r
17056 The sequence is hashed, looking for <i style='mso-bidi-font-style:normal'>ktuples</i>
\r
17057 words. Dynamic programming is only carried out on the <i style='mso-bidi-font-style:
\r
17058 normal'>ndiag</i> best scoring diagonals. This is much faster but less accurate
\r
17059 than the two previous. This mode is controlled by the parameters <b>-ktuple,
\r
17060 -diag_mode and -ndiag<o:p></o:p></b></span></p>
\r
17062 <p class=flagdescription><span class=StyleflagdescriptionBoldItalicChar><span
\r
17063 lang=EN-US>cfasta_pair_wise</span></span><span lang=EN-US>: c stands for
\r
17064 checked. It is the same algorithm. The dynamic programming is made on the <i
\r
17065 style='mso-bidi-font-style:normal'>ndiag</i> best diagonals, and then on the
\r
17066 2*ndiags, and so on until the scores converge. Complexity will depend on the
\r
17067 level of divergence of the sequences, but will usually be L*log(L), with an
\r
17068 accuracy comparable to the two first mode ( this was checked on BaliBase). This
\r
17069 mode is controlled by the parameters <b>-ktuple, -diag_mode and
\96ndiag<o:p></o:p></b></span></p>
\r
17071 <p class=Note><span lang=EN-US style='mso-ansi-language:EN-US'>Note: Users may
\r
17072 find by looking into the code that other modes with fancy names exists
\r
17073 (viterby_pair_wise
\85) Unless mentioned in this documentation, these modes are
\r
17074 not supported.<o:p></o:p></span></p>
\r
17076 <p class=flag><a name="_Toc235958581"></a><a name="_Toc102494804"></a><a
\r
17077 name="_Toc101065270"><span style='mso-bookmark:_Toc102494804'><span
\r
17078 style='mso-bookmark:_Toc235958581'><span lang=AF>-ktuple</span></span></span></a></p>
\r
17080 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span
\r
17081 style='mso-spacerun:yes'> </span>-ktuple=<value><o:p></o:p></span></p>
\r
17083 <p class=instruction><span lang=EN-US>Default: -ktuple=1 or 2</span></p>
\r
17085 <p class=flagdescription><span lang=EN-US>Indicates the ktuple size for
\r
17086 cfasta_pair_wise dp_mode and fasta_pair_wise. It is set to 1 for proteins, and
\r
17087 2 for DNA. The alphabet used for protein can be a degenerated version, set with
\r
17088 <b><u>-sim_matrix.</u></b>. </span></p>
\r
17090 <p class=flag><a name="_Toc235958582"></a><a name="_Toc102494805"></a><a
\r
17091 name="_Toc101065271"><span style='mso-bookmark:_Toc102494805'><span
\r
17092 style='mso-bookmark:_Toc235958582'><span lang=AF>-ndiag</span></span></span></a></p>
\r
17094 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span
\r
17095 style='mso-spacerun:yes'> </span>-ndiag=<value><o:p></o:p></span></p>
\r
17097 <p class=instruction><span lang=EN-US>Default: -ndiag=0</span></p>
\r
17099 <p class=flagdescription><span lang=EN-US>Indicates the number of diagonals
\r
17100 used by the <i>fasta_pair_wise</i> algorithm (cf <b>-dp_mode</b>). When<span
\r
17101 style='mso-spacerun:yes'> </span><b>-ndiag=0</b>, n_diag=Log (length of the
\r
17102 smallest sequence)+1. </span></p>
\r
17104 <p class=Note><span lang=EN-US style='mso-ansi-language:EN-US'>When
\96ndiag and
\r
17105 \96diag_threshold are set, diagonals are selected if and only if they fulfill
\r
17106 both conditions.<o:p></o:p></span></p>
\r
17108 <p class=flag><a name="_Toc235958583"></a><a name="_Toc102494806"></a><a
\r
17109 name="_Toc101065272"><span style='mso-bookmark:_Toc102494806'><span
\r
17110 style='mso-bookmark:_Toc235958583'><span lang=AF>-diag_mode</span></span></span></a></p>
\r
17112 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span
\r
17113 style='mso-spacerun:yes'> </span>-diag_mode=<value><o:p></o:p></span></p>
\r
17115 <p class=instruction><span lang=EN-US>Default: -diag_mode=0</span></p>
\r
17117 <p class=flagdescription><span lang=EN-US>Indicates the manner in which
\r
17118 diagonals are scored during the fasta hashing. </span></p>
\r
17120 <p class=flagdescription><span lang=EN-US>0: indicates that the score of a
\r
17121 diagonal is equal to the sum of the scores of the exact matches it contains. </span></p>
\r
17123 <p class=flagdescription><span lang=EN-US>1 indicates that this score is set
\r
17124 equal to the score of the best uninterrupted segment (useful when dealing with
\r
17125 fragments of sequences).</span></p>
\r
17127 <p class=flag><a name="_Toc235958584"></a><a name="_Toc102494807"></a><a
\r
17128 name="_Toc101065273"><span style='mso-bookmark:_Toc102494807'><span
\r
17129 style='mso-bookmark:_Toc235958584'><span lang=AF>-diag_threshold</span></span></span></a></p>
\r
17131 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span
\r
17132 style='mso-spacerun:yes'> </span>-diag_threshold=<value><o:p></o:p></span></p>
\r
17134 <p class=instruction><span lang=EN-US>Default: -diag_threshold=0</span></p>
\r
17136 <p class=flagdescription><span lang=EN-US>Sets the value of the threshold when
\r
17137 selecting diagonals. </span></p>
\r
17139 <p class=flagdescription><span lang=EN-US>0: indicates that
\96ndiag should be
\r
17140 used to select the diagonals (cf
\96ndiag section).</span></p>
\r
17142 <p class=flag><a name="_Toc235958585"></a><a name="_Toc102494808"></a><a
\r
17143 name="_Toc101065274"><span style='mso-bookmark:_Toc102494808'><span
\r
17144 style='mso-bookmark:_Toc235958585'><span lang=AF>-sim_matrix</span></span></span></a></p>
\r
17146 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span
\r
17147 style='mso-spacerun:yes'> </span>-sim_matrix=<string><o:p></o:p></span></p>
\r
17149 <p class=instruction><span lang=EN-US>Default: -sim_matrix=vasiliky</span></p>
\r
17151 <p class=flagdescription><span lang=EN-US>Indicates the manner in which the
\r
17152 amino acid alphabet is degenerated when hashing in the fasta_pairwise dynamic
\r
17153 programming. Standard ClustalW matrices are all valid. They are used to define
\r
17154 groups of amino acids having positive substitution values. In T-Coffee, the
\r
17155 default is a 13 letter grouping named Vasiliky, with residues grouped as
\r
17156 follows:</span></p>
\r
17158 <p class=example2><span lang=EN-US>rk, de, qh, vilm, fy (other residues kept
\r
17159 alone).</span></p>
\r
17161 <p class=flagdescription><span lang=EN-US>This alphabet is set with the flag <b>-sim_matrix=vasiliky</b>.
\r
17162 In order to keep the alphabet non degenerated, <b>-sim_matrix=idmat </b>can be
\r
17163 used to retain the standard alphabet.</span></p>
\r
17165 <p class=flag><a name="_Toc235958586"></a><a name="_Toc102494809"></a><a
\r
17166 name="_Toc101065275"><span style='mso-bookmark:_Toc102494809'><span
\r
17167 style='mso-bookmark:_Toc235958586'><span lang=AF>-matrix [CW]</span></span></span></a></p>
\r
17169 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span
\r
17170 style='mso-spacerun:yes'> </span>-matrix=<blosum62mt><o:p></o:p></span></p>
\r
17172 <p class=instruction><span lang=EN-US>Default: -matrix=blosum62mt</span></p>
\r
17174 <p class=flagdescription><span lang=EN-US>The usage of this flag has been
\r
17175 modified from previous versions, due to frequent mistakes in its usage. This
\r
17176 flag sets the matrix that will be used by alignment methods within t_coffee
\r
17177 (slow_pair, lalign_id_pair). It does not affect external methods (like
\r
17178 clustal_pair, clustal_aln
\85). </span></p>
\r
17180 <p class=flagdescription><span lang=EN-US>Users can also provide their own
\r
17181 matrices, using the matrix format described in the appendix.</span></p>
\r
17183 <p class=flag><a name="_Toc235958587"></a><a name="_Toc102494810"></a><a
\r
17184 name="_Toc101065276"><span style='mso-bookmark:_Toc102494810'><span
\r
17185 style='mso-bookmark:_Toc235958587'><span lang=AF>-nomatch</span></span></span></a></p>
\r
17187 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span
\r
17188 style='mso-spacerun:yes'> </span>-nomatch=<positive value><o:p></o:p></span></p>
\r
17190 <p class=instruction><span lang=EN-US>Default: -nomatch=0</span></p>
\r
17192 <p class=flagdescription><span lang=EN-US>Indicates the penalty to associate
\r
17193 with a match. When using a library, all matches are positive or equal to 0.
\r
17194 Matches equal to 0 are unsupported by the library but non-penalized. Setting
\r
17195 nomatch to a non-negative value makes it possible to penalize these null
\r
17196 matches and prevent unrelated sequences from being aligned (this can be useful
\r
17197 when the alignments are meant to be used for structural modeling).</span></p>
\r
17199 <p class=flag><a name="_Toc235958588"></a><a name="_Toc102494811"></a><a
\r
17200 name="_Toc101065277"><span style='mso-bookmark:_Toc102494811'><span
\r
17201 style='mso-bookmark:_Toc235958588'><span lang=AF>-gapopen</span></span></span></a></p>
\r
17203 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span
\r
17204 style='mso-spacerun:yes'> </span>-gapopen=<negative value><o:p></o:p></span></p>
\r
17206 <p class=instruction><span lang=EN-US>Default: -gapopen=0</span></p>
\r
17208 <p class=flagdescription><span lang=EN-US>Indicates the penalty applied for
\r
17209 opening a gap. The penalty must be negative. If no value is provided when using
\r
17210 a substitution matrix, a value will be automatically computed.</span></p>
\r
17212 <p class=flagdescription><span lang=EN-US>Here are some guidelines regarding
\r
17213 the tuning of gapopen and gapext. In T-Coffee matches get a score between 0
\r
17214 (match) and 1000 (match perfectly consistent with the library). The default
\r
17215 cosmetic penalty is set to -50 (5% of a perfect match). If you want to tune
\r
17216 -gapoen and see a strong effect, you should therefore consider values between 0
\r
17217 and -1000. </span></p>
\r
17219 <p class=flag><a name="_Toc235958589"></a><a name="_Toc102494812"></a><a
\r
17220 name="_Toc101065278"><span style='mso-bookmark:_Toc102494812'><span
\r
17221 style='mso-bookmark:_Toc235958589'><span lang=AF>-gapext</span></span></span></a></p>
\r
17223 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span
\r
17224 style='mso-spacerun:yes'> </span>-gapext=<negative value><o:p></o:p></span></p>
\r
17226 <p class=instruction><span lang=EN-US>Default: -gapext=0</span></p>
\r
17228 <p class=flagdescription><span lang=EN-US>Indicates the penalty applied for
\r
17229 extending a gap (cf <b><u>-gapopen</u></b>)</span></p>
\r
17231 <p class=flag><a name="_Toc235958590"></a><a name="_Toc102494813"></a><a
\r
17232 name="_Toc101065279"><span style='mso-bookmark:_Toc102494813'><span
\r
17233 style='mso-bookmark:_Toc235958590'><span lang=AF>-fgapopen</span></span></span></a></p>
\r
17235 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Unsupported<o:p></o:p></span></p>
\r
17237 <p class=flag><a name="_Toc235958591"></a><a name="_Toc102494814"></a><a
\r
17238 name="_Toc101065280"><span style='mso-bookmark:_Toc102494814'><span
\r
17239 style='mso-bookmark:_Toc235958591'><span lang=AF>-fgapext</span></span></span></a></p>
\r
17241 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Unsupported<o:p></o:p></span></p>
\r
17243 <p class=flag><a name="_Toc235958592"></a><a name="_Toc102494815"></a><a
\r
17244 name="_Toc101065281"><span style='mso-bookmark:_Toc102494815'><span
\r
17245 style='mso-bookmark:_Toc235958592'><span lang=AF>-cosmetic_penalty</span></span></span></a></p>
\r
17247 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span
\r
17248 style='mso-spacerun:yes'> </span>-cosmetic_penalty=<negative value><o:p></o:p></span></p>
\r
17250 <p class=instruction><span lang=EN-US>Default: -cosmetic_penalty=-50</span></p>
\r
17252 <p class=flagdescription><span lang=EN-US>Indicates the penalty applied for
\r
17253 opening a gap. This penalty is set to a very low value. It will only have an
\r
17254 influence on the portions of the alignment that are unalignable. It will not
\r
17255 make them more correct, but only more pleasing to the eye ( i.e. Avoid
\r
17256 stretches of lonely residues).</span></p>
\r
17258 <p class=flagdescription><span lang=EN-US>The cosmetic penalty is automatically
\r
17259 turned off if a substitution matrix is used rather than a library.</span></p>
\r
17261 <p class=flag><a name="_Toc235958593"></a><a name="_Toc102494816"></a><a
\r
17262 name="_Toc101065282"><span style='mso-bookmark:_Toc102494816'><span
\r
17263 style='mso-bookmark:_Toc235958593'><span lang=AF>-tg_mode</span></span></span></a></p>
\r
17265 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span
\r
17266 style='mso-spacerun:yes'> </span>-tg_mode=<0, 1, or 2><o:p></o:p></span></p>
\r
17268 <p class=instruction><span lang=EN-US>Default: -tg_mode=1</span></p>
\r
17270 <p class=flagdescription><span lang=EN-US>0: terminal gaps penalized with <span
\r
17271 class=StyleflagdescriptionBoldItalicChar>-gapopen + -gapext*len<o:p></o:p></span></span></p>
\r
17273 <p class=flagdescription><span lang=EN-US>1: terminal gaps penalized with a <span
\r
17274 class=StyleflagdescriptionBoldItalicChar>-gapext*len<o:p></o:p></span></span></p>
\r
17276 <p class=flagdescription><span lang=EN-US>2: terminal gaps unpenalized.</span></p>
\r
17278 <p class=flagdescription><span lang=EN-US><o:p> </o:p></span></p>
\r
17280 <h3><a name="_Toc235958594"></a><a name="_Toc102494817"></a><a
\r
17281 name="_Toc102494375"></a><a name="_Toc101065283"><span style='mso-bookmark:
\r
17282 _Toc102494375'><span style='mso-bookmark:_Toc102494817'><span style='mso-bookmark:
\r
17283 _Toc235958594'><span lang=EN-US>Weighting Schemes</span></span></span></span></a></h3>
\r
17285 <p class=flag><a name="_Toc235958595"></a><a name="_Toc102494818"></a><a
\r
17286 name="_Toc101065284"><span style='mso-bookmark:_Toc102494818'><span
\r
17287 style='mso-bookmark:_Toc235958595'><span lang=AF>-seq_weight</span></span></span></a></p>
\r
17289 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:
\r
17290 -seq_weight=<t_coffee or <file_name>><o:p></o:p></span></p>
\r
17292 <p class=instruction><span lang=EN-US>Default: -seq_weight=t_coffee</span></p>
\r
17294 <p class=flagdescription><span lang=EN-US>These are the individual weights
\r
17295 assigned to each sequence. The t_coffee weights try to compensate the bias in
\r
17296 consistency caused by redundancy in the sequences.</span></p>
\r
17298 <p class=Formula><span lang=EN-US><span style='mso-tab-count:1'> </span>sim(A,B)=%similarity
\r
17299 between A and B, between 0 and 1. </span></p>
\r
17301 <p class=Formula><span lang=EN-US><span style='mso-tab-count:1'> </span>weight(A)=1/sum(sim(A,X)^3)</span></p>
\r
17303 <p class=flagdescription><span lang=EN-US>Weights are normalized so that their
\r
17304 sum equals the number of sequences. They are applied onto the primary library
\r
17305 in the following manner:</span></p>
\r
17307 <p class=Formula><span lang=EN-US><span style='mso-tab-count:1'> </span>res_score(Ax,By)=Min(weight(A),
\r
17308 weight(B))*res_score(Ax, By)</span></p>
\r
17310 <p class=flagdescription><span lang=EN-US>These are very simple weights. Their
\r
17311 main goal is to prevent a single sequence present in many copies to dominate
\r
17312 the alignment.</span></p>
\r
17314 <p class=Note><span lang=EN-US style='mso-ansi-language:EN-US'>Note: The
\r
17315 library output by -out_lib is the un-weighted<span style='mso-spacerun:yes'>
\r
17316 </span>library. <o:p></o:p></span></p>
\r
17318 <p class=Note><span lang=EN-US style='mso-ansi-language:EN-US'>Note: Weights
\r
17319 can be output using the -outseqweight flag.<o:p></o:p></span></p>
\r
17321 <p class=Note><span lang=EN-US style='mso-ansi-language:EN-US'>Note: You can
\r
17322 use your own weights (see the format section). <o:p></o:p></span></p>
\r
17324 <p class=MyNormal><span lang=AF><o:p> </o:p></span></p>
\r
17326 <h3><a name="_Toc235958596"></a><a name="_Toc102494819"></a><a
\r
17327 name="_Toc102494376"></a><a name="_Toc101065285"><span style='mso-bookmark:
\r
17328 _Toc102494376'><span style='mso-bookmark:_Toc102494819'><span style='mso-bookmark:
\r
17329 _Toc235958596'><span lang=EN-US>Multiple Alignment Computation</span></span></span></span></a></h3>
\r
17331 <p class=flag><a name="_Toc235958597"></a><a name="_Toc102494820"></a><a
\r
17332 name="_Toc101065286"><span style='mso-bookmark:_Toc102494820'><span
\r
17333 style='mso-bookmark:_Toc235958597'><span lang=AF>-msa_mode</span></span></span></a></p>
\r
17335 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:
\r
17336 -msa_mode=<tree,graph,precomputed><o:p></o:p></span></p>
\r
17338 <p class=instruction><span lang=EN-US>Default: -evaluate_mode=tree</span></p>
\r
17340 <p class=flagdescription><span lang=EN-US>Unsupported</span></p>
\r
17342 <p class=flag><a name="_Toc102494821"></a><a name="_Toc101065287"></a><a
\r
17343 name="_Toc235958598"><span style='mso-bookmark:_Toc101065287'><span
\r
17344 style='mso-bookmark:_Toc102494821'><span lang=AF>-one2all</span></span></span></a><span
\r
17345 style='mso-bookmark:_Toc101065287'><span style='mso-bookmark:_Toc102494821'></span></span></p>
\r
17347 <p class=flagusage><span style='mso-bookmark:_Toc101065287'><span
\r
17348 style='mso-bookmark:_Toc102494821'><span lang=EN-US style='mso-ansi-language:
\r
17349 EN-US'>Usage: -one2all=<name><o:p></o:p></span></span></span></p>
\r
17351 <p class=instruction><span style='mso-bookmark:_Toc101065287'><span
\r
17352 style='mso-bookmark:_Toc102494821'><span lang=EN-US>Default: not used</span></span></span></p>
\r
17354 <p class=flagdescription><span style='mso-bookmark:_Toc101065287'><span
\r
17355 style='mso-bookmark:_Toc102494821'><span lang=EN-US>Will generate a one to all
\r
17356 library with respect to the specified sequence and will then align all the
\r
17357 sequences in turn to that sequence, in a sequence determined by the order in
\r
17358 which the sequences were provided.<span style='mso-spacerun:yes'> </span></span></span></span></p>
\r
17360 <p class=flagdescription><span style='mso-bookmark:_Toc101065287'><span
\r
17361 style='mso-bookmark:_Toc102494821'><b style='mso-bidi-font-weight:normal'><span
\r
17362 lang=EN-US>
\96profile_comparison =profile</span></b><span lang=EN-US>, the MSAs
\r
17363 provided via
\96profile are vectorized and the function specified by
\r
17364 \96profile_comparison is used to make profile profile alignments. In that case,
\r
17365 the complexity is NL^2</span></span></span></p>
\r
17367 <p class=flag><span style='mso-bookmark:_Toc101065287'><span style='mso-bookmark:
\r
17368 _Toc102494821'><a name="_Toc235958599"><span lang=AF>-profile</span></a></span></span><span
\r
17369 style='mso-bookmark:_Toc235958599'><span lang=AF>_comparison</span></span></p>
\r
17371 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:
\r
17372 -profile_mode=<fullN,profile><o:p></o:p></span></p>
\r
17374 <p class=instruction><span lang=EN-US>Default: -profile_mode=full50</span></p>
\r
17376 <p class=flagdescription><span lang=EN-US>The profile mode flag controls the
\r
17377 multiple profile alignments in T-Coffee. There are two instances where t_coffee
\r
17378 can make multiple profile alignments:</span></p>
\r
17380 <p class=flagdescription><span lang=EN-US>1-When N, the number of sequences is
\r
17381 higher than <b style='mso-bidi-font-weight:normal'>
\96maxnseq, </b>the program
\r
17382 switches to its multiple profile alignment mode (t_coffee_dpa).</span></p>
\r
17384 <p class=flagdescription><span lang=EN-US>2-When MSAs are provided via the <b
\r
17385 style='mso-bidi-font-weight:normal'>
\96profile</b> flag or via <b
\r
17386 style='mso-bidi-font-weight:normal'>
\96profile1</b> and <b style='mso-bidi-font-weight:
\r
17387 normal'>
\96profile2</b>. </span></p>
\r
17389 <p class=flagdescription><span lang=EN-US>In these situations, the
\r
17390 \96profile_mode value influences the alignment computation, these values are:</span></p>
\r
17392 <p class=flagdescription><b style='mso-bidi-font-weight:normal'><span
\r
17393 lang=EN-US>
\96profile_comparison =profile</span></b><span lang=EN-US>, the MSAs
\r
17394 provided via
\96profile are vectorized and the function specified by
\r
17395 \96profile_comparison is used to make profile profile alignments. In that case,
\r
17396 the complexity is NL^2</span></p>
\r
17398 <p class=flagdescription><span class=ListChar><b style='mso-bidi-font-weight:
\r
17399 normal'><span lang=EN-US style='font-size:12.0pt;mso-bidi-font-size:10.0pt'>-profile_comparison=fullN</span></b></span><span
\r
17400 lang=EN-US>, N is an integer value that can omitted. <i style='mso-bidi-font-style:
\r
17401 normal'>Full</i> indicates that given two profiles, the alignment will be based
\r
17402 on a library that includes every possible pair of sequences between the two
\r
17403 profiles. If N is set, then the library will be restricted to the N most
\r
17404 similar pairs of sequences between the two profiles, as judged from a measure
\r
17405 made on a pairwise alignment of these two profiles.</span></p>
\r
17407 <p class=flag><a name="_Toc235958600"></a><a name="_Toc102494822"></a><a
\r
17408 name="_Toc101065288"><span style='mso-bookmark:_Toc102494822'><span
\r
17409 style='mso-bookmark:_Toc235958600'><span lang=AF>-profile_</span></span></span></a><span
\r
17410 style='mso-bookmark:_Toc235958600'><span lang=AF>mode</span></span></p>
\r
17412 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:
\r
17413 -profile_mode=<cw_profile_profile, muscle_profile_profile, multi_channel><o:p></o:p></span></p>
\r
17415 <p class=instruction><span lang=EN-US>Default: -profile_mode=cw_profile_profile</span></p>
\r
17417 <p class=flagdescription><span lang=EN-US>When <b style='mso-bidi-font-weight:
\r
17418 normal'>
\96profile_comparison=profile</b>, this flag selects a profile scoring
\r
17419 function.</span></p>
\r
17421 <h3><a name="_Toc235958601"></a><a name="_Toc102494823"></a><a
\r
17422 name="_Toc102494377"></a><a name="_Toc101065289"><span style='mso-bookmark:
\r
17423 _Toc102494377'><span style='mso-bookmark:_Toc102494823'><span style='mso-bookmark:
\r
17424 _Toc235958601'><span lang=EN-US>Alignment Post-Processing</span></span></span></span></a></h3>
\r
17426 <p class=flag><a name="_Toc235958602"></a><a name="_Toc102494824"></a><a
\r
17427 name="_Toc101065290"><span style='mso-bookmark:_Toc102494824'><span
\r
17428 style='mso-bookmark:_Toc235958602'><span lang=AF>-clean_aln</span></span></span></a></p>
\r
17430 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span
\r
17431 style='mso-spacerun:yes'> </span>-clean_aln<span style='mso-spacerun:yes'>
\r
17432 </span><o:p></o:p></span></p>
\r
17434 <p class=instruction><span lang=EN-US>Default:-clean_aln</span></p>
\r
17436 <p class=flagdescription><span lang=EN-US>This flag causes T-Coffee to
\r
17437 post-process the multiple alignment. Residues that have a reliability score
\r
17438 smaller or equal to -clean_threshold (as given by an evaluation that uses
\r
17439 -clean_evaluate_mode)<span style='mso-spacerun:yes'> </span>are realigned to
\r
17440 the rest of the alignment. Residues with a score higher than the threshold
\r
17441 constitute a rigid framework that cannot be altered.</span></p>
\r
17443 <p class=flagdescription><span lang=EN-US>The cleaning algorithm is greedy. It
\r
17444 starts from the top left segment of low constituency residues and works its way
\r
17445 left to right, top to bottom along the alignment. You can require this
\r
17446 operation to be carried out for several cycles using the -clean_iterations
\r
17449 <p class=flagdescription><span lang=EN-US>The rationale behind this operation
\r
17450 is mostly cosmetic. In order to ensure a decent looking alignment, the gop is
\r
17451 set to -20 and the gep to -1. There is no penalty for terminal gaps, and the
\r
17452 matrix is blosum62mt.</span></p>
\r
17454 <p class=Note><span lang=EN-US style='mso-ansi-language:EN-US'>Note: Gaps are
\r
17455 always considered to have a reliability score of 0.<o:p></o:p></span></p>
\r
17457 <p class=Note><span class=WarningChar><span lang=EN-US>Note: The use of the
\r
17458 cleaning option can result in memory overflow when aligning large</span></span><span
\r
17459 lang=EN-US style='mso-ansi-language:EN-US'> </span><span class=WarningChar><span
\r
17460 lang=EN-US>sequences,<o:p></o:p></span></span></p>
\r
17462 <p class=flag><a name="_Toc235958603"></a><a name="_Toc102494825"></a><a
\r
17463 name="_Toc101065291"><span style='mso-bookmark:_Toc102494825'><span
\r
17464 style='mso-bookmark:_Toc235958603'><span lang=AF>-clean_threshold</span></span></span></a></p>
\r
17466 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span
\r
17467 style='mso-spacerun:yes'> </span>-clean_threshold=<0-9><span
\r
17468 style='mso-spacerun:yes'> </span><o:p></o:p></span></p>
\r
17470 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Default:-clean_aln=1<o:p></o:p></span></p>
\r
17472 <p class=MyNormal><span lang=AF>See -clean_aln for details.</span></p>
\r
17474 <p class=flag><a name="_Toc235958604"></a><a name="_Toc102494826"></a><a
\r
17475 name="_Toc101065292"><span style='mso-bookmark:_Toc102494826'><span
\r
17476 style='mso-bookmark:_Toc235958604'><span lang=AF>-clean_iteration</span></span></span></a></p>
\r
17478 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span
\r
17479 style='mso-spacerun:yes'> </span>-clean_iteration=<value between 1 and
\r
17480 ><span style='mso-spacerun:yes'> </span><o:p></o:p></span></p>
\r
17482 <p class=instruction><span lang=EN-US>Default:-clean_iteration=1</span></p>
\r
17484 <p class=MyNormal><span lang=AF>See -clean_aln for details.</span></p>
\r
17486 <p class=flag><a name="_Toc235958605"></a><a name="_Toc102494827"></a><a
\r
17487 name="_Toc101065293"><span style='mso-bookmark:_Toc102494827'><span
\r
17488 style='mso-bookmark:_Toc235958605'><span lang=AF>-clean_evaluation_mode</span></span></span></a></p>
\r
17490 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span
\r
17491 style='mso-spacerun:yes'> </span>-clean_iteration=<evaluation_mode
\r
17492 ><span style='mso-spacerun:yes'> </span><o:p></o:p></span></p>
\r
17494 <p class=instruction><span lang=EN-US>Default:-clean_iteration=t_coffee_non_extended</span></p>
\r
17496 <p class=flagdescription><span lang=EN-US>Indicates the mode used for the
\r
17497 evaluation that will indicate the segments that should be realigned. See
\r
17498 -evaluation_mode for the list of accepted modes.</span></p>
\r
17500 <p class=flag><a name="_Toc235958606"></a><a name="_Toc102494828"></a><a
\r
17501 name="_Toc101065294"><span style='mso-bookmark:_Toc102494828'><span
\r
17502 style='mso-bookmark:_Toc235958606'><span lang=AF>-iterate</span></span></span></a></p>
\r
17504 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:
\r
17505 -iterate=<integer><o:p></o:p></span></p>
\r
17507 <p class=instruction><span lang=EN-US>Default: -iterate=0</span></p>
\r
17509 <p class=flagdescription><span lang=EN-US>Sequences are extracted in turn and
\r
17510 realigned to the MSA. If iterate is set to -1, each sequence is realigned,
\r
17511 otherwise the number of iterations is set by
\96iterate.</span></p>
\r
17513 <h2><a name="_Toc235958607"></a><a name="_Toc102494829"></a><a
\r
17514 name="_Toc102494378"></a><a name="_Toc101065295"><span style='mso-bookmark:
\r
17515 _Toc102494378'><span style='mso-bookmark:_Toc102494829'><span style='mso-bookmark:
\r
17516 _Toc235958607'><span lang=EN-US>CPU Control</span></span></span></span></a></h2>
\r
17518 <h3><a name="_Toc235958608"></a><a name="_Toc102494830"></a><a
\r
17519 name="_Toc102494379"></a><a name="_Toc101065296"><span style='mso-bookmark:
\r
17520 _Toc102494379'><span style='mso-bookmark:_Toc102494830'><span style='mso-bookmark:
\r
17521 _Toc235958608'><span lang=EN-US>Multithreading</span></span></span></span></a></h3>
\r
17523 <p class=flag><a name="_Toc235958609"></a><a name="_Toc102494831"></a><a
\r
17524 name="_Toc101065297"><span style='mso-bookmark:_Toc102494831'><span
\r
17525 style='mso-bookmark:_Toc235958609'><span lang=AF>-multi_core </span></span></span></a></p>
\r
17527 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span
\r
17528 style='mso-spacerun:yes'> </span>-multi_core=</span> templates_jobs_relax_msa<span
\r
17529 lang=EN-US style='mso-ansi-language:EN-US'><o:p></o:p></span></p>
\r
17531 <p class=instruction><span lang=EN-US>Default: 0</span></p>
\r
17533 <p class=flagdescription><span lang=EN-US>Specifies that the steps of T-Coffee
\r
17534 that should be multi threaded. by default all relevant steps are.</span></p>
\r
17536 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
17537 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
17538 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
17539 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
17541 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:
\r
17542 t_coffee sample_seq2.fasta -multi_core jobs</span></p>
\r
17546 <p class=flag><a name="_Toc235958610"></a><a name="_Toc102494832"></a><a
\r
17547 name="_Toc102494380"></a><a name="_Toc101065298"><span style='mso-bookmark:
\r
17548 _Toc102494380'><span style='mso-bookmark:_Toc102494832'><span style='mso-bookmark:
\r
17549 _Toc235958610'><span lang=AF>-n_core </span></span></span></span></a></p>
\r
17551 <p class=flagusage><span style='mso-bookmark:_Toc101065298'><span
\r
17552 style='mso-bookmark:_Toc102494380'><span style='mso-bookmark:_Toc102494832'><span
\r
17553 style='mso-bookmark:_Toc235958610'><span lang=EN-US style='mso-ansi-language:
\r
17554 EN-US'>Usage:<span style='mso-spacerun:yes'> </span>-n_core=</span><span
\r
17555 lang=EN-US> </span><number of cores></span></span></span></span><span
\r
17556 style='mso-bookmark:_Toc101065298'><span style='mso-bookmark:_Toc102494380'><span
\r
17557 style='mso-bookmark:_Toc102494832'><span style='mso-bookmark:_Toc235958610'><span
\r
17558 lang=EN-US style='mso-ansi-language:EN-US'><o:p></o:p></span></span></span></span></span></p>
\r
17560 <p class=instruction><span style='mso-bookmark:_Toc101065298'><span
\r
17561 style='mso-bookmark:_Toc102494380'><span style='mso-bookmark:_Toc102494832'><span
\r
17562 style='mso-bookmark:_Toc235958610'><span lang=EN-US>Default: 0</span></span></span></span></span></p>
\r
17564 <p class=flagdescription><span style='mso-bookmark:_Toc101065298'><span
\r
17565 style='mso-bookmark:_Toc102494380'><span style='mso-bookmark:_Toc102494832'><span
\r
17566 style='mso-bookmark:_Toc235958610'><span lang=EN-US>Default indicates that all
\r
17567 cores will be used, as indicated by the environment via:</span></span></span></span></span></p>
\r
17569 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
17570 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
17571 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
17572 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
17574 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span
\r
17575 style='mso-bookmark:_Toc101065298'><span style='mso-bookmark:_Toc102494380'><span
\r
17576 style='mso-bookmark:_Toc102494832'><span style='mso-bookmark:_Toc235958610'><span
\r
17577 lang=EN-US>PROMPT: t_coffee sample_seq2.fasta -multi_core jobs</span></span></span></span></span></p>
\r
17581 <h3><span style='mso-bookmark:_Toc101065298'><span style='mso-bookmark:_Toc102494380'><span
\r
17582 style='mso-bookmark:_Toc102494832'><span style='mso-bookmark:_Toc235958610'><span
\r
17583 lang=EN-US><o:p> </o:p></span></span></span></span></span></h3>
\r
17585 <h3><span style='mso-bookmark:_Toc101065298'><span style='mso-bookmark:_Toc102494380'><span
\r
17586 style='mso-bookmark:_Toc102494832'><span style='mso-bookmark:_Toc235958610'><span
\r
17587 lang=EN-US>Limits</span></span></span></span></span></h3>
\r
17589 <p class=flag><a name="_Toc235958611"></a><a name="_Toc102494833"></a><a
\r
17590 name="_Toc101065299"><span style='mso-bookmark:_Toc102494833'><span
\r
17591 style='mso-bookmark:_Toc235958611'><span lang=AF>-mem_mode</span></span></span></a></p>
\r
17593 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span
\r
17594 style='mso-spacerun:yes'> </span>deprecated</span><span lang=EN-US
\r
17595 style='mso-ansi-language:EN-US;mso-bidi-font-weight:bold'><o:p></o:p></span></p>
\r
17597 <p class=flag><a name="_Toc235958612"></a><a name="_Toc102494834"></a><a
\r
17598 name="_Toc101065300"><span style='mso-bookmark:_Toc102494834'><span
\r
17599 style='mso-bookmark:_Toc235958612'><span lang=AF>-ulimit</span></span></span></a></p>
\r
17601 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span
\r
17602 style='mso-spacerun:yes'> </span>-ulimit=<value><o:p></o:p></span></p>
\r
17604 <p class=instruction><span lang=EN-US>Default: -ulimit=0</span></p>
\r
17606 <p class=flagdescription><span lang=EN-US>Specifies the upper limit of memory
\r
17607 usage (in Megabytes). Processes exceeding this limit will automatically exit. A
\r
17608 value 0 indicates that no limit applies.</span></p>
\r
17610 <p class=flag><a name="_Toc235958613"></a><a name="_Toc102494835"></a><a
\r
17611 name="_Toc101065301"><span style='mso-bookmark:_Toc102494835'><span
\r
17612 style='mso-bookmark:_Toc235958613'><span lang=AF>-maxlen</span></span></span></a></p>
\r
17614 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span
\r
17615 style='mso-spacerun:yes'> </span>-maxlen=<value, 0=nolimit><o:p></o:p></span></p>
\r
17617 <p class=instruction><span lang=EN-US>Default: -maxlen=1000</span><span
\r
17618 lang=EN-US style='mso-bidi-font-weight:bold'><o:p></o:p></span></p>
\r
17620 <p class=flagdescription><span lang=EN-US>Indicates the maximum length of the
\r
17621 sequences. <a name="_Toc101065302"></a></span></p>
\r
17623 <h3><span style='mso-bookmark:_Toc101065302'><a name="_Toc235958614"></a><a
\r
17624 name="_Toc102494836"></a><a name="_Toc102494381"><span style='mso-bookmark:
\r
17625 _Toc102494836'><span style='mso-bookmark:_Toc235958614'><span lang=EN-US>Aligning
\r
17626 more than 100 sequences with DPA</span></span></span></a></span></h3>
\r
17628 <p class=flag><a name="_Toc235958615"></a><a name="_Toc102494837"></a><a
\r
17629 name="_Toc101065303"><span style='mso-bookmark:_Toc102494837'><span
\r
17630 style='mso-bookmark:_Toc235958615'><span lang=AF>-maxnseq</span></span></span></a></p>
\r
17632 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span
\r
17633 style='mso-spacerun:yes'> </span>-maxnseq=<value, 0=nolimit><o:p></o:p></span></p>
\r
17635 <p class=instruction><span lang=EN-US>Default: -maxnseq=50</span></p>
\r
17637 <p class=flagdescription><span lang=EN-US>Indicates the maximum number of
\r
17638 sequences before triggering the use of t_coffee_dpa.</span></p>
\r
17640 <p class=flag><a name="_Toc235958616"></a><a name="_Toc102494838"></a><a
\r
17641 name="_Toc101065304"><span style='mso-bookmark:_Toc102494838'><span
\r
17642 style='mso-bookmark:_Toc235958616'><span lang=AF>-dpa_master_aln</span></span></span></a></p>
\r
17644 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:
\r
17645 -dpa_master_aln=<File, method><o:p></o:p></span></p>
\r
17647 <p class=instruction><span lang=EN-US>Default: -dpa_master_aln=NO</span></p>
\r
17649 <p class=flagdescription><span lang=EN-US>When using dpa, t_coffee needs a seed
\r
17650 alignment that can be computed using any appropriate method. By default,
\r
17651 t_coffee computes a fast approximate alignment.</span></p>
\r
17653 <p class=flagdescription><span lang=EN-US>A pre-alignment can be provided
\r
17654 through this flag, as well as any program using the following syntax:</span></p>
\r
17656 <p class=example2><span lang=EN-US>your_script
\96in <fasta_file> -out
\r
17657 <file_name></span></p>
\r
17659 <p class=flag><a name="_Toc235958617"></a><a name="_Toc102494839"></a><a
\r
17660 name="_Toc101065305"><span style='mso-bookmark:_Toc102494839'><span
\r
17661 style='mso-bookmark:_Toc235958617'><span lang=AF>-dpa_maxnseq</span></span></span></a></p>
\r
17663 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:
\r
17664 -dpa_maxnseq=<integer value><o:p></o:p></span></p>
\r
17666 <p class=instruction><span lang=EN-US>Default: -dpa_maxnseq=30</span></p>
\r
17668 <p class=flagdescription><span lang=EN-US>Maximum number of sequences aligned
\r
17669 simultaneously when DPA is ran. Given the tree computed from the master
\r
17670 alignment, a node is sent to computation if it controls more than <b
\r
17671 style='mso-bidi-font-weight:normal'>
\96dpa_maxnseq</b> OR if it controls a pair
\r
17672 of sequences having less than <b style='mso-bidi-font-weight:normal'>
\96dpa_min_score2</b>
\r
17673 percent ID.<a name="_Toc101065306"></a></span></p>
\r
17675 <p class=flag><span style='mso-bookmark:_Toc101065306'><a name="_Toc235958618"></a><a
\r
17676 name="_Toc102494840"><span style='mso-bookmark:_Toc235958618'><span lang=AF>-dpa_min_score1</span></span></a></span></p>
\r
17678 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:
\r
17679 -dpa_min_score1=<integer value><o:p></o:p></span></p>
\r
17681 <p class=instruction><span lang=EN-US>Default: -dpa_min_score1=95</span></p>
\r
17683 <p class=flagdescription><span lang=EN-US>Threshold for not realigning the
\r
17684 sequences within the master alignment. Given this alignment and the associated
\r
17685 tree, sequences below a node are not realigned if none of them has less than<b
\r
17686 style='mso-bidi-font-weight:normal'>
\96dpa_min_score1</b> % identity.<a
\r
17687 name="_Toc101065307"></a></span></p>
\r
17689 <p class=flag><span style='mso-bookmark:_Toc101065307'><a name="_Toc235958619"></a><a
\r
17690 name="_Toc102494841"><span style='mso-bookmark:_Toc235958619'><span lang=AF>-dpa_min_score2</span></span></a></span></p>
\r
17692 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:
\r
17693 -dpa_min_score2<o:p></o:p></span></p>
\r
17695 <p class=instruction><span lang=EN-US>Default: -dpa_min_score2</span></p>
\r
17697 <p class=flagdescription><span lang=EN-US>Maximum number of sequences aligned
\r
17698 simultaneously when DPA is ran. Given the tree computed from the master
\r
17699 alignment, a node is sent to computation if it controls more than <b
\r
17700 style='mso-bidi-font-weight:normal'>
\96dpa_maxnseq</b> OR if it controls a pair
\r
17701 of sequences having less than <b style='mso-bidi-font-weight:normal'>
\96dpa_min_score2</b>
\r
17702 percent ID.<a name="_Toc101065308"></a></span></p>
\r
17704 <p class=flag><span style='mso-bookmark:_Toc101065308'><a name="_Toc235958620"></a><a
\r
17705 name="_Toc102494842"><span style='mso-bookmark:_Toc235958620'><span lang=AF>-dap_tree
\r
17706 [NOT IMPLEMENTED]</span></span></a></span></p>
\r
17708 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span
\r
17709 style='mso-spacerun:yes'> </span>-dpa_tree=<filename><o:p></o:p></span></p>
\r
17711 <p class=instruction><span lang=EN-US>Default: -unset</span></p>
\r
17713 <p class=flagdescription><span lang=EN-US>Guide tree used in DPA. This is a
\r
17714 newick tree where the distance associated with each node is set to the minimum
\r
17715 pairwise distance among all considered sequences.</span></p>
\r
17717 <h2><a name="_Toc235958621"></a><a name="_Toc102494843"></a><a
\r
17718 name="_Toc102494382"></a><a name="_Toc101065309"><span style='mso-bookmark:
\r
17719 _Toc102494382'><span style='mso-bookmark:_Toc102494843'><span style='mso-bookmark:
\r
17720 _Toc235958621'><span lang=EN-US>Using Structures</span></span></span></span></a><a
\r
17721 name="_Toc101065310"></a></h2>
\r
17723 <h3><span style='mso-bookmark:_Toc101065310'><a name="_Toc235958622"></a><a
\r
17724 name="_Toc102494844"></a><a name="_Toc102494383"><span style='mso-bookmark:
\r
17725 _Toc102494844'><span style='mso-bookmark:_Toc235958622'><span lang=EN-US>Generic</span></span></span></a></span></h3>
\r
17727 <p class=flag><a name="_Toc235958623"><span lang=AF>-mode</span></a></p>
\r
17729 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage: -mode=3dcoffee<o:p></o:p></span></p>
\r
17731 <p class=instruction><span lang=EN-US>Default: turned off</span></p>
\r
17733 <p class=flagdescription><span lang=EN-US>Runs t_coffee with the 3dcoffee mode
\r
17734 (cf next section).</span></p>
\r
17736 <p class=flag><a name="_Toc235958624"></a><a name="_Toc102494846"></a><a
\r
17737 name="_Toc101065312"><span style='mso-bookmark:_Toc102494846'><span
\r
17738 style='mso-bookmark:_Toc235958624'><span lang=AF>-check_pdb_status</span></span></span></a></p>
\r
17740 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:
\r
17741 -check_pdb_status<o:p></o:p></span></p>
\r
17743 <p class=instruction><span lang=EN-US>Default: turned off</span></p>
\r
17745 <p class=flagdescription><span lang=EN-US>Forces t_coffee to run
\r
17746 extract_from_pdb to check the pdb status of each sequence. This can
\r
17747 considerably slow down the program.</span></p>
\r
17749 <p class=flagdescription><span lang=EN-US><o:p> </o:p></span></p>
\r
17751 <h3><a name="_Toc235958625"></a><a name="_Toc102494847"></a><a
\r
17752 name="_Toc102494384"></a><a name="_Toc101065313"><span style='mso-bookmark:
\r
17753 _Toc102494384'><span style='mso-bookmark:_Toc102494847'><span style='mso-bookmark:
\r
17754 _Toc235958625'><span lang=EN-US>3D Coffee: Using SAP</span></span></span></span></a></h3>
\r
17756 <p class=flagdescription><span lang=EN-US>It is possible to use t_coffee to
\r
17757 compute multiple structural alignments. To do so, ensure that you have the sap
\r
17758 program installed.</span></p>
\r
17760 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
17761 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
17762 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
17763 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
17765 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:
\r
17766 t_coffee
\96pdb=struc1.pdb,struc2.pdb,struc3.pdb -method sap_pair</span></p>
\r
17770 <p class=flagdescription><span lang=EN-US>Will combine the pairwise alignments
\r
17771 produced by SAP.<span style='mso-spacerun:yes'> </span>There are currently
\r
17772 four methods that can be interfaced with t_coffee:</span></p>
\r
17774 <p class=flagdescription style='text-indent:28.25pt'><span lang=EN-US>sap_pair:
\r
17775 that uses the sap algorithm</span></p>
\r
17777 <p class=flagdescription style='text-indent:28.25pt'><span lang=EN-US>align_pdb:
\r
17778 uses a t_coffee implementation of sap, not as accurate.</span></p>
\r
17780 <p class=flagdescription style='text-indent:28.25pt'><span lang=EN-US>tmaliagn_pair
\r
17781 (http://zhang.bioinformatics.ku.edu/TM-align/)</span></p>
\r
17783 <p class=flagdescription style='text-indent:28.25pt'><span lang=EN-US>mustang_pair
\r
17784 (http://www.cs.mu.oz.au/~arun/mustang)</span></p>
\r
17786 <p class=flagdescription><span lang=EN-US>When providing a PDB file, the
\r
17787 computation is only carried out on the first chain of this file. If your
\r
17788 original file contains several chain, you should extract the chain you want to
\r
17789 work on. You can use <b style='mso-bidi-font-weight:normal'>t_coffee
\96other_pg
\r
17790 extract_from_pdb </b>or any pdb handling program.</span></p>
\r
17792 <p class=flagdescription><span lang=EN-US>If you are working with public PDB
\r
17793 files, you can use the PDB identifier and specify the chain by adding its index
\r
17794 to the identifier (i.e. 1pdbC). If your structure is an NMR structure, you are
\r
17795 advised to provide the program with one structure only.</span></p>
\r
17797 <p class=flagdescription><span lang=EN-US>If you wish to align only a portion
\r
17798 of the structure, you should extract it yourself from the pdb file, using <b
\r
17799 style='mso-bidi-font-weight:normal'>t_coffee
\96other_pg extract_from_pdb </b>or
\r
17800 any pdb handling program.</span></p>
\r
17802 <p class=flagdescription><span lang=EN-US>You can provide t_coffee with a
\r
17803 mixture of sequences and structure. In this case, you should use the special
\r
17806 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
17807 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
17808 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
17809 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
17811 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:
\r
17812 t_coffee
\96mode 3dcoffee
\96seq 3d_sample3.fasta -template_file
\r
17813 template_file.template</span></p>
\r
17817 <h3><a name="_Toc235958626"></a><a name="_Toc102494848"></a><a
\r
17818 name="_Toc102494385"></a><a name="_Toc101065314"><span style='mso-bookmark:
\r
17819 _Toc102494385'><span style='mso-bookmark:_Toc102494848'><span style='mso-bookmark:
\r
17820 _Toc235958626'><span lang=EN-US>Using/finding PDB templates for the Sequences</span></span></span></span></a></h3>
\r
17822 <p class=flag><a name="_Toc235958627"></a><a name="_Toc102494849"></a><a
\r
17823 name="_Toc101065315"><span style='mso-bookmark:_Toc102494849'><span
\r
17824 style='mso-bookmark:_Toc235958627'><span lang=AF>-template_file</span></span></span></a></p>
\r
17826 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US;mso-bidi-font-weight:
\r
17827 bold'>Usage</span><span lang=EN-US style='mso-ansi-language:EN-US'>:
\r
17828 -template_file =<o:p></o:p></span></p>
\r
17830 <p class=flagusage style='text-indent:28.25pt'><span lang=EN-US
\r
17831 style='mso-ansi-language:EN-US'><filename, <o:p></o:p></span></p>
\r
17833 <p class=flagusage style='margin-left:77.95pt'><span lang=EN-US
\r
17834 style='mso-ansi-language:EN-US'>SCRIPT_scriptame, <o:p></o:p></span></p>
\r
17836 <p class=flagusage style='margin-left:77.95pt'><span lang=EN-US
\r
17837 style='mso-ansi-language:EN-US'>SELF_TAG <o:p></o:p></span></p>
\r
17839 <p class=flagusage style='margin-left:77.95pt'><span lang=EN-US
\r
17840 style='mso-ansi-language:EN-US'>SEQFILE_TAG_filename,<o:p></o:p></span></p>
\r
17842 <p class=flagusage style='margin-left:77.95pt'><span lang=EN-US
\r
17843 style='mso-ansi-language:EN-US'>no><o:p></o:p></span></p>
\r
17845 <p class=instruction><span lang=EN-US>Default: no</span></p>
\r
17847 <p class=flagdescription><span lang=EN-US>This flag instructs t_coffee on the
\r
17848 templates that will be used when combining several types of information. For
\r
17849 instance, when using structural information, this file will indicate the
\r
17850 structural template that corresponds to your sequences. The identifier T
\r
17851 indicates that the file should be a FASTA like file, formatted as follows.
\r
17852 There are several ways to pass the templates:</span></p>
\r
17854 <p class=flagheading2><span lang=EN-US>Predefined Modes</span></p>
\r
17856 <p class=MyNormaBoldl><span lang=AF>EXPRESSO: will use the EBI server to find
\r
17857 _P_ templates</span></p>
\r
17859 <p class=MyNormaBoldl><span lang=AF>PSIBLAST: will use the EBI sever to find
\r
17860 profiles </span></p>
\r
17862 <p class=MyNormaBoldl><span lang=AF><o:p> </o:p></span></p>
\r
17864 <p class=flagheading2><span lang=EN-US>File name</span></p>
\r
17866 <p class=flagdescription><span lang=EN-US>This file contains the
\r
17867 sequence/template association it uses a FASTA-like format, as follows:</span></p>
\r
17869 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
\r
17870 mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
\r
17871 background:#E6E6E6'>
\r
17873 <p class=examplefileCxSpFirst><span lang=EN-US>><sequence name> _P_
\r
17874 <pdb template></span></p>
\r
17876 <p class=examplefileCxSpMiddle><span lang=EN-US>><sequence name> _G_
\r
17877 <gene template></span></p>
\r
17879 <p class=examplefileCxSpMiddle><span lang=EN-US>><sequence name> _R_
\r
17880 <MSA template></span></p>
\r
17882 <p class=examplefileCxSpMiddle><span lang=EN-US>><sequence name> _F_
\r
17883 <RNA Secondary Structure></span></p>
\r
17885 <p class=examplefileCxSpMiddle><span lang=EN-US>><sequence name> _T_
\r
17886 <Transmembrane Secondary Structure></span></p>
\r
17888 <p class=examplefileCxSpMiddle><span lang=EN-US>><sequence name> _E_
\r
17889 <Protein Secondary Structure></span></p>
\r
17891 <p class=examplefileCxSpLast><span lang=EN-US><o:p> </o:p></span></p>
\r
17895 <p class=flagdescription><span lang=EN-US>Each template will be used in place
\r
17896 of the sequence with the appropriate method. For instance, structural templates
\r
17897 will be aligned with sap_pair and the information thus generated will be
\r
17898 transferred onto the alignment.</span></p>
\r
17900 <p class=flagdescription><span lang=EN-US>Note the following rule:</span></p>
\r
17902 <p class=flagdescription><span lang=EN-US><span style='mso-tab-count:1'> </span>-Each
\r
17903 sequence can have one template of each type (structural, genomics
\85)</span></p>
\r
17905 <p class=flagdescription><span lang=EN-US><span style='mso-tab-count:1'> </span>-Each
\r
17906 sequence can only have one template of a given type</span></p>
\r
17908 <p class=flagdescription><span lang=EN-US><span style='mso-tab-count:1'> </span>-Several
\r
17909 sequences can share the same template</span></p>
\r
17911 <p class=flagdescription><span lang=EN-US><span style='mso-tab-count:1'> </span>-All
\r
17912 the sequences do not need to have a template</span></p>
\r
17914 <p class=flagdescription><span lang=EN-US>The type of template on which a
\r
17915 method works is declared with the SEQ_TYPE parameter in the method
\r
17916 configuration file:</span></p>
\r
17918 <p class=flagdescription><span lang=EN-US><span style='mso-tab-count:1'> </span>SEQ_TYPE<span
\r
17919 style='mso-tab-count:1'> </span>S: a method that uses sequences </span></p>
\r
17921 <p class=flagdescription><span lang=EN-US><span style='mso-tab-count:1'> </span>SEQ_TYPE<span
\r
17922 style='mso-tab-count:1'> </span>PS: a pairwise method that aligns
\r
17923 sequences and structures</span></p>
\r
17925 <p class=flagdescription><span lang=EN-US><span style='mso-tab-count:1'> </span>SEQ_TYPE<span
\r
17926 style='mso-tab-count:1'> </span>P: a method that aligns structures
\r
17927 (sap for instance)</span></p>
\r
17929 <p class=flagdescription><span lang=EN-US>There are 4 tags identifying the
\r
17930 template type:</span></p>
\r
17932 <p class=flagdescription style='text-indent:28.25pt'><span lang=EN-US>_P_<span
\r
17933 style='mso-tab-count:1'> </span>Structural templates: a pdb identifier
\r
17934 OR a pdb file</span></p>
\r
17936 <p class=flagdescription style='margin-left:106.2pt;text-indent:-35.4pt'><span
\r
17937 lang=EN-US>_G_<span style='mso-tab-count:1'> </span>Genomic templates: a
\r
17938 protein sequence where boundary amino-acid have been recoded with ( o:0, i:1,
\r
17941 <p class=flagdescription style='text-indent:28.25pt'><span lang=EN-US>_R_<span
\r
17942 style='mso-tab-count:1'> </span>Profile Templates: a file containing a
\r
17943 multiple sequence alignment</span></p>
\r
17945 <p class=flagdescription style='text-indent:28.25pt'><span lang=EN-US>_F_<span
\r
17946 style='mso-tab-count:1'> </span>RNA secondary Structures</span></p>
\r
17948 <p class=flagdescription style='text-indent:28.25pt'><span lang=EN-US><o:p> </o:p></span></p>
\r
17950 <p class=flagdescription><span lang=EN-US>More than one template file can be
\r
17951 provided. There is no need to have one template for every sequence in the
\r
17952 dataset. </span></p>
\r
17954 <p class=flagdescription style='text-indent:28.25pt'><span lang=EN-US>_P_, _G_,
\r
17955 and _R_ are known as <b style='mso-bidi-font-weight:normal'>template TAGS<o:p></o:p></b></span></p>
\r
17957 <p class=flagheading2><span lang=EN-US>2-SCRIPT_<scriptname></span></p>
\r
17959 <p class=flagdescription><span lang=EN-US>Indicates that filename is a script
\r
17960 that will be used to generate a valid template file. The script will run on a
\r
17961 file containing all your sequences using the following syntax:</span></p>
\r
17963 <p class=example2><span lang=EN-US>scriptname
\96infile=<your sequences>
\r
17964 -outfile=<template_file></span></p>
\r
17966 <p class=flagdescription><span lang=EN-US>It is also possible to pass some
\r
17967 parameters, use @ as a separator and # in place of the = sign. For instance, if
\r
17968 you want to call the a script named blast.pl with the foloowing parameters;</span></p>
\r
17970 <p class=example2><span lang=EN-US>blast.pl -db=pdb -dir=/local/test</span></p>
\r
17972 <p class=flagdescription><span lang=EN-US>Use</span></p>
\r
17974 <p class=example2><span lang=EN-US>SCRIPT_blast.pl@db#pdb@dir#/local/test</span></p>
\r
17976 <p class=flagdescription><span lang=EN-US>Bear in mind that the input output
\r
17977 flags will then be concatenated to this command line so that t_coffee ends up
\r
17978 calling the program using the following system call:</span></p>
\r
17980 <p class=example2><span lang=EN-US>blast.pl -db=pdb -dir=/local/test
\r
17981 -infile=<some tmp file> -outfile=<another tmp file></span></p>
\r
17983 <p class=flagdescription><span lang=EN-US><o:p> </o:p></span></p>
\r
17985 <p class=flagheading2><span lang=EN-US>3-SELF_TAG</span></p>
\r
17987 <p class=flagdescription><span lang=EN-US>TAG can take the value of any of the known
\r
17988 TAGS (_S_, _G_, _P_). SELF indicates that the original name of the sequence
\r
17989 will be used to fetch the template: </span></p>
\r
17991 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
17992 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
17993 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
17994 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
17996 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:
\r
17997 t_coffee 3d_sample2.fasta
\96template_file SELF_P_</span></p>
\r
18001 <p class=flagdescription><span lang=EN-US>The previous command will work
\r
18002 because the sequences in 3d_sample3 are named </span></p>
\r
18004 <p class=flagheading2><span lang=EN-US>4-SEQFILE_TAG_filename</span></p>
\r
18006 <p class=flagdescription><span lang=EN-US>Use this flag if your templates are
\r
18007 in filename, and are named according to the sequences. For instance, if your
\r
18008 protein sequences have been recoded with Exon/Intron information, you should
\r
18009 have the recoded sequences names according to the original:</span></p>
\r
18011 <p class=example2><span lang=EN-US>SEQFILE_G_recodedprotein.fasta<span
\r
18012 style='mso-tab-count:1'> </span></span></p>
\r
18014 <p class=flag><a name="_Toc235958628"></a><a name="_Toc102494850"></a><a
\r
18015 name="_Toc101065316"><span style='mso-bookmark:_Toc102494850'><span
\r
18016 style='mso-bookmark:_Toc235958628'><span lang=AF>-struc_to_use</span></span></span></a></p>
\r
18018 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:
\r
18019 -struc_to_use=<struc1, struc2
\85><o:p></o:p></span></p>
\r
18021 <p class=instruction><span lang=EN-US>Default: -struc_to_use=NULL</span></p>
\r
18023 <p class=flagdescription><span lang=EN-US>Restricts the 3Dcoffee to a set of
\r
18024 pre-defined structures.</span></p>
\r
18026 <h2><a name="_Toc235958629"></a><a name="_Toc102494851"></a><a
\r
18027 name="_Toc102494386"></a><a name="_Toc101065317"><span style='mso-bookmark:
\r
18028 _Toc102494386'><span style='mso-bookmark:_Toc102494851'><span style='mso-bookmark:
\r
18029 _Toc235958629'><span lang=EN-US>Multiple Local Alignments</span></span></span></span></a></h2>
\r
18031 <p class=MyNormal><span lang=AF>It is possible to compute multiple local alignments,
\r
18032 using the moca routine. MOCA is a routine that allows extracting all the local
\r
18033 alignments that show some similarity with another predefined fragment.</span></p>
\r
18035 <p class=MyNormal><span lang=AF>'mocca' is a perl script that calls t-coffee
\r
18036 and provides it with the appropriate parameters.</span></p>
\r
18038 <p class=flag><a name="_Toc235958630"></a><a name="_Toc102494852"></a><a
\r
18039 name="_Toc101065318"><span style='mso-bookmark:_Toc102494852'><span
\r
18040 style='mso-bookmark:_Toc235958630'><span lang=AF>-domain</span></span></span></a><span
\r
18041 style='mso-bookmark:_Toc102494852'><span style='mso-bookmark:_Toc235958630'><span
\r
18042 lang=AF>/-mocca</span></span></span></p>
\r
18044 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:
\r
18045 -domain<o:p></o:p></span></p>
\r
18047 <p class=instruction><span lang=EN-US>Default: not set</span></p>
\r
18049 <p class=flagdescription><span lang=EN-US>This flag indicates that t_coffee
\r
18050 will run using the domain mode. All the sequences will be concatenated, and the
\r
18051 resulting sequence will be compared to itself using lalign_rs_s_pair mode
\r
18052 (lalign of the sequence against itself using keeping the lalign raw score).
\r
18053 This step is the most computer intensive, and it is advisable to save the
\r
18054 resulting file.</span></p>
\r
18056 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
18057 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
18058 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
18059 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
18061 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:
\r
18062 t_coffee -in Ssample_seq1.fasta,Mlalign_rs_s_pair
\r
18063 -out_lib=sample_lib1.mocca_lib -domain -start=100 -len=50 </span></p>
\r
18067 <p class=flagdescription><span lang=EN-US>This instruction will use the
\r
18068 fragment 100-150 on the concatenated sequences, as a template for the extracted
\r
18069 repeats. The extraction will only be made once. The library will be placed in
\r
18070 the file <lib name>.</span></p>
\r
18072 <p class=flagdescription><span lang=EN-US><o:p> </o:p></span></p>
\r
18074 <p class=flagdescription><span lang=EN-US>If you want, you can test other
\r
18075 coordinates for the repeat, such as </span></p>
\r
18077 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
18078 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
18079 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
18080 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
18082 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:
\r
18083 t_coffee -in sample_lib1.mocca_lib -domain -start=100 -len=60 </span></p>
\r
18087 <p class=flagdescription><span lang=EN-US>This run will use the fragment
\r
18088 100-160, and will be much faster because it does not need to re-compute the
\r
18089 lalign library. </span></p>
\r
18091 <p class=flag><a name="_Toc235958631"></a><a name="_Toc102494853"></a><a
\r
18092 name="_Toc101065319"><span style='mso-bookmark:_Toc102494853'><span
\r
18093 style='mso-bookmark:_Toc235958631'><span lang=AF>-start</span></span></span></a></p>
\r
18095 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:
\r
18096 -start=<int value><o:p></o:p></span></p>
\r
18098 <p class=instruction><span lang=EN-US>Default: not set</span></p>
\r
18100 <p class=flagdescription><span lang=EN-US>This flag indicates the starting
\r
18101 position of the portion of sequence that will be used as a template for the
\r
18102 repeat extraction. The value assumes that all the sequences have been
\r
18103 concatenated, and is given on the resulting sequence.</span></p>
\r
18105 <p class=flag><a name="_Toc235958632"></a><a name="_Toc102494854"></a><a
\r
18106 name="_Toc101065320"><span style='mso-bookmark:_Toc102494854'><span
\r
18107 style='mso-bookmark:_Toc235958632'><span lang=AF>-len</span></span></span></a></p>
\r
18109 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:
\r
18110 -len=<int value><o:p></o:p></span></p>
\r
18112 <p class=instruction><span lang=EN-US>Default: not set</span></p>
\r
18114 <p class=flagdescription><span lang=EN-US>This flag indicates the length of the
\r
18115 portion of sequence that will be used as a template.</span></p>
\r
18117 <p class=flag><a name="_Toc235958633"></a><a name="_Toc102494855"></a><a
\r
18118 name="_Toc101065321"><span style='mso-bookmark:_Toc102494855'><span
\r
18119 style='mso-bookmark:_Toc235958633'><span lang=AF>-scale</span></span></span></a></p>
\r
18121 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:
\r
18122 -scale=<int value><o:p></o:p></span></p>
\r
18124 <p class=instruction><span lang=EN-US>Default: -scale=-100</span></p>
\r
18126 <p class=flagdescription><span lang=EN-US>This flag indicates the value of the
\r
18127 threshold for extracting the repeats. The actual threshold is equal to:</span></p>
\r
18129 <p class=flagdescription><span lang=EN-US><span style='mso-tab-count:1'> </span>motif_len*scale</span></p>
\r
18131 <p class=flagdescription><span lang=EN-US>Increase the scale </span><span
\r
18132 lang=EN-US style='font-family:Wingdings;mso-ascii-font-family:"Times New Roman";
\r
18133 mso-hansi-font-family:"Times New Roman";mso-char-type:symbol;mso-symbol-font-family:
\r
18134 Wingdings'><span style='mso-char-type:symbol;mso-symbol-font-family:Wingdings'>ó</span></span><span
\r
18135 lang=EN-US>Increase sensitivity </span><span lang=EN-US style='font-family:
\r
18136 Wingdings;mso-ascii-font-family:"Times New Roman";mso-hansi-font-family:"Times New Roman";
\r
18137 mso-char-type:symbol;mso-symbol-font-family:Wingdings'><span style='mso-char-type:
\r
18138 symbol;mso-symbol-font-family:Wingdings'>ó</span></span><span lang=EN-US> More
\r
18139 alignments( i.e. -50).</span></p>
\r
18141 <p class=flag><a name="_Toc235958634"></a><a name="_Toc102494856"></a><a
\r
18142 name="_Toc101065322"><span style='mso-bookmark:_Toc102494856'><span
\r
18143 style='mso-bookmark:_Toc235958634'><span lang=AF>-domain_interactive [Examples]</span></span></span></a></p>
\r
18145 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:
\r
18146 -domain_interactive<o:p></o:p></span></p>
\r
18148 <p class=instruction><span lang=EN-US>Default: unset</span></p>
\r
18150 <p class=flagdescription><span lang=EN-US>Launches an interactive mocca
\r
18151 session.</span></p>
\r
18153 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
18154 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
18155 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
18156 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
18158 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:
\r
18159 t_coffee -in Lsample_lib3.tc_lib,Mlalign_rs_s_pair -domain -start=100 -len=60</span></p>
\r
18163 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
\r
18164 mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
\r
18165 background:#E6E6E6;margin-left:0mm;margin-right:10.0mm'>
\r
18167 <p class=examplefilesmallCxSpFirst><span lang=EN-US>TOLB_ECOLI_212_26<span
\r
18168 style='mso-tab-count:3'> </span><span
\r
18169 style='mso-spacerun:yes'> </span>211 SKLAYVTFESGR--SALVIQTLANGAVRQV-ASFPRHNGAPAFSPDGSKLAFA</span></p>
\r
18171 <p class=examplefilesmallCxSpMiddle><span lang=EN-US>TOLB_ECOLI_165_218<span
\r
18172 style='mso-spacerun:yes'> </span>164 TRIAYVVQTNGGQFPYELRVSDYDGYNQFVVHRSPQPLMSPAWSPDGSKLAYV</span></p>
\r
18174 <p class=examplefilesmallCxSpMiddle><span lang=EN-US>TOLB_ECOLI_256_306<span
\r
18175 style='mso-spacerun:yes'> </span>255 SKLAFALSKTGS--LNLYVMDLASGQIRQV-TDGRSNNTEPTWFPDSQNLAFT</span></p>
\r
18177 <p class=examplefilesmallCxSpMiddle><span lang=EN-US>TOLB_ECOLI_307_350<span
\r
18178 style='mso-spacerun:yes'> </span>306 -------DQAGR--PQVYKVNINGGAPQRI-TWEGSQNQDADVSSDGKFMVMV</span></p>
\r
18180 <p class=examplefilesmallCxSpMiddle><span lang=EN-US>TOLB_ECOLI_351_393<span
\r
18181 style='mso-spacerun:yes'> </span>350 -------SNGGQ--QHIAKQDLATGGV-QV-LSSTFLDETPSLAPNGTMVIYS<span
\r
18182 style='mso-spacerun:yes'> </span></span></p>
\r
18184 <p class=examplefilesmallCxSpMiddle><span lang=EN-US><span
\r
18185 style='mso-spacerun:yes'> </span>1<span
\r
18186 style='mso-spacerun:yes'> </span>*<span
\r
18187 style='mso-spacerun:yes'> </span><span
\r
18188 style='mso-spacerun:yes'> </span>*<span style='mso-spacerun:yes'>
\r
18189 </span>:<span style='mso-spacerun:yes'> </span><span
\r
18190 style='mso-spacerun:yes'> </span>.<span style='mso-spacerun:yes'>
\r
18191 </span>.:.<span style='mso-spacerun:yes'> </span>:<span
\r
18192 style='mso-spacerun:yes'> </span></span></p>
\r
18194 <p class=examplefilesmallCxSpMiddle><span lang=EN-US><o:p> </o:p></span></p>
\r
18196 <p class=examplefilesmallCxSpMiddle><span lang=EN-US><span
\r
18197 style='mso-spacerun:yes'> </span>MENU: Type Letter Flag[number] and
\r
18198 Return: ex |10</span></p>
\r
18200 <p class=examplefilesmallCxSpMiddle><span lang=EN-US><span
\r
18201 style='mso-spacerun:yes'> </span>|x<span style='mso-spacerun:yes'>
\r
18202 </span>-->Set<span style='mso-spacerun:yes'> </span>the START to x</span></p>
\r
18204 <p class=examplefilesmallCxSpMiddle><span lang=EN-US><span
\r
18205 style='mso-spacerun:yes'> </span>>x<span
\r
18206 style='mso-spacerun:yes'> </span>-->Set<span
\r
18207 style='mso-spacerun:yes'> </span>the LEN<span style='mso-spacerun:yes'>
\r
18208 </span>to x</span></p>
\r
18210 <p class=examplefilesmallCxSpMiddle><span lang=EN-US><span
\r
18211 style='mso-spacerun:yes'> </span>Cx<span style='mso-spacerun:yes'>
\r
18212 </span>-->Set<span style='mso-spacerun:yes'> </span>the sCale to x</span></p>
\r
18214 <p class=examplefilesmallCxSpMiddle><span lang=EN-US><span
\r
18215 style='mso-spacerun:yes'> </span>Sname<span style='mso-spacerun:yes'>
\r
18216 </span>-->Save<span style='mso-spacerun:yes'> </span>the<span
\r
18217 style='mso-spacerun:yes'> </span>Alignment </span></p>
\r
18219 <p class=examplefilesmallCxSpMiddle><span lang=EN-US><span
\r
18220 style='mso-spacerun:yes'> </span>Bx<span style='mso-spacerun:yes'>
\r
18221 </span>-->Save<span style='mso-spacerun:yes'> </span>Goes back x it </span></p>
\r
18223 <p class=examplefilesmallCxSpMiddle><span lang=EN-US><span
\r
18224 style='mso-spacerun:yes'> </span>return<span style='mso-spacerun:yes'>
\r
18225 </span>-->Compute the<span style='mso-spacerun:yes'> </span>Alignment</span></p>
\r
18227 <p class=examplefilesmallCxSpMiddle><span lang=EN-US><span
\r
18228 style='mso-spacerun:yes'> </span>X<span style='mso-spacerun:yes'>
\r
18229 </span>-->eXit</span></p>
\r
18231 <p class=examplefilesmallCxSpMiddle><span lang=EN-US><o:p> </o:p></span></p>
\r
18233 <p class=examplefilesmallCxSpMiddle><span lang=EN-US>[ITERATION<span
\r
18234 style='mso-spacerun:yes'> </span>1] [START=211] [LEN= 50] [SCALE=-100]<span
\r
18235 style='mso-spacerun:yes'> </span>YOUR CHOICE:</span></p>
\r
18237 <p class=examplefilesmallCxSpMiddle><span lang=EN-US>For instance, to set the
\r
18238 length of the domain to 40, type: </span></p>
\r
18240 <p class=examplefilesmallCxSpMiddle><span lang=EN-US><o:p> </o:p></span></p>
\r
18242 <p class=examplefilesmallCxSpMiddle><span lang=EN-US>[ITERATION<span
\r
18243 style='mso-spacerun:yes'> </span>1] [START=211] [LEN= 50] [SCALE=-100]<span
\r
18244 style='mso-spacerun:yes'> </span>YOUR CHOICE:>40[return]</span></p>
\r
18246 <p class=examplefilesmallCxSpMiddle><span lang=EN-US>[return]</span></p>
\r
18248 <p class=examplefilesmallCxSpMiddle><span lang=EN-US><o:p> </o:p></span></p>
\r
18250 <p class=examplefilesmallCxSpMiddle><span lang=EN-US>Which will generate:</span></p>
\r
18252 <p class=examplefilesmallCxSpMiddle><span lang=EN-US><o:p> </o:p></span></p>
\r
18254 <p class=examplefilesmallCxSpMiddle><span lang=EN-US>TOLB_ECOLI_212_252<span
\r
18255 style='mso-spacerun:yes'> </span>211
\r
18256 SKLAYVTFESGRSALVIQTLANGAVRQVASFPRHNGAPAF<span style='mso-spacerun:yes'>
\r
18257 </span>251</span></p>
\r
18259 <p class=examplefilesmallCxSpMiddle><span lang=EN-US>TOLB_ECOLI_256_296<span
\r
18260 style='mso-spacerun:yes'> </span>255
\r
18261 SKLAFALSKTGSLNLYVMDLASGQIRQVTDGRSNNTEPTW<span style='mso-spacerun:yes'>
\r
18262 </span>295</span></p>
\r
18264 <p class=examplefilesmallCxSpMiddle><span lang=EN-US>TOLB_ECOLI_300_340<span
\r
18265 style='mso-spacerun:yes'> </span>299
\r
18266 QNLAFTSDQAGRPQVYKVNINGGAPQRITWEGSQNQDADV<span style='mso-spacerun:yes'>
\r
18267 </span>339</span></p>
\r
18269 <p class=examplefilesmallCxSpMiddle><span lang=EN-US>TOLB_ECOLI_344_383<span
\r
18270 style='mso-spacerun:yes'> </span>343
\r
18271 KFMVMVSSNGGQQHIAKQDLATGGV-QVLSSTFLDETPSL<span style='mso-spacerun:yes'>
\r
18272 </span>382</span></p>
\r
18274 <p class=examplefilesmallCxSpMiddle><span lang=EN-US>TOLB_ECOLI_387_427<span
\r
18275 style='mso-spacerun:yes'> </span>386
\r
18276 TMVIYSSSQGMGSVLNLVSTDGRFKARLPATDGQVKFPAW<span style='mso-spacerun:yes'>
\r
18277 </span>426</span></p>
\r
18279 <p class=examplefilesmallCxSpMiddle><span lang=EN-US><span
\r
18280 style='mso-spacerun:yes'> </span>1<span
\r
18281 style='mso-spacerun:yes'> </span>:<span style='mso-spacerun:yes'>
\r
18282 </span>:<span style='mso-spacerun:yes'> </span>:<span
\r
18283 style='mso-spacerun:yes'> </span><span
\r
18284 style='mso-spacerun:yes'> </span>::<span style='mso-spacerun:yes'>
\r
18285 </span>.<span style='mso-spacerun:yes'> </span>40</span></p>
\r
18287 <p class=examplefilesmallCxSpMiddle><span lang=EN-US><o:p> </o:p></span></p>
\r
18289 <p class=examplefilesmallCxSpMiddle><span lang=EN-US><o:p> </o:p></span></p>
\r
18291 <p class=examplefilesmallCxSpMiddle><span lang=EN-US><o:p> </o:p></span></p>
\r
18293 <p class=examplefilesmallCxSpMiddle><span lang=EN-US><o:p> </o:p></span></p>
\r
18295 <p class=examplefilesmallCxSpMiddle><span lang=EN-US><span
\r
18296 style='mso-spacerun:yes'> </span>MENU: Type Letter Flag[number] and
\r
18297 Return: ex |10</span></p>
\r
18299 <p class=examplefilesmallCxSpMiddle><span lang=EN-US><span
\r
18300 style='mso-spacerun:yes'> </span>|x<span style='mso-spacerun:yes'>
\r
18301 </span>-->Set<span style='mso-spacerun:yes'> </span>the START to x</span></p>
\r
18303 <p class=examplefilesmallCxSpMiddle><span lang=EN-US><span
\r
18304 style='mso-spacerun:yes'> </span>>x<span
\r
18305 style='mso-spacerun:yes'> </span>-->Set<span
\r
18306 style='mso-spacerun:yes'> </span>the LEN<span style='mso-spacerun:yes'>
\r
18307 </span>to x</span></p>
\r
18309 <p class=examplefilesmallCxSpMiddle><span lang=EN-US><span
\r
18310 style='mso-spacerun:yes'> </span>Cx<span style='mso-spacerun:yes'>
\r
18311 </span>-->Set<span style='mso-spacerun:yes'> </span>the sCale to x</span></p>
\r
18313 <p class=examplefilesmallCxSpMiddle><span lang=EN-US><span
\r
18314 style='mso-spacerun:yes'> </span>Sname<span style='mso-spacerun:yes'>
\r
18315 </span>-->Save<span style='mso-spacerun:yes'> </span>the<span
\r
18316 style='mso-spacerun:yes'> </span>Alignment </span></p>
\r
18318 <p class=examplefilesmallCxSpMiddle><span lang=EN-US><span
\r
18319 style='mso-spacerun:yes'> </span><span style='mso-spacerun:yes'>
\r
18320 </span>Bx<span style='mso-spacerun:yes'> </span>-->Save<span
\r
18321 style='mso-spacerun:yes'> </span>Goes back x it </span></p>
\r
18323 <p class=examplefilesmallCxSpMiddle><span lang=EN-US><span
\r
18324 style='mso-spacerun:yes'> </span>return<span style='mso-spacerun:yes'>
\r
18325 </span>-->Compute the<span style='mso-spacerun:yes'> </span>Alignment</span></p>
\r
18327 <p class=examplefilesmallCxSpMiddle><span lang=EN-US><span
\r
18328 style='mso-spacerun:yes'> </span>X<span style='mso-spacerun:yes'>
\r
18329 </span>-->eXit</span></p>
\r
18331 <p class=examplefilesmallCxSpMiddle><span lang=EN-US><o:p> </o:p></span></p>
\r
18333 <p class=examplefilesmallCxSpLast><span lang=EN-US>[ITERATION<span
\r
18334 style='mso-spacerun:yes'> </span>3] [START=211] [LEN= 40] [SCALE=-100]<span
\r
18335 style='mso-spacerun:yes'> </span>YOUR CHOICE: </span></p>
\r
18339 <p class=MyNormal><span lang=AF><o:p> </o:p></span></p>
\r
18341 <p class=flagdescription><span lang=EN-US>If you want to indicate the
\r
18342 coordinates, relative to a specific sequence, type:</span></p>
\r
18344 <p class=example2><span lang=EN-US><span style='mso-tab-count:1'> </span>|<seq_name>:start</span></p>
\r
18346 <p class=flagdescription><span lang=EN-US>Type S<your name> to save the
\r
18347 current alignment, and extract a new motif. </span></p>
\r
18349 <p class=flagdescription><span lang=EN-US>Type X when you are done.</span></p>
\r
18351 <h2><a name="_Toc235958635"></a><a name="_Toc102494857"></a><a
\r
18352 name="_Toc102494387"></a><a name="_Toc101065323"><span style='mso-bookmark:
\r
18353 _Toc102494387'><span style='mso-bookmark:_Toc102494857'><span style='mso-bookmark:
\r
18354 _Toc235958635'><span lang=EN-US>Output Control</span></span></span></span></a></h2>
\r
18356 <h3><a name="_Toc235958636"></a><a name="_Toc102494858"></a><a
\r
18357 name="_Toc102494388"></a><a name="_Toc101065324"><span style='mso-bookmark:
\r
18358 _Toc102494388'><span style='mso-bookmark:_Toc102494858'><span style='mso-bookmark:
\r
18359 _Toc235958636'><span lang=EN-US>Generic</span></span></span></span></a></h3>
\r
18361 <p class=flag><a name="_Toc235958637"></a><a name="_Toc102494859"><span
\r
18362 style='mso-bookmark:_Toc235958637'><span lang=AF>Conventions Regarding
\r
18363 Filenames</span></span></a></p>
\r
18365 <p class=MyNormal><span lang=AF>stdout, stderr, stdin, no, /dev/null are valid
\r
18366 filenames. They cause the corresponding file to be output in stderr or stdout,
\r
18367 for an input file, stdin causes the program to requests the corresponding file
\r
18368 through pipe. No causes a suppression of the output, as does /dev/null.</span></p>
\r
18370 <p class=flag><a name="_Toc235958638"></a><a name="_Toc102494860"><span
\r
18371 style='mso-bookmark:_Toc235958638'><span lang=AF>Identifying the Output files
\r
18372 automatically</span></span></a></p>
\r
18374 <p class=MyNormal><span lang=AF>In the t_coffee output, each output appears in
\r
18375 a line:</span></p>
\r
18377 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
\r
18378 mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
\r
18379 background:#E6E6E6'>
\r
18381 <p class=examplefile><span lang=EN-US>##### FILENAME <name> TYPE
\r
18382 <Type> FORMAT <Format></span></p>
\r
18386 <p class=flag><a name="_Toc102494861"></a><a name="_Toc102494389"></a><a
\r
18387 name="_Toc101065325"></a><a name="_Toc235958639"><span style='mso-bookmark:
\r
18388 _Toc101065325'><span style='mso-bookmark:_Toc102494389'><span style='mso-bookmark:
\r
18389 _Toc102494861'><span lang=AF>-no_warning</span></span></span></span></a><span
\r
18390 style='mso-bookmark:_Toc101065325'><span style='mso-bookmark:_Toc102494389'><span
\r
18391 style='mso-bookmark:_Toc102494861'></span></span></span></p>
\r
18393 <p class=flagusage><span style='mso-bookmark:_Toc101065325'><span
\r
18394 style='mso-bookmark:_Toc102494389'><span style='mso-bookmark:_Toc102494861'><span
\r
18395 lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span
\r
18396 style='mso-spacerun:yes'> </span>-no_warning<o:p></o:p></span></span></span></span></p>
\r
18398 <p class=instruction><span style='mso-bookmark:_Toc101065325'><span
\r
18399 style='mso-bookmark:_Toc102494389'><span style='mso-bookmark:_Toc102494861'><span
\r
18400 lang=EN-US>Default: Switched off</span></span></span></span></p>
\r
18402 <p class=flagdescription><span style='mso-bookmark:_Toc101065325'><span
\r
18403 style='mso-bookmark:_Toc102494389'><span style='mso-bookmark:_Toc102494861'><span
\r
18404 lang=EN-US>Suppresseswarning output.<i style='mso-bidi-font-style:normal'><o:p></o:p></i></span></span></span></span></p>
\r
18406 <h3><span style='mso-bookmark:_Toc101065325'><span style='mso-bookmark:_Toc102494389'><span
\r
18407 style='mso-bookmark:_Toc102494861'><span lang=EN-US><o:p> </o:p></span></span></span></span></h3>
\r
18409 <h3><span style='mso-bookmark:_Toc101065325'><span style='mso-bookmark:_Toc102494389'><span
\r
18410 style='mso-bookmark:_Toc102494861'><a name="_Toc235958640"><span lang=EN-US>Alignments</span></a></span></span></span></h3>
\r
18412 <p class=flag><a name="_Toc235958641"></a><a name="_Toc102494862"></a><a
\r
18413 name="_Toc101065326"><span style='mso-bookmark:_Toc102494862'><span
\r
18414 style='mso-bookmark:_Toc235958641'><span lang=AF>-outfile</span></span></span></a></p>
\r
18416 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span
\r
18417 style='mso-spacerun:yes'> </span>-outfile=<out_aln file,default,no><o:p></o:p></span></p>
\r
18419 <p class=instruction><span lang=EN-US>Default:-outfile=default</span></p>
\r
18421 <p class=flagdescription><span lang=EN-US>Indicates the name of the alignment
\r
18422 output by t_coffee. If the default is used, the alignment is named <i
\r
18423 style='mso-bidi-font-style:normal'><your sequences>.aln<o:p></o:p></i></span></p>
\r
18425 <p class=flag><a name="_Toc235958642"></a><a name="_Toc102494863"></a><a
\r
18426 name="_Toc101065327"><span style='mso-bookmark:_Toc102494863'><span
\r
18427 style='mso-bookmark:_Toc235958642'><span lang=AF>-output</span></span></span></a></p>
\r
18429 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span
\r
18430 style='mso-spacerun:yes'> </span>-output=<format1,format2,...> <o:p></o:p></span></p>
\r
18432 <p class=instruction><span lang=EN-US>Default:-output=clustalw</span></p>
\r
18434 <p class=flagdescription><span lang=EN-US>Indicates the format used for
\r
18435 outputting the -outfile.</span></p>
\r
18437 <p class=flagdescription><span lang=EN-US>Supported formats are:</span></p>
\r
18439 <p class=flagdescription><span lang=EN-US><span style='mso-tab-count:1'> </span></span></p>
\r
18441 <p class=flagdescriptionid1><span lang=EN-US>clustalw_aln, clustalw<span
\r
18442 style='mso-tab-count:1'> </span>: ClustalW format.</span></p>
\r
18444 <p class=flagdescriptionid1><span lang=EN-US>gcg, msf_aln<span
\r
18445 style='mso-spacerun:yes'> </span><span style='mso-tab-count:1'> </span><span
\r
18446 style='mso-tab-count:1'> </span>: MSF alignment.</span></p>
\r
18448 <p class=flagdescriptionid1><span lang=EN-US>pir_aln<span style='mso-tab-count:
\r
18449 3'> </span>: pir alignment.</span></p>
\r
18451 <p class=flagdescriptionid1><span lang=EN-US>fasta_aln<span style='mso-tab-count:
\r
18452 2'> </span>: fasta alignment.</span></p>
\r
18454 <p class=flagdescriptionid1><span lang=EN-US>phylip<span style='mso-tab-count:
\r
18455 3'> </span>: Phylip format.</span></p>
\r
18457 <p class=flagdescriptionid1><span lang=EN-US>pir_seq<span style='mso-tab-count:
\r
18458 3'> </span>: pir sequences (no gap).</span></p>
\r
18460 <p class=flagdescriptionid1><span lang=EN-US>fasta_seq<span style='mso-tab-count:
\r
18461 2'> </span>: fasta sequences (no gap).</span></p>
\r
18463 <p class=flagdescription><span lang=EN-US><span style='mso-tab-count:2'> </span></span></p>
\r
18465 <p class=flagdescription><span lang=EN-US>As well as:</span></p>
\r
18467 <p class=flagdescription><span lang=EN-US><o:p> </o:p></span></p>
\r
18469 <p class=flagdescriptionid1><span lang=EN-US>score_ascii<span style='mso-tab-count:
\r
18470 1'> </span>: causes the output of a reliability flag </span></p>
\r
18472 <p class=flagdescriptionid1><span lang=EN-US>score_html<span style='mso-tab-count:
\r
18473 1'> </span>: causes the output to be a reliability plot in HTML</span></p>
\r
18475 <p class=flagdescriptionid1><span lang=EN-US>score_pdf<span style='mso-tab-count:
\r
18476 1'> </span>: idem in PDF (if ps2pdf is installed on your system).</span></p>
\r
18478 <p class=flagdescriptionid1><span lang=EN-US>score_ps<span style='mso-tab-count:
\r
18479 1'> </span><span style='mso-tab-count:1'> </span>:
\r
18480 idem in postscript.</span></p>
\r
18482 <p class=flagdescription><span lang=EN-US><o:p> </o:p></span></p>
\r
18484 <p class=flagdescription><span lang=EN-US>More than one format can be
\r
18485 indicated:</span></p>
\r
18487 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
18488 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
18489 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
18490 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
18492 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:
\r
18493 t_coffee sample_seq1.fasta -output=clustalw,gcg, score_html </span></p>
\r
18497 <p class=flagdescription><span lang=EN-US>A publication describing the CORE
\r
18498 index is available on:</span></p>
\r
18500 <p class=MyNormal><span lang=AF><a
\r
18501 href="http://www.tcoffee.org/Publications/Pdf/core.pp.pdf"><span lang=EN-US
\r
18502 style='mso-ansi-language:EN-US'>http://www.tcoffee.org/Publications/Pdf/core.pp.pdf</span></a></span></p>
\r
18504 <p class=flag><a name="_Toc235958643"></a><a name="_Toc102494864"></a><a
\r
18505 name="_Toc101065328"><span style='mso-bookmark:_Toc102494864'><span
\r
18506 style='mso-bookmark:_Toc235958643'><span lang=AF>-outseqweight</span></span></span></a></p>
\r
18508 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span
\r
18509 style='mso-spacerun:yes'> </span>-outseqweight=<filename><o:p></o:p></span></p>
\r
18511 <p class=instruction><span lang=EN-US>Default: not used</span></p>
\r
18513 <p class=flagdescription><span lang=EN-US>Indicates the name of the file in
\r
18514 which the sequences weights should be saved..</span></p>
\r
18516 <p class=flag><a name="_Toc235958644"></a><a name="_Toc102494865"></a><a
\r
18517 name="_Toc101065329"><span style='mso-bookmark:_Toc102494865'><span
\r
18518 style='mso-bookmark:_Toc235958644'><span lang=AF>-case</span></span></span></a></p>
\r
18520 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span
\r
18521 style='mso-spacerun:yes'> </span>-case=<keep,upper,lower><o:p></o:p></span></p>
\r
18523 <p class=instruction><span lang=EN-US>Default: -case=keep</span></p>
\r
18525 <p class=MyNormal><span lang=AF>Instructs the program on the case to be used in
\r
18526 the output file (Clustalw uses upper case). The default keeps the case and
\r
18527 makes it possible to maintain a mixture of upper and lower case residues.</span></p>
\r
18529 <p class=MyNormal><span lang=AF>If you need to change the case of your file,
\r
18530 you can use seq_reformat:</span></p>
\r
18532 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
18533 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
18534 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
18535 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
18537 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:
\r
18538 t_coffee
\96other_pg seq_reformat
\96in sample_aln1.aln
\96action +lower
\96output
\r
18539 clustalw </span></p>
\r
18543 <p class=flag><a name="_Toc235958645"></a><a name="_Toc102494866"></a><a
\r
18544 name="_Toc101065330"><span style='mso-bookmark:_Toc102494866'><span
\r
18545 style='mso-bookmark:_Toc235958645'><span lang=AF>-cpu</span></span></span></a></p>
\r
18547 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span
\r
18548 style='mso-spacerun:yes'> </span>deprecated<o:p></o:p></span></p>
\r
18550 <p class=flag><a name="_Toc235958646"></a><a name="_Toc102494867"><span
\r
18551 style='mso-bookmark:_Toc235958646'><span lang=AF>-outseqweight</span></span></a></p>
\r
18553 <p class=MyNormal><span lang=AF>Usage: -outseqweight=<name of the file
\r
18554 containing the weights applied></span></p>
\r
18556 <p class=MyNormal><span lang=AF>Default: -outseqweight=no</span></p>
\r
18558 <p class=MyNormal><span lang=AF>Will cause the program to output the weights
\r
18559 associated with every sequence in the dataset.</span></p>
\r
18561 <p class=flag><a name="_Toc235958647"></a><a name="_Toc102494868"></a><a
\r
18562 name="_Toc101065331"><span style='mso-bookmark:_Toc102494868'><span
\r
18563 style='mso-bookmark:_Toc235958647'><span lang=AF>-outorder [cw]</span></span></span></a></p>
\r
18565 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span
\r
18566 style='mso-spacerun:yes'> </span>-outorder=<input OR aligned OR
\r
18567 filename> <o:p></o:p></span></p>
\r
18569 <p class=instruction><span lang=EN-US>Default:-outorder=input</span></p>
\r
18571 <p class=flagdescription><span lang=EN-US>Sets the order of the sequences in
\r
18572 the output alignment: <b>-outorder=input</b> means the sequences are kept in
\r
18573 the original order. <b>-outorder=aligned</b> means the sequences come in the
\r
18574 order indicated by the tree. This order can be seen as a one-dimensional
\r
18575 projection of the tree distances. <b style='mso-bidi-font-weight:normal'>
\96outdorder=<filename></b>Filename
\r
18576 is a legal fasta file, whose order will be used in the final alignment.</span></p>
\r
18578 <p class=flag><a name="_Toc235958648"><span lang=AF>-inorder [cw]</span></a></p>
\r
18580 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span
\r
18581 style='mso-spacerun:yes'> </span>-inorder=<input OR aligned> <o:p></o:p></span></p>
\r
18583 <p class=instruction><span lang=EN-US>Default:-inorder=aligned</span></p>
\r
18585 <p class=flagdescription><span lang=EN-US>Multiple alignments based on dynamic
\r
18586 programming depend slightly on the order in which the incoming sequences are
\r
18587 provided. To prevent this effect sequences are arbitrarily sorted at the
\r
18588 beginning of the program (-inorder=aligned). However, this affects the sequence
\r
18589 order within the library. You can switch this off by ststing
\96inorder=input.</span></p>
\r
18591 <p class=flag><a name="_Toc235958649"></a><a name="_Toc102494869"><span
\r
18592 style='mso-bookmark:_Toc235958649'><span lang=AF>-seqnos</span></span></a></p>
\r
18594 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span
\r
18595 style='mso-spacerun:yes'> </span>-seqnos=<on or off> <o:p></o:p></span></p>
\r
18597 <p class=instruction><span lang=EN-US>Default:-seqnos=off</span></p>
\r
18599 <p class=MyNormal><span lang=AF>Causes the output alignment to contain residue
\r
18600 numbers at the end of each line:</span></p>
\r
18602 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
\r
18603 mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
\r
18604 background:#E6E6E6'>
\r
18606 <p class=examplefileCxSpFirst><span lang=EN-US>T-COFFEE</span></p>
\r
18608 <p class=examplefileCxSpMiddle><span lang=EN-US>seq1 aaa---aaaa--------aa 9</span></p>
\r
18610 <p class=examplefileCxSpMiddle><span lang=EN-US>seq2 a-----aa-----------a 4</span></p>
\r
18612 <p class=examplefileCxSpMiddle><span lang=EN-US><o:p> </o:p></span></p>
\r
18614 <p class=examplefileCxSpMiddle><span lang=EN-US>seq1 a-----------------a 11</span></p>
\r
18616 <p class=examplefileCxSpLast><span lang=EN-US>seq2 aaaaaaaaaaaaaaaaaaa 19</span></p>
\r
18620 <h3><a name="_Toc235958650"></a><a name="_Toc102494870"></a><a
\r
18621 name="_Toc102494390"></a><a name="_Toc101065332"><span style='mso-bookmark:
\r
18622 _Toc102494390'><span style='mso-bookmark:_Toc102494870'><span style='mso-bookmark:
\r
18623 _Toc235958650'><span lang=EN-US>Libraries</span></span></span></span></a></h3>
\r
18625 <p class=MyNormal><span lang=AF>Although, it does not necessarily do so
\r
18626 explicitly, T-Coffee always end up combining libraries. Libraries are
\r
18627 collections of pairs of residues. Given a set of libraries, T-Coffee makes an
\r
18628 attempt to assemble the alignment with the highest level of consistence. You
\r
18629 can think of the alignment as a timetable. Each library pair would be a request
\r
18630 from students or teachers, and the job of T-Coffee would be to assemble the
\r
18631 time table that makes as many people as possible happy
\85</span></p>
\r
18633 <p class=flag><a name="_Toc235958651"></a><a name="_Toc102494871"><span
\r
18634 style='mso-bookmark:_Toc235958651'><span lang=AF>-out_lib</span></span></a></p>
\r
18636 <p class=MyNormal><span lang=AF>Usage:<span style='mso-spacerun:yes'>
\r
18637 </span>-out_lib=<name of the library,default,no> </span></p>
\r
18639 <p class=MyNormal><span lang=AF>Default:-out_lib=default</span></p>
\r
18641 <p class=MyNormal><span lang=AF><o:p> </o:p></span></p>
\r
18643 <p class=flagdescription><span lang=EN-US>Sets the name of the library output.
\r
18644 Default implies <run_name>.tc_lib</span></p>
\r
18646 <p class=flag><a name="_Toc235958652"></a><a name="_Toc102494872"></a><a
\r
18647 name="_Toc101065333"><span style='mso-bookmark:_Toc102494872'><span
\r
18648 style='mso-bookmark:_Toc235958652'><span lang=AF>-lib_only</span></span></span></a></p>
\r
18650 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:<span
\r
18651 style='mso-spacerun:yes'> </span>-lib_only<o:p></o:p></span></p>
\r
18653 <p class=instruction><span lang=EN-US>Default: unset</span></p>
\r
18655 <p class=flagdescription><span lang=EN-US>Causes the program to stop once the
\r
18656 library has been computed. Must be used in conjunction with the flag <b
\r
18657 style='mso-bidi-font-weight:normal'>
\96out_lib</b></span></p>
\r
18659 <h3><a name="_Toc235958653"></a><a name="_Toc102494873"></a><a
\r
18660 name="_Toc102494391"></a><a name="_Toc101065334"><span style='mso-bookmark:
\r
18661 _Toc102494391'><span style='mso-bookmark:_Toc102494873'><span style='mso-bookmark:
\r
18662 _Toc235958653'><span lang=EN-US>Trees</span></span></span></span></a></h3>
\r
18664 <p class=flag><a name="_Toc235958654"></a><a name="_Toc102494874"></a><a
\r
18665 name="_Toc101065335"><span style='mso-bookmark:_Toc102494874'><span
\r
18666 style='mso-bookmark:_Toc235958654'><span lang=AF>-newtree</span></span></span></a></p>
\r
18668 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:
\r
18669 -newtree=<tree file><o:p></o:p></span></p>
\r
18671 <p class=instruction><span lang=EN-US>Default: No file specified</span></p>
\r
18673 <p class=flagdescription><span lang=EN-US>Indicates the name of the file into
\r
18674 which the guide tree will be written. The default will be
\r
18675 <sequence_name>.dnd, or <run_name.dnd>. The tree is written in the
\r
18676 parenthesis format known as newick or <st1:place w:st="on"><st1:State w:st="on">New
\r
18677 Hampshire</st1:State></st1:place> and used by Phylips (see the format
\r
18678 section).</span></p>
\r
18680 <div style='mso-element:para-border-div;border:solid windowtext 1.5pt;
\r
18681 padding:0mm 0mm 0mm 0mm;background:#F7CBB7'>
\r
18683 <p class=Warning><span lang=EN-US>Do NOT confuse this guide tree with a
\r
18684 phylogenetic tree.</span></p>
\r
18688 <h2><a name="_Toc235958655"></a><a name="_Toc102494875"></a><a
\r
18689 name="_Toc102494392"></a><a name="_Toc101065336"><span style='mso-bookmark:
\r
18690 _Toc102494392'><span style='mso-bookmark:_Toc102494875'><span style='mso-bookmark:
\r
18691 _Toc235958655'><span lang=EN-US>Reliability Estimation</span></span></span></span></a></h2>
\r
18693 <h3><a name="_Toc235958656"></a><a name="_Toc102494876"></a><a
\r
18694 name="_Toc102494393"></a><a name="_Toc101065337"><span style='mso-bookmark:
\r
18695 _Toc102494393'><span style='mso-bookmark:_Toc102494876'><span style='mso-bookmark:
\r
18696 _Toc235958656'><span lang=EN-US>CORE Computation</span></span></span></span></a></h3>
\r
18698 <p class=MyNormal><span lang=AF>The CORE is an index that indicates the
\r
18699 consistency between the library of piarwise alignments and the final multiple
\r
18700 alignment. Our experiment indicate that the higher this consistency, the more
\r
18701 reliable the alignment. A publication describing the CORE index can be found
\r
18704 <p class=MyNormal><a name="_Toc102494877"></a><a name="_Toc101065338"><span
\r
18705 style='mso-bookmark:_Toc102494877'></span></a><a
\r
18706 href="http://www.tcoffee.org/Publications/Pdf/core.pp.pdf"><span
\r
18707 style='mso-bookmark:_Toc101065338'><span style='mso-bookmark:_Toc102494877'><span
\r
18708 lang=EN-US style='mso-ansi-language:EN-US'>http://www.tcoffee.org/Publications/Pdf/core.pp.pdf</span></span></span><span
\r
18709 style='mso-bookmark:_Toc101065338'><span style='mso-bookmark:_Toc102494877'></span></span></a><span
\r
18710 style='mso-bookmark:_Toc101065338'><span style='mso-bookmark:_Toc102494877'></span></span></p>
\r
18712 <p class=flag><span style='mso-bookmark:_Toc101065338'><span style='mso-bookmark:
\r
18713 _Toc102494877'><a name="_Toc235958657"><span lang=AF>-evaluate_mode</span></a></span></span></p>
\r
18715 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:
\r
18716 -evaluate_mode=<t_coffee_fast,t_coffee_slow,t_coffee_non_extended ><o:p></o:p></span></p>
\r
18718 <p class=instruction><span lang=EN-US>Default: -evaluate_mode=t_coffee_fast</span></p>
\r
18720 <p class=flagdescription><span lang=EN-US>This flag indicates the mode used to
\r
18721 normalize the t_coffee score when computing the reliability score. </span></p>
\r
18723 <p class=flagdescription><i style='mso-bidi-font-style:normal'><span
\r
18724 lang=EN-US>t_coffee_fast</span></i><span lang=EN-US>: Normalization is made
\r
18725 using the highest score in the MSA. This evaluation mode was validated and in
\r
18726 our hands, pairs of residues with a score of 5 or higher have 90 % chances to
\r
18727 be correctly aligned to one another. </span></p>
\r
18729 <p class=flagdescription><i style='mso-bidi-font-style:normal'><span
\r
18730 lang=EN-US>t_coffee_slow:</span></i><span lang=EN-US> Normalization is made
\r
18731 using the library. This usually results in lower score and a scoring scheme
\r
18732 more sensitive to the number of sequences in the dataset. Note that this
\r
18733 scoring scheme is not any more slower, thanks to the implementation of a faster
\r
18734 heuristic algorithm. </span></p>
\r
18736 <p class=flagdescription><i style='mso-bidi-font-style:normal'><span
\r
18737 lang=EN-US>t_coffee_non_extended:</span></i><span lang=EN-US> the score of each
\r
18738 residue is the ratio between the sum of its non extended scores with the column
\r
18739 and the sum of all its possible non extended scores.</span></p>
\r
18741 <p class=flagdescription><span lang=EN-US>These modes will be useful when
\r
18742 generating colored version of the output, with the <b style='mso-bidi-font-weight:
\r
18743 normal'>
\96output</b> flag:</span></p>
\r
18745 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
18746 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
18747 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
18748 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
18750 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:
\r
18751 t_coffee sample_seq1.fasta
\96evaluate_mode t_coffee_slow
\96output score_ascii,
\r
18752 score_html </span></p>
\r
18754 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:
\r
18755 t_coffee sample_seq1.fasta
\96evaluate_mode t_coffee_fast
\96output score_ascii,
\r
18756 score_html </span></p>
\r
18758 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:
\r
18759 t_coffee sample_seq1.fasta
\96evaluate_mode t_coffee_non_extended
\96output
\r
18760 score_ascii, score_html </span></p>
\r
18764 <h2><a name="_Toc235958658"></a><a name="_Toc102494878"></a><a
\r
18765 name="_Toc102494394"></a><a name="_Toc101065339"><span style='mso-bookmark:
\r
18766 _Toc102494394'><span style='mso-bookmark:_Toc102494878'><span style='mso-bookmark:
\r
18767 _Toc235958658'><span lang=EN-US>Generic Output</span></span></span></span></a></h2>
\r
18769 <p class=flag><a name="_Toc235958659"></a><a name="_Toc102494879"><span
\r
18770 style='mso-bookmark:_Toc235958659'><span lang=AF>-run_name</span></span></a></p>
\r
18772 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:
\r
18773 -run_name=<your run name><o:p></o:p></span></p>
\r
18775 <p class=instruction><span lang=EN-US>Default: no default set</span></p>
\r
18777 <p class=MyNormal><span lang=AF>This flag causes the prefix <your
\r
18778 sequences> to be replaced by <your run name> when renaming the default
\r
18779 output files.</span></p>
\r
18781 <p class=flag><a name="_Toc235958660"></a><a name="_Toc102494880"></a><a
\r
18782 name="_Toc101065340"><span style='mso-bookmark:_Toc102494880'><span
\r
18783 style='mso-bookmark:_Toc235958660'><span lang=AF>-quiet</span></span></span></a></p>
\r
18785 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:
\r
18786 -quiet=<stderr,stdout,file name OR nothing>.<o:p></o:p></span></p>
\r
18788 <p class=instruction><span lang=EN-US>Default:-quiet=stderr</span></p>
\r
18790 <p class=flagdescription><span lang=EN-US>Redirects the standard output to
\r
18791 either a file. <b>-quiet</b> on its own redirect the output to /dev/null.</span></p>
\r
18793 <p class=flag><a name="_Toc235958661"></a><a name="_Toc102494881"><span
\r
18794 style='mso-bookmark:_Toc235958661'><span lang=AF>-align [CW]</span></span></a></p>
\r
18796 <p class=MyNormal><span lang=AF>This flag indicates that the program must
\r
18797 produce the alignment. It is here for compatibility with ClustalW.</span></p>
\r
18799 <h2><a name="_Toc235958662"><span lang=EN-US>APDB, iRMSD and tRMSD Parameters</span></a></h2>
\r
18801 <p class=MyNormal><span lang=AF><o:p> </o:p></span></p>
\r
18803 <div style='mso-element:para-border-div;border:solid windowtext 1.5pt;
\r
18804 padding:0mm 0mm 0mm 0mm;background:#F7CBB7'>
\r
18806 <p class=Warning><span lang=EN-US>Warning: These flags will only work within
\r
18807 the APDB package that can be invoked via the
\96other_pg parameter of T-Coffee:</span></p>
\r
18809 <p class=Warning><span lang=EN-US><span style='mso-tab-count:2'> </span><span
\r
18810 style='mso-spacerun:yes'> </span>t_coffee
\96other_pg apdb
\96aln <your aln></span></p>
\r
18812 <p class=Warning><span lang=EN-US><o:p> </o:p></span></p>
\r
18816 <p class=flag><a name="_Toc235958663"><span lang=AF>-quiet [Same as T-Coffee]</span></a></p>
\r
18818 <p class=flag><a name="_Toc235958664"><span lang=AF>-run_name [Same as
\r
18819 T-Coffee]</span></a></p>
\r
18821 <p class=flag><a name="_Toc235958665"><span lang=AF>-aln</span></a></p>
\r
18823 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:
\r
18824 -aln=<file_name>.<o:p></o:p></span></p>
\r
18826 <p class=instruction><span lang=EN-US>Default:none</span></p>
\r
18828 <p class=flagdescription><span lang=EN-US>Indicates the name of the file
\r
18829 containing the sequences that need to be evaluated. The sequences whose
\r
18830 structure is meant to be used must be named according to their PDB identifier. </span></p>
\r
18832 <p class=flagdescription><span lang=EN-US>The format can be FASTA, CLUSTAL or
\r
18833 any of the formats supported by T-Coffee. APDB only evaluates residues in
\r
18834 capital and ignores those in lower case. If your sequences are in lower case,
\r
18835 you can upper case them using seq_reformat:</span></p>
\r
18837 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
18838 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
18839 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
18840 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
18842 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:
\r
18843 t_coffee
\96other_pg seq_reformat
\96in 3d_sample4.aln
\96action +upper
\96output
\r
18844 clustalw > 3d_sample4.cw_aln</span></p>
\r
18848 <p class=flagdescription><span lang=EN-US>The alignment can then be evaluated
\r
18849 using the defaultr of APDB:</span></p>
\r
18851 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
18852 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
18853 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
18854 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
18856 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:
\r
18857 t_coffee
\96other_pg apdb
\96aln 3d_sample4.aln</span></p>
\r
18861 <p class=flagdescription><span lang=EN-US>The alignment can contain as many
\r
18862 structures as you wish.</span></p>
\r
18864 <p class=flag><a name="_Toc235958666"><span lang=AF>-n_excluded_nb</span></a></p>
\r
18866 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:
\r
18867 -n_excluded_nb=<integer>.<o:p></o:p></span></p>
\r
18869 <p class=instruction><span lang=EN-US>Default:1</span></p>
\r
18871 <p class=flagdescription><span lang=EN-US>When evaluating the local score of a
\r
18872 pair of aligned residues, the residues immediately next to that column should
\r
18873 not contribute to the measure. By default the first to the left and first to
\r
18874 the right are excluded.</span></p>
\r
18876 <p class=flag><a name="_Toc235958667"><span lang=AF>-maximum_distance</span></a></p>
\r
18878 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:
\r
18879 -maximum_distance=<float>.<o:p></o:p></span></p>
\r
18881 <p class=instruction><span lang=EN-US>Default:10</span></p>
\r
18883 <p class=flagdescription><span lang=EN-US>Size of the neighborhood considered
\r
18884 around every residue. If .-local_mode is set to sphere, -maximum_distance is
\r
18885 the radius of a sphere centered around each residue. If
\96local_mode is set to
\r
18886 window, then
\96maximum_distance is the size of the half window (i.e.
\r
18887 window_size=-maximum_distance*2+1).</span></p>
\r
18889 <p class=flag><a name="_Toc235958668"><span lang=AF>-similarity_threshold</span></a></p>
\r
18891 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:
\r
18892 -similarity_threshold=<integer>.<o:p></o:p></span></p>
\r
18894 <p class=instruction><span lang=EN-US>Default:70</span></p>
\r
18896 <p class=flagdescription><span lang=EN-US>Fraction of the neighborhood that
\r
18897 must be supportive for a pair of residue to be considered correct in APDB. The
\r
18898 neighborhood is a sphere defined by
\96maximum_distance, and the support is
\r
18899 defined by
\96md_threshold.</span></p>
\r
18901 <p class=flag><a name="_Toc235958669"><span lang=AF>-local_mode</span></a></p>
\r
18903 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:
\r
18904 -local_mode=<sphere,window>.<o:p></o:p></span></p>
\r
18906 <p class=instruction><span lang=EN-US>Default:sphere</span></p>
\r
18908 <p class=flagdescription><span lang=EN-US>Defines the shape of a neighborhood,
\r
18909 either as a sphere or as a window.</span></p>
\r
18911 <p class=flag><a name="_Toc235958670"><span lang=AF>-filter</span></a></p>
\r
18913 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:
\r
18914 -filter=<0.00-1.00>.<o:p></o:p></span></p>
\r
18916 <p class=instruction><span lang=EN-US>Default:1.00</span></p>
\r
18918 <p class=flagdescription><span lang=EN-US>Defines the centiles that should be
\r
18919 kept when making the local measure. Foir instance, -filter=0.90 means that the
\r
18920 the 10 last centiles will be removed from the evaluation. The filtration is
\r
18921 carried out on the iRMSD values.</span></p>
\r
18923 <p class=flag><a name="_Toc235958671"><span lang=AF>-print_rapdb [Unsupported]</span></a></p>
\r
18925 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:
\r
18926 -print_rapdb (FLAG)<o:p></o:p></span></p>
\r
18928 <p class=instruction><span lang=EN-US>Default:off</span></p>
\r
18930 <p class=flagdescription><span lang=EN-US>This causes the prints out of the
\r
18931 exact neighborhood of every considered pair of residues.</span></p>
\r
18933 <p class=flag><a name="_Toc235958672"><span lang=AF>-outfile [Same as T-Coffee]</span></a></p>
\r
18935 <p class=MyNormal><span lang=AF>This flag is meant to control the output name
\r
18936 of the colored APDB output. This file will either display the local APDB score
\r
18937 or the local iRMD, depending on the value of
\96color_mode. The default format is
\r
18938 defined by
\96ouptut and is score_html.</span></p>
\r
18940 <p class=flag><a name="_Toc235958673"><span lang=AF>-color_mode</span></a></p>
\r
18942 <p class=flagusage><span lang=EN-US style='mso-ansi-language:EN-US'>Usage:
\r
18943 -color_mode=<apdb, irmsd><o:p></o:p></span></p>
\r
18945 <p class=instruction><span lang=EN-US>Default:apdb</span></p>
\r
18947 <p class=MyNormal><span lang=AF>This flag is meant to control the colored APDB
\r
18948 output (local score). This file will either display the local APDB score or the
\r
18949 local iRMD.</span></p>
\r
18951 <div style='mso-element:para-border-div;border:solid windowtext 3.0pt;
\r
18952 padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#CCCCCC;margin-left:0mm;margin-right:
\r
18955 <p class=ChapterTitle><a name="_Toc235958674"><span lang=EN-US>Building a
\r
18956 Server</span></a></p>
\r
18960 <p class=MyNormal><span lang=AF>We maintain a T-Coffee server (www.tcoffee.org).
\r
18961 We will be pleased to provide anyone who wants to set up a similar service with
\r
18962 the sources</span></p>
\r
18964 <h3><a name="_Toc102494884"></a><a name="_Toc102494396"></a><a
\r
18965 name="_Toc235958675"><span style='mso-bookmark:_Toc102494396'><span
\r
18966 style='mso-bookmark:_Toc102494884'><span lang=EN-US>Environment Variables</span></span></span></a><span
\r
18967 style='mso-bookmark:_Toc102494396'><span style='mso-bookmark:_Toc102494884'></span></span></h3>
\r
18969 <p class=MyNormal><span style='mso-bookmark:_Toc102494396'><span
\r
18970 style='mso-bookmark:_Toc102494884'><span lang=AF>T-Coffee stores a lots of
\r
18971 information in locations that may be unsuitable when running a server. </span></span></span></p>
\r
18973 <p class=MyNormal><span style='mso-bookmark:_Toc102494396'><span
\r
18974 style='mso-bookmark:_Toc102494884'><span lang=AF>By default, T-Coffee will
\r
18975 generate and rely on the follwing directory structure:</span></span></span></p>
\r
18977 <p class=example><span style='mso-bookmark:_Toc102494396'><span
\r
18978 style='mso-bookmark:_Toc102494884'><span lang=EN-US>/home/youraccount/<span
\r
18979 style='mso-tab-count:2'> </span>#HOME_4_TCOFFEE</span></span></span></p>
\r
18981 <p class=example><span style='mso-bookmark:_Toc102494396'><span
\r
18982 style='mso-bookmark:_Toc102494884'><span lang=EN-US>HOME_4_TCOFFEE/.t_coffee/ <span
\r
18983 style='mso-tab-count:1'> </span>#DIR_4_TCOFFEE</span></span></span></p>
\r
18985 <p class=example><span style='mso-bookmark:_Toc102494396'><span
\r
18986 style='mso-bookmark:_Toc102494884'><span lang=EN-US>DIR_4_TCOFFEE/cache<span
\r
18987 style='mso-tab-count:2'> </span>#CACHE_4_TCOFFEE</span></span></span></p>
\r
18989 <p class=example><span style='mso-bookmark:_Toc102494396'><span
\r
18990 style='mso-bookmark:_Toc102494884'><span lang=EN-US>DIR_4_TCOFFEE/tmp<span
\r
18991 style='mso-tab-count:2'> </span>#TMP_4_TCOFFEE</span></span></span></p>
\r
18993 <p class=example><span style='mso-bookmark:_Toc102494396'><span
\r
18994 style='mso-bookmark:_Toc102494884'><span lang=EN-US>DIR_4_TCOFFEE/methods<span
\r
18995 style='mso-tab-count:2'> </span>#METHOS_4_TCOFFEE</span></span></span></p>
\r
18997 <p class=example><span style='mso-bookmark:_Toc102494396'><span
\r
18998 style='mso-bookmark:_Toc102494884'><span lang=EN-US>DIR_4_TCOFFEE/mcoffee<span
\r
18999 style='mso-tab-count:2'> </span>#MCOFFEE_4_TCOFFEE</span></span></span></p>
\r
19001 <p class=MyNormal><span style='mso-bookmark:_Toc102494396'><span
\r
19002 style='mso-bookmark:_Toc102494884'><span lang=AF><o:p> </o:p></span></span></span></p>
\r
19004 <p class=MyNormal><span style='mso-bookmark:_Toc102494396'><span
\r
19005 style='mso-bookmark:_Toc102494884'><span lang=AF>By default, all these
\r
19006 directories are automatically created, following the dependencies suggested
\r
19007 here. </span></span></span></p>
\r
19009 <p class=MyNormal><span style='mso-bookmark:_Toc102494396'><span
\r
19010 style='mso-bookmark:_Toc102494884'><span lang=AF>The first step is the
\r
19011 determination of the HOME. By default the program tries to use HOME_4_TCOFFEE,
\r
19012 then the HOME variable and TMP or TEMP if HOME is not set on your system or
\r
19013 your account. It is your responsibility to make sure that one of these
\r
19014 variables is set to some valid location where the T-Coffee process is allowed
\r
19015 to read and write.</span></span></span></p>
\r
19017 <p class=MyNormal><span style='mso-bookmark:_Toc102494396'><span
\r
19018 style='mso-bookmark:_Toc102494884'><span lang=AF>If no valid location can be
\r
19019 found for HOME_4_TCOFFEE, the program exits. If you are running T-Coffee on a
\r
19020 server, we recommend to hard set the following locations, where your scratch is
\r
19021 a valid location. </span></span></span></p>
\r
19023 <p class=MyNormal><span style='mso-bookmark:_Toc102494396'><span
\r
19024 style='mso-bookmark:_Toc102494884'><span lang=AF><o:p> </o:p></span></span></span></p>
\r
19026 <p class=example><span style='mso-bookmark:_Toc102494396'><span
\r
19027 style='mso-bookmark:_Toc102494884'><span lang=EN-US>HOME_4_TCOFFEE=
\94your scratch
\94</span></span></span></p>
\r
19029 <p class=example><span style='mso-bookmark:_Toc102494396'><span
\r
19030 style='mso-bookmark:_Toc102494884'><span lang=EN-US>TMP_4_TCOFFEE=
\94your
\r
19031 scratch
\94</span></span></span></p>
\r
19033 <p class=example><span style='mso-bookmark:_Toc102494396'><span
\r
19034 style='mso-bookmark:_Toc102494884'><span lang=EN-US>DIR_4_TCOFFEE=
\94your
\r
19035 scratch
\94</span></span></span></p>
\r
19037 <p class=example><span style='mso-bookmark:_Toc102494396'><span
\r
19038 style='mso-bookmark:_Toc102494884'><span lang=EN-US>CACHE_4_TCOFFEE=
\94your
\r
19039 scratch
\94</span></span></span></p>
\r
19041 <p class=example><span style='mso-bookmark:_Toc102494396'><span
\r
19042 style='mso-bookmark:_Toc102494884'><span lang=EN-US>NO_ERROR_REPORT_4_TCOFFEE=1</span></span></span></p>
\r
19044 <p class=MyNormal><span style='mso-bookmark:_Toc102494396'><span
\r
19045 style='mso-bookmark:_Toc102494884'><span lang=AF>Note that<span
\r
19046 style='mso-spacerun:yes'> </span>it is a good idea to have a cron job that
\r
19047 cleans up this scratch area, once in a while. </span></span></span></p>
\r
19049 <p class=MyNormal><span style='mso-bookmark:_Toc102494396'><span
\r
19050 style='mso-bookmark:_Toc102494884'><span lang=AF><o:p> </o:p></span></span></span></p>
\r
19052 <h3><span style='mso-bookmark:_Toc102494396'><span style='mso-bookmark:_Toc102494884'><a
\r
19053 name="_Toc235958676"><span lang=EN-US>Output of the .dnd file.</span></a></span></span></h3>
\r
19055 <p class=MyNormal><span lang=AF>A common source of error when running a server:
\r
19056 T-Coffee MUST output the .dnd file because it re-reads it to carry out the
\r
19057 progressive alignment. By default T-Coffee outputs this file in the directory
\r
19058 where the process is running. If the T-Coffee process does not have permission
\r
19059 to write in that directory, the computation will abort...</span></p>
\r
19061 <p class=MyNormal><span lang=AF>To avoid this, simply specify the name of the
\r
19062 output tree: </span></p>
\r
19064 <p class=MyNormal><span lang=AF><span style='mso-tab-count:1'> </span>-newtree=<writable
\r
19065 file (usually in /tmp)></span></p>
\r
19067 <p class=MyNormal><span lang=AF>Chose the name so that two processes may not
\r
19068 over-write each other dnd file. </span></p>
\r
19070 <h3><a name="_Toc235958677"></a><a name="_Toc102494885"></a><a
\r
19071 name="_Toc102494397"><span style='mso-bookmark:_Toc102494885'><span
\r
19072 style='mso-bookmark:_Toc235958677'><span lang=EN-US>Permissions</span></span></span></a></h3>
\r
19074 <p class=MyNormal><span lang=AF>The t_coffee process MUST be allowed to write
\r
19075 in some scratch area, even when it is ran by Mr nobody... Make sure the /tmp/
\r
19076 partition is not protected.</span></p>
\r
19078 <h3><a name="_Toc235958678"></a><a name="_Toc102494886"></a><a
\r
19079 name="_Toc102494398"><span style='mso-bookmark:_Toc102494886'><span
\r
19080 style='mso-bookmark:_Toc235958678'><span lang=EN-US>Other Programs</span></span></span></a></h3>
\r
19082 <p class=MyNormal><span lang=AF>T-Coffee may call various programs while it
\r
19083 runs (lalign2list by defaults). Make sure your process knows where to find
\r
19084 these executables.</span></p>
\r
19086 <div style='mso-element:para-border-div;border:solid windowtext 3.0pt;
\r
19087 padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#CCCCCC;margin-left:0mm;margin-right:
\r
19090 <p class=ChapterTitle><a name="_Toc235958679"></a><a name="_Toc102494887"></a><a
\r
19091 name="_Toc101065353"><span style='mso-bookmark:_Toc102494887'><span
\r
19092 style='mso-bookmark:_Toc235958679'><span lang=EN-US>F</span></span></span></a><span
\r
19093 style='mso-bookmark:_Toc235958679'><span lang=EN-US>ormats</span></span></p>
\r
19097 <h2><a name="_Toc235958680"></a><a name="_Toc102494888"></a><a
\r
19098 name="_Toc102494399"></a><a name="_Toc101065354"><span style='mso-bookmark:
\r
19099 _Toc102494399'><span style='mso-bookmark:_Toc102494888'><span style='mso-bookmark:
\r
19100 _Toc235958680'><span lang=EN-US>Parameter files</span></span></span></span></a></h2>
\r
19102 <p class=MyNormal><span lang=AF>Parameter files used with -parameters,
\r
19103 -t_coffee_defaults, -dali_defaults... Must contain a valid parameter string
\r
19104 where line breaks are allowed. These files cannot contain any comment, the
\r
19105 recommended format is one parameter per line:</span></p>
\r
19107 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
\r
19108 mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
\r
19109 background:#E6E6E6'>
\r
19111 <p class=examplefileCxSpFirst><span lang=EN-US><span style='mso-tab-count:1'> </span><parameter
\r
19112 name>=<value1>,<value2>....</span></p>
\r
19114 <p class=examplefileCxSpLast><span lang=EN-US><span style='mso-tab-count:1'> </span><parameter
\r
19115 name>=.....</span></p>
\r
19119 <h2><a name="_Toc235958681"></a><a name="_Toc102494889"></a><a
\r
19120 name="_Toc102494400"></a><a name="_Toc101065355"><span style='mso-bookmark:
\r
19121 _Toc102494400'><span style='mso-bookmark:_Toc102494889'><span style='mso-bookmark:
\r
19122 _Toc235958681'><span lang=EN-US>Sequence Name Handling</span></span></span></span></a></h2>
\r
19124 <p class=MyNormal><span lang=AF>Sequence name handling is meant to be fully
\r
19125 consistent with ClustalW (Version 1.75). This implies that in some cases the
\r
19126 names of your sequences may be edited when coming out of the program. Five
\r
19127 rules apply:</span></p>
\r
19129 <p class=MyNormal><span lang=AF><o:p> </o:p></span></p>
\r
19131 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
\r
19132 mso-border-alt:solid windowtext .5pt;padding:1.0pt 1.0pt 1.0pt 1.0pt'>
\r
19134 <p class=Noteboxtitle style='border:none;mso-border-alt:solid windowtext .5pt;
\r
19135 padding:0mm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'><span lang=EN-US>Naming
\r
19136 Your Sequences the <st1:Street w:st="on"><st1:address w:st="on">Right Way</st1:address></st1:Street></span></p>
\r
19138 <p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;
\r
19139 padding:0mm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'><span lang=EN-US>1-No
\r
19142 <p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;
\r
19143 padding:0mm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'><span lang=EN-US>Names
\r
19144 that do contain spaces, for instance:</span></p>
\r
19146 <p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;
\r
19147 padding:0mm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'><span lang=EN-US><span
\r
19148 style='mso-tab-count:1'> </span>>seq1 human_myc</span></p>
\r
19150 <p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;
\r
19151 padding:0mm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'><span lang=EN-US>will be
\r
19152 turned into</span></p>
\r
19154 <p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;
\r
19155 padding:0mm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'><span lang=EN-US><span
\r
19156 style='mso-tab-count:1'> </span>>seq1</span></p>
\r
19158 <p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;
\r
19159 padding:0mm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'><span lang=EN-US>It is
\r
19160 your responsibility to make sure that the names you provide are not ambiguous
\r
19161 after such an editing. This editing is consistent with Clustalw (Version 1.75)</span></p>
\r
19163 <p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;
\r
19164 padding:0mm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'><span lang=EN-US><o:p> </o:p></span></p>
\r
19166 <p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;
\r
19167 padding:0mm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'><span lang=EN-US>2-No
\r
19168 Strange Character</span></p>
\r
19170 <p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;
\r
19171 padding:0mm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'><span lang=EN-US>Some non
\r
19172 alphabetical characters are replaced with underscores. These are: ';:()'</span></p>
\r
19174 <p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;
\r
19175 padding:0mm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'><span lang=EN-US>Other
\r
19176 characters are legal and will be kept unchanged. This editing is meant to keep
\r
19177 in line with Clustalw (Version 1.75).</span></p>
\r
19179 <p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;
\r
19180 padding:0mm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'><span lang=EN-US><o:p> </o:p></span></p>
\r
19182 <p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;
\r
19183 padding:0mm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'><span lang=EN-US>3-> is
\r
19184 NEVER legal (except as a header token in a FASTA file)</span></p>
\r
19186 <p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;
\r
19187 padding:0mm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'><span lang=EN-US><o:p> </o:p></span></p>
\r
19189 <p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;
\r
19190 padding:0mm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'><span lang=EN-US>4-Name
\r
19191 length must be below 100 characters, although 15 is recommended for
\r
19192 compatibility with other programs.</span></p>
\r
19194 <p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;
\r
19195 padding:0mm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'><span lang=EN-US>5-Duplicated
\r
19196 sequences will be renamed (i.e. sequences with the same name in the same
\r
19197 dataset) are allowed but will be renamed according to their original order.
\r
19198 When sequences come from multiple sources via the
\96in flag, consistency of the
\r
19199 renaming is not guaranteed. You should avoid duplicated sequences as they will
\r
19200 cause your input to differ from your output thus making it difficult to track
\r
19205 <h2><a name="_Toc235958682"></a><a name="_Toc102494890"></a><a
\r
19206 name="_Toc102494401"></a><a name="_Toc101065356"><span style='mso-bookmark:
\r
19207 _Toc102494401'><span style='mso-bookmark:_Toc102494890'><span style='mso-bookmark:
\r
19208 _Toc235958682'><span lang=EN-US>Automatic Format Recognition</span></span></span></span></a></h2>
\r
19210 <p class=MyNormal><span lang=AF>Most common formats are automatically
\r
19211 recognized by t_coffee. See -in and the next section for more details. If your
\r
19212 format is not recognized, use readseq or clustalw to switch to another format.
\r
19213 We recommend Fasta.</span></p>
\r
19215 <h2><a name="_Toc235958683"></a><a name="_Toc102494891"></a><a
\r
19216 name="_Toc102494402"></a><a name="_Toc101065357"><span style='mso-bookmark:
\r
19217 _Toc102494402'><span style='mso-bookmark:_Toc102494891'><span style='mso-bookmark:
\r
19218 _Toc235958683'><span lang=EN-US>Structures</span></span></span></span></a></h2>
\r
19220 <p class=MyNormal><span lang=AF>PDB format is recognized by T-Coffee. T-Coffee
\r
19221 uses extract_from_pdb (cf
\96other_pg flag). extract_from_pdb is a small embeded
\r
19222 module that can be used on its own to extract information from pdb files.</span></p>
\r
19224 <h2><a name="_Toc235958684"><span lang=EN-US>RNA Structures</span></a></h2>
\r
19226 <p class=MyNormal><span lang=AF>RNA structures can either be coded as T-Coffee
\r
19227 libraries, with each line indicating two paired residues, or as alifold output.
\r
19228 The selex format is also partly supported (see the seq_reformat tutorial on RNA
\r
19229 sequences handling).</span></p>
\r
19231 <h2><a name="_Toc235958685"></a><a name="_Toc102494892"></a><a
\r
19232 name="_Toc102494403"></a><a name="_Toc101065358"><span style='mso-bookmark:
\r
19233 _Toc102494403'><span style='mso-bookmark:_Toc102494892'><span style='mso-bookmark:
\r
19234 _Toc235958685'><span lang=EN-US>Sequences</span></span></span></span></a></h2>
\r
19236 <p class=MyNormal><span lang=AF>Sequences can come in the following formats:
\r
19237 fasta, pir, swiss-prot, clustal aln, msf aln and t_coffee aln. These formats
\r
19238 are the one automatically recognized. Please replace the '*' sign sometimes
\r
19239 used for stop codons with an X.</span></p>
\r
19241 <h2><a name="_Toc235958686"></a><a name="_Toc102494893"></a><a
\r
19242 name="_Toc102494404"></a><a name="_Toc101065359"><span style='mso-bookmark:
\r
19243 _Toc102494404'><span style='mso-bookmark:_Toc102494893'><span style='mso-bookmark:
\r
19244 _Toc235958686'><span lang=EN-US>Alignments</span></span></span></span></a></h2>
\r
19246 <p class=MyNormal><span lang=AF>Alignments can come in the following formats:
\r
19247 msf, ClustalW, Fasta, Pir and t_coffee. The t_coffee format is very similar to
\r
19248 the ClustalW format, but slightly more flexible. Any interleaved format with
\r
19249 sequence name on each line will be correctly parsed:</span></p>
\r
19251 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
\r
19252 mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
\r
19253 background:#E6E6E6'>
\r
19255 <p class=examplefileCxSpFirst><span lang=EN-US><empy line> <span
\r
19256 style='mso-tab-count:1'> </span>[Facultative]n</span></p>
\r
19258 <p class=examplefileCxSpMiddle><span lang=EN-US><line of text> <span
\r
19259 style='mso-tab-count:1'> </span>[Required]</span></p>
\r
19261 <p class=examplefileCxSpMiddle><span lang=EN-US><line of text><span
\r
19262 style='mso-tab-count:3'> </span>[Facultative]n</span></p>
\r
19264 <p class=examplefileCxSpMiddle><span lang=EN-US><empty line><span
\r
19265 style='mso-tab-count:3'> </span>[Required]</span></p>
\r
19267 <p class=examplefileCxSpMiddle><span lang=EN-US><empty line><span
\r
19268 style='mso-tab-count:3'> </span>[Facultative]n</span></p>
\r
19270 <p class=examplefileCxSpMiddle><span lang=EN-US><seq1
\r
19271 name><space><seq1></span></p>
\r
19273 <p class=examplefileCxSpMiddle><span lang=EN-US><seq2
\r
19274 name><space><seq2></span></p>
\r
19276 <p class=examplefileCxSpMiddle><span lang=EN-US><seq3
\r
19277 name><space><seq3></span></p>
\r
19279 <p class=examplefileCxSpMiddle><span lang=EN-US><empty line><span
\r
19280 style='mso-tab-count:3'> </span>[Required]</span></p>
\r
19282 <p class=examplefileCxSpMiddle><span lang=EN-US><empty line><span
\r
19283 style='mso-tab-count:3'> </span>[Facultative]n</span></p>
\r
19285 <p class=examplefileCxSpMiddle><span lang=EN-US><seq1
\r
19286 name><space><seq1></span></p>
\r
19288 <p class=examplefileCxSpMiddle><span lang=EN-US><seq2
\r
19289 name><space><seq2></span></p>
\r
19291 <p class=examplefileCxSpMiddle><span lang=EN-US><seq3
\r
19292 name><space><seq3></span></p>
\r
19294 <p class=examplefileCxSpMiddle><span lang=EN-US><empty line><span
\r
19295 style='mso-tab-count:3'> </span>[Required]</span></p>
\r
19297 <p class=examplefileCxSpLast><span lang=EN-US><empty line><span
\r
19298 style='mso-tab-count:3'> </span>[Facultative]n</span></p>
\r
19302 <p class=MyNormal><span lang=AF>An empty line is a line that does NOT contain
\r
19303 amino-acid. A line that contains the ClustalW annotation (.:*) is empty.</span></p>
\r
19305 <p class=MyNormal><span lang=AF>Spaces are forbidden in the name. When the
\r
19306 alignment is being read, non character signs are ignored in the sequence field
\r
19307 (such as numbers, annotation
\85).</span></p>
\r
19309 <p class=Note><span lang=EN-US style='mso-ansi-language:EN-US'>Note: a
\r
19310 different number of lines in the different blocks will cause the program to
\r
19311 crash or hang.<o:p></o:p></span></p>
\r
19313 <h2><a name="_Toc235958687"></a><a name="_Toc102494894"></a><a
\r
19314 name="_Toc102494405"></a><a name="_Toc101065360"><span style='mso-bookmark:
\r
19315 _Toc102494405'><span style='mso-bookmark:_Toc102494894'><span style='mso-bookmark:
\r
19316 _Toc235958687'><span lang=EN-US>Libraries</span></span></span></span></a></h2>
\r
19318 <h3><a name="_Toc235958688"></a><a name="_Toc102494895"></a><a
\r
19319 name="_Toc102494406"><span style='mso-bookmark:_Toc102494895'><span
\r
19320 style='mso-bookmark:_Toc235958688'><span lang=EN-US>T-COFFEE_LIB_FORMAT_01</span></span></span></a></h3>
\r
19322 <p class=MyNormal><span lang=AF>This is currently the only supported format.</span></p>
\r
19324 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
\r
19325 mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
\r
19326 background:#E6E6E6'>
\r
19328 <p class=examplefileCxSpFirst><span lang=EN-US>!<space> TC_LIB_FORMAT_01</span></p>
\r
19330 <p class=examplefileCxSpMiddle><span lang=EN-US><nseq></span></p>
\r
19332 <p class=examplefileCxSpMiddle><span lang=EN-US><seq1 name> <seq1
\r
19333 length> <seq1></span></p>
\r
19335 <p class=examplefileCxSpMiddle><span lang=EN-US><seq2 name> <seq2
\r
19336 length> <seq2></span></p>
\r
19338 <p class=examplefileCxSpMiddle><span lang=EN-US><seq3 name> <seq3
\r
19339 length> <seq3></span></p>
\r
19341 <p class=examplefileCxSpMiddle><span lang=EN-US>!Comment</span></p>
\r
19343 <p class=examplefileCxSpMiddle><span lang=EN-US>(!Comment)n</span></p>
\r
19345 <p class=examplefileCxSpMiddle><span lang=EN-US>#Si1 Si2</span></p>
\r
19347 <p class=examplefileCxSpMiddle><span lang=EN-US>Ri1 Ri2 V1 (V2, V3)</span></p>
\r
19349 <p class=examplefileCxSpMiddle><span lang=EN-US>#1 2</span></p>
\r
19351 <p class=examplefileCxSpMiddle><span lang=EN-US>12 13 99 (12/0 vs 13/1, weight
\r
19354 <p class=examplefileCxSpMiddle><span lang=EN-US>12 14 70</span></p>
\r
19356 <p class=examplefileCxSpMiddle><span lang=EN-US>15 16 56</span></p>
\r
19358 <p class=examplefileCxSpMiddle><span lang=EN-US>#1 3</span></p>
\r
19360 <p class=examplefileCxSpMiddle><span lang=EN-US>12 13 99 </span></p>
\r
19362 <p class=examplefileCxSpMiddle><span lang=EN-US>12 14 70</span></p>
\r
19364 <p class=examplefileCxSpMiddle><span lang=EN-US>15 16 56</span></p>
\r
19366 <p class=examplefileCxSpLast><span lang=EN-US>!<space>SEQ_1_TO_N </span></p>
\r
19370 <p class=MyNormal><span lang=AF>Si1: index of Sequence 1</span></p>
\r
19372 <p class=MyNormal><span lang=AF>Ri1: index of residue 1 in seq1</span></p>
\r
19374 <p class=MyNormal><span lang=AF>V1: Integer Value: Weight</span></p>
\r
19376 <p class=MyNormal><span lang=AF>V2, V3: optional values</span></p>
\r
19378 <p class=Note><span lang=EN-US style='mso-ansi-language:EN-US'>Note 1: There is
\r
19379 a space between the ! And SEQ_1_TO_N<o:p></o:p></span></p>
\r
19381 <p class=Note><span lang=EN-US style='mso-ansi-language:EN-US'>Note 2: The last
\r
19382 line (! SEQ_1_TO_N) indicates that:<o:p></o:p></span></p>
\r
19384 <p class=MyNormal><span lang=AF>Sequences and residues are numbered from 1 to
\r
19385 N, unless the token SEQ_1_TO_N is omitted, in which case the sequences are
\r
19386 numbered from 0 to N-1, and residues are from 1 to N.</span></p>
\r
19388 <p class=MyNormal><span lang=AF>Residues do not need to be sorted, and neither
\r
19389 do the sequences. The same pair can appear several times in the library. For
\r
19390 instance, the following file would be legal:</span></p>
\r
19392 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
\r
19393 mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
\r
19394 background:#E6E6E6'>
\r
19396 <p class=examplefileCxSpFirst><span lang=EN-US>#1 2</span></p>
\r
19398 <p class=examplefileCxSpMiddle><span lang=EN-US>12 13 99</span></p>
\r
19400 <p class=examplefileCxSpMiddle><span lang=EN-US>#1 2</span></p>
\r
19402 <p class=examplefileCxSpMiddle><span lang=EN-US>15 16 99 </span></p>
\r
19404 <p class=examplefileCxSpMiddle><span lang=EN-US>#1 1</span></p>
\r
19406 <p class=examplefileCxSpLast><span lang=EN-US>12 14 70</span></p>
\r
19410 <p class=MyNormal><a name="_Toc102494896"></a><a name="_Toc102494407"><span
\r
19411 style='mso-bookmark:_Toc102494896'><span lang=AF>It is also poosible to declare
\r
19412 ranges of resdues rather than single pairs. For instance, the following:</span></span></a></p>
\r
19414 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
\r
19415 mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
\r
19416 background:#E6E6E6'>
\r
19418 <p class=examplefileCxSpFirst><span style='mso-bookmark:_Toc102494407'><span
\r
19419 style='mso-bookmark:_Toc102494896'><span lang=EN-US>#0 1</span></span></span></p>
\r
19421 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494407'><span
\r
19422 style='mso-bookmark:_Toc102494896'><span lang=EN-US>+BLOCK+<span
\r
19423 style='mso-spacerun:yes'> </span>10 12 14 99</span></span></span></p>
\r
19425 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494407'><span
\r
19426 style='mso-bookmark:_Toc102494896'><span lang=EN-US>+BLOCK+<span
\r
19427 style='mso-spacerun:yes'> </span>15 30 40 99</span></span></span></p>
\r
19429 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494407'><span
\r
19430 style='mso-bookmark:_Toc102494896'><span lang=EN-US>#0 2</span></span></span></p>
\r
19432 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494407'><span
\r
19433 style='mso-bookmark:_Toc102494896'><span lang=EN-US>15 16 99 </span></span></span></p>
\r
19435 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494407'><span
\r
19436 style='mso-bookmark:_Toc102494896'><span lang=EN-US>#0 1</span></span></span></p>
\r
19438 <p class=examplefileCxSpLast><span style='mso-bookmark:_Toc102494407'><span
\r
19439 style='mso-bookmark:_Toc102494896'><span lang=EN-US>12 14 70</span></span></span></p>
\r
19443 <p class=MyNormal><span style='mso-bookmark:_Toc102494407'><span
\r
19444 style='mso-bookmark:_Toc102494896'><span lang=AF>The first statement BLOCK
\r
19445 declares a BLOCK of length 10, that starts on position 12 of sequence 1 and
\r
19446 position 14 of sequence 2 and where each pair of residues within the block has
\r
19447 a score of 99. The second BLOCK starts on residue 30 of 1, residue 40 of 2 and
\r
19448 extends for 15 residues.</span></span></span></p>
\r
19450 <p class=MyNormal><span style='mso-bookmark:_Toc102494407'><span
\r
19451 style='mso-bookmark:_Toc102494896'><span lang=AF>Blocks can overalp and be
\r
19452 incompatible with one another, just like single constraints.</span></span></span></p>
\r
19454 <p class=MyNormal><span style='mso-bookmark:_Toc102494407'><span
\r
19455 style='mso-bookmark:_Toc102494896'><span lang=AF><span
\r
19456 style='mso-spacerun:yes'> </span></span></span></span></p>
\r
19458 <h3><span style='mso-bookmark:_Toc102494407'><span style='mso-bookmark:_Toc102494896'><a
\r
19459 name="_Toc235958689"><span lang=EN-US>T-COFFEE_LIB_FORMAT_02</span></a></span></span></h3>
\r
19461 <p class=MyNormal><span lang=AF>A simpler format is being developed, however it
\r
19462 is not yet fully supported and is only mentioned here for development purpose.</span></p>
\r
19464 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
\r
19465 mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
\r
19466 background:#E6E6E6'>
\r
19468 <p class=examplefileCxSpFirst><span lang=EN-US>! TC_LIB_FORMAT_02</span></p>
\r
19470 <p class=examplefileCxSpMiddle><span lang=EN-US>#S1 SEQ1 [OPTIONAL]</span></p>
\r
19472 <p class=examplefileCxSpMiddle><span lang=EN-US>#S2 SEQ2 [OPTIONAL]</span></p>
\r
19474 <p class=examplefileCxSpMiddle><span lang=EN-US>...</span></p>
\r
19476 <p class=examplefileCxSpMiddle><span lang=EN-US>!comment [OPTIONAL]</span></p>
\r
19478 <p class=examplefileCxSpMiddle><span lang=EN-US>S1 R1 Ri1 S2 R2 Ri2 V1 (V2 V3)</span></p>
\r
19480 <p class=examplefileCxSpMiddle><span lang=EN-US>=> <st1:place w:st="on">N R1</st1:place>
\r
19481 Ri1 S2 R2 Ri2 V1 (V2 V3)</span></p>
\r
19483 <p class=examplefileCxSpLast><span lang=EN-US>...</span></p>
\r
19487 <p class=MyNormal><span lang=AF>S1, S2: name of sequence 1 and 2</span></p>
\r
19489 <p class=MyNormal><span lang=AF>SEQ1: sequence of S1</span></p>
\r
19491 <p class=MyNormal><span lang=AF>Ri1, Ri2: index of the residues in their
\r
19492 respective sequence</span></p>
\r
19494 <p class=MyNormal><span lang=AF>R1, R2: Residue type</span></p>
\r
19496 <p class=MyNormal><span lang=AF>V1, V2, V3: integer Values (V2 and V3 are
\r
19497 optional)</span></p>
\r
19499 <p class=MyNormal><span lang=AF>Value1, Value 2 and Value3 are optional.</span></p>
\r
19501 <h2><a name="_Toc101065361"></a><a name="_Toc235958690"></a><a
\r
19502 name="_Toc102494897"></a><a name="_Toc102494408"><span style='mso-bookmark:
\r
19503 _Toc102494897'><span style='mso-bookmark:_Toc235958690'><span style='mso-bookmark:
\r
19504 _Toc101065361'><span lang=EN-US>Library List</span></span></span></span></a><span
\r
19505 style='mso-bookmark:_Toc101065361'></span></h2>
\r
19507 <p class=MyNormal><span style='mso-bookmark:_Toc101065361'><span lang=AF>These
\r
19508 are lists of pairs of sequences that must be used to compute a library. The
\r
19509 format is:</span></span></p>
\r
19511 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
\r
19512 mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
\r
19513 background:#E6E6E6'>
\r
19515 <p class=examplefileCxSpFirst><span style='mso-bookmark:_Toc101065361'><span
\r
19516 lang=EN-US><nseq> <S1> <S2></span></span></p>
\r
19518 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065361'><span
\r
19519 lang=EN-US>2 hamg2 globav</span></span></p>
\r
19521 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065361'><span
\r
19522 lang=EN-US>3 hamgw hemog singa</span></span></p>
\r
19524 <p class=examplefileCxSpLast><span style='mso-bookmark:_Toc101065361'><span
\r
19525 lang=EN-US>...</span></span></p>
\r
19529 <h2><span style='mso-bookmark:_Toc101065361'><a name="_Toc235958691"></a><a
\r
19530 name="_Toc102494898"></a><a name="_Toc102494409"><span style='mso-bookmark:
\r
19531 _Toc102494898'><span style='mso-bookmark:_Toc235958691'><span lang=EN-US>Substitution
\r
19532 matrices.</span></span></span></a></span></h2>
\r
19534 <p class=MyNormal><span lang=AF>If the required substitution matrix is not available,
\r
19535 write your own in a file using the following format:</span></p>
\r
19537 <h3><a name="_Toc235958692"></a><a name="_Toc102494899"></a><a
\r
19538 name="_Toc102494410"></a><a name="_Toc101065362"><span style='mso-bookmark:
\r
19539 _Toc102494410'><span style='mso-bookmark:_Toc102494899'><span style='mso-bookmark:
\r
19540 _Toc235958692'><span lang=EN-US>ClustalW Style</span></span></span></span></a><span
\r
19541 style='mso-bookmark:_Toc102494410'><span style='mso-bookmark:_Toc102494899'><span
\r
19542 style='mso-bookmark:_Toc235958692'><span lang=EN-US> [Deprecated]</span></span></span></span></h3>
\r
19544 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
\r
19545 mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
\r
19546 background:#E6E6E6'>
\r
19548 <p class=examplefileCxSpFirst><span lang=EN-US># CLUSTALW_MATRIX FORMAT</span></p>
\r
19550 <p class=examplefileCxSpMiddle><span lang=EN-US>$</span></p>
\r
19552 <p class=examplefileCxSpMiddle><span lang=EN-US>v1</span></p>
\r
19554 <p class=examplefileCxSpMiddle><span lang=EN-US>v2 v3</span></p>
\r
19556 <p class=examplefileCxSpMiddle><span lang=EN-US>v4 v5 v6</span></p>
\r
19558 <p class=examplefileCxSpMiddle><span lang=EN-US>...</span></p>
\r
19560 <p class=examplefileCxSpLast><span lang=EN-US>$</span></p>
\r
19564 <p class=MyNormal><span lang=AF>v1, v2... are integers, possibly negatives.</span></p>
\r
19566 <p class=MyNormal><span lang=AF>The order of the amino acids is:
\r
19567 ABCDEFGHIKLMNQRSTVWXYZ, which means that v1 is the substitution value for A vs
\r
19568 A, v2 for A vs B, v3 for B vs B, v4 for A vs C and so on.</span></p>
\r
19570 <h3><a name="_Toc235958693"></a><a name="_Toc102494900"></a><a
\r
19571 name="_Toc102494411"></a><a name="_Toc101065363"><span style='mso-bookmark:
\r
19572 _Toc102494411'><span style='mso-bookmark:_Toc102494900'><span style='mso-bookmark:
\r
19573 _Toc235958693'><span lang=EN-US>BLAST Format [Recommended]</span></span></span></span></a></h3>
\r
19575 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
\r
19576 mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
\r
19577 background:#E6E6E6'>
\r
19579 <p class=examplefileCxSpFirst><span lang=EN-US># BLAST_MATRIX FORMAT</span></p>
\r
19581 <p class=examplefileCxSpMiddle><span lang=EN-US># ALPHABET=AGCT</span></p>
\r
19583 <p class=examplefileCxSpMiddle><span lang=EN-US><span
\r
19584 style='mso-spacerun:yes'> </span>A G C T</span></p>
\r
19586 <p class=examplefileCxSpMiddle><span lang=EN-US>A 0 1 2 3</span></p>
\r
19588 <p class=examplefileCxSpMiddle><span lang=EN-US>G 0 2 3 4</span></p>
\r
19590 <p class=examplefileCxSpMiddle><span lang=EN-US>C 1 1 2 3</span></p>
\r
19592 <p class=examplefileCxSpLast><span lang=EN-US>...</span></p>
\r
19596 <p class=MyNormal><span lang=AF>The alphabet can be freely defined</span></p>
\r
19598 <h2><a name="_Toc235958694"></a><a name="_Toc102494901"></a><a
\r
19599 name="_Toc102494412"></a><a name="_Toc101065364"><span style='mso-bookmark:
\r
19600 _Toc102494412'><span style='mso-bookmark:_Toc102494901'><span style='mso-bookmark:
\r
19601 _Toc235958694'><span lang=EN-US>Sequences Weights</span></span></span></span></a></h2>
\r
19603 <p class=MyNormal><span lang=AF>Create your own weight file, using the
\r
19604 -seq_weight flag:</span></p>
\r
19606 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
\r
19607 mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
\r
19608 background:#E6E6E6'>
\r
19610 <p class=examplefileCxSpFirst><span lang=EN-US># SINGLE_SEQ_WEIGHT_FORMAT_01</span></p>
\r
19612 <p class=examplefileCxSpMiddle><span lang=EN-US>seq_name1 v1</span></p>
\r
19614 <p class=examplefileCxSpMiddle><span lang=EN-US>seq_name2 v2</span></p>
\r
19616 <p class=examplefileCxSpLast><span lang=EN-US>...</span></p>
\r
19620 <p class=MyNormal><span lang=AF>No duplicate allowed. Sequences not included in
\r
19621 the set of sequences provided to t_coffee will be ignored. Order is free. V1 is
\r
19622 a float. Un-weighted sequences will see their weight set to 1.</span></p>
\r
19624 <span lang=AF style='font-size:11.0pt;font-family:"Times New Roman";mso-fareast-font-family:
\r
19625 "Times New Roman";mso-bidi-font-family:"Courier New";mso-ansi-language:AF;
\r
19626 mso-fareast-language:EN-US;mso-bidi-language:AR-SA'><br clear=all
\r
19627 style='page-break-before:always'>
\r
19630 <div style='mso-element:para-border-div;border:solid windowtext 3.0pt;
\r
19631 padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#CCCCCC;margin-left:0mm;margin-right:
\r
19634 <p class=ChapterTitle><a name="_Toc235958695"><span lang=EN-US>Known Problems</span></a></p>
\r
19638 <p class=MyNormal><span lang=AF>1-Sensitivity to sequence order: It is
\r
19639 difficult to implement a MSA algorithm totally insensitive to the order of
\r
19640 input of the sequences. In t_coffee, robustness is increased by sorting the
\r
19641 sequences alphabetically before aligning them. Beware that this can result in
\r
19642 confusing output where sequences with similar name are unexpectedly close to
\r
19643 one another in the final alignment.</span></p>
\r
19645 <p class=MyNormal><span lang=AF>2-Nucleotides sequences with long stretches of
\r
19646 Ns will cause problems to lalign, especially when using Mocca. To avoid any
\r
19647 problem, filter out these nucleotides before running mocca.</span></p>
\r
19649 <p class=MyNormal><span lang=AF>3-Stop codons are sometimes coded with '*' in
\r
19650 protein sequences. This will cause the program to crash or hang. Please replace
\r
19651 the '*' signs with an X.</span></p>
\r
19653 <p class=MyNormal><span lang=AF>4-Results can differ from one architecture to
\r
19654 another, due rounding differences. This is caused by the tree estimation
\r
19655 procedcure. If you want to make sure an alignment is reproducible, you should
\r
19656 keep the associated dendrogram.</span></p>
\r
19658 <p class=MyNormal><span lang=AF>5-Deploying the program on a </span></p>
\r
19660 <div style='mso-element:para-border-div;border:solid windowtext 3.0pt;
\r
19661 padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#CCCCCC;margin-left:0mm;margin-right:
\r
19664 <p class=ChapterTitle><a name="_Toc235958696"><span lang=EN-US>Technical Notes</span></a></p>
\r
19668 <p class=MyNormal><span lang=AF>These notes are only meant for internal
\r
19669 development.</span></p>
\r
19671 <h2><a name="_Toc235958697"></a><a name="_Toc102494904"></a><a
\r
19672 name="_Toc102494413"><span style='mso-bookmark:_Toc102494904'><span
\r
19673 style='mso-bookmark:_Toc235958697'><span lang=EN-US>Development</span></span></span></a></h2>
\r
19675 <p class=MyNormal><span lang=AF>The following examples are only meant for
\r
19676 internal development, and are used to insure stability from release to release</span></p>
\r
19678 <h4><span lang=AF>profile2list</span></h4>
\r
19680 <p class=MyNormal><span lang=AF>prf1: profile containing one structure</span></p>
\r
19682 <p class=MyNormal><span lang=AF>prf2: profile containing one structure</span></p>
\r
19684 <p class=MyNormal><span lang=AF><o:p> </o:p></span></p>
\r
19686 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
19687 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
19688 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
19689 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
19691 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:
\r
19692 t_coffee<span style='mso-spacerun:yes'>
\r
19693 </span>Rsample_profile1.aln,Rsample_profile2.aln -mode=3dcoffee
\r
19694 -outfile=aligned_prf.aln</span></p>
\r
19696 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US><o:p> </o:p></span></p>
\r
19700 <h3><a name="_Toc235958698"></a><a name="_Toc102494905"></a><a
\r
19701 name="_Toc102494414"><span style='mso-bookmark:_Toc102494905'><span
\r
19702 style='mso-bookmark:_Toc235958698'><span lang=EN-US>Command Line List</span></span></span></a></h3>
\r
19704 <p class=MyNormal><span lang=AF>These command lines have been checked before
\r
19705 every release (along with the other CL in this documentation:</span></p>
\r
19707 <p class=MyNormal><span lang=AF><o:p> </o:p></span></p>
\r
19709 <p class=MyNormal><span lang=AF>-external methods;</span></p>
\r
19711 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
19712 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
19713 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
19714 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
19716 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US><span
\r
19717 style='mso-tab-count:1'> </span>PROMPT: t_coffee sample_seq1.fasta
\96in=Mclustalw_pair,Mclustalw_msa,Mslow_pair
\r
19718 \96outfile=clustal_text</span></p>
\r
19722 <p class=MyNormal><span lang=AF>-fugue_client</span></p>
\r
19724 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
19725 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
19726 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
19727 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
19729 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:
\r
19730 t_coffee
\96in Ssample_seq5.fasta Pstruc4.pdb Mfugue_pair</span></p>
\r
19734 <p class=MyNormal><span lang=AF>-A list of command lines kindly provided by
\r
19735 James Watson (used to crash the pg before version 3.40)</span></p>
\r
19737 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
19738 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
19739 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
19740 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
19742 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:
\r
19743 t_coffee -in Sseq.fas P2PTC Mfugue_pair</span></p>
\r
19745 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:
\r
19746 t_coffee -in S2seqs.fas Mfugue_pair -template_file SELF_P_</span></p>
\r
19748 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:
\r
19749 t_coffee -mode 3dcoffee -in Sseq.fas P2PTC</span></p>
\r
19751 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:
\r
19752 t_coffee -mode 3dcoffee -in S2seqs.fas -template_file SELF_P_</span></p>
\r
19756 <p class=MyNormal><span lang=AF>-A list of command lines that crashed the
\r
19757 program before 3.81</span></p>
\r
19759 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
19760 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
19761 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
19762 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
19764 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:
\r
19765 t_coffee sample_seq6.fasta
\96in Mfast_pair Msap_pair Mfugue_pair
\96template_file
\r
19766 template_file6.template </span></p>
\r
19770 <p class=MsoBodyText><span lang=EN-US><span style='mso-tab-count:1'> </span>-A
\r
19771 command line to read
\93relaxed
\94 pdb files...</span></p>
\r
19773 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
19774 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
19775 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
19776 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
19778 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:
\r
19779 t_coffee
\96in Msap_pair Ssample_seq7.fasta
\96template_file
\r
19780 template_file7.template
\96weight 1001
\96out_lib test_lib7.tc_lib
\96lib_only </span></p>
\r
19784 <p class=MsoBodyText><span lang=EN-US><span style='mso-tab-count:1'> </span>-Parsing
\r
19785 of MARNA libraries</span></p>
\r
19787 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
19788 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
19789 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
19790 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
19792 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:
\r
19793 t_coffee
\96in Lmarna.tc_lib
\96outfile maran.test</span></p>
\r
19797 <p class=MsoBodyText><span lang=EN-US><span style='mso-tab-count:1'> </span>-Parsing
\r
19798 of long sequence lines:</span></p>
\r
19800 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
\r
19801 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
\r
19802 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0mm 10.0pt 0mm;
\r
19803 background:#FFFFCC;margin-left:20.0mm;margin-right:0mm'>
\r
19805 <p class=MyExample style='margin-left:0mm;background:#FFFFCC'><span lang=EN-US>PROMPT:
\r
19806 t_coffee
\96in Asample_aln5.aln
\96outfile test.aln</span></p>
\r
19810 <p class=MsoBodyText><span lang=EN-US><o:p> </o:p></span></p>
\r
19812 <div style='mso-element:para-border-div;border:solid windowtext 3.0pt;
\r
19813 padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#CCCCCC;margin-left:0mm;margin-right:
\r
19816 <p class=ChapterTitle><a name="_Toc235958699"></a><a name="_Toc102494906"><span
\r
19817 style='mso-bookmark:_Toc235958699'><span lang=EN-US>To D</span></span></a><span
\r
19818 style='mso-bookmark:_Toc235958699'><span lang=EN-US>o
\85</span></span></p>
\r
19822 <p class=MyNormal><span lang=AF>-implement UPGMA tree computation</span></p>
\r
19824 <p class=MyNormal><span lang=AF>-implement seq2dpa_tree</span></p>
\r
19826 <p class=MyNormal><span lang=AF>-debug dpa</span></p>
\r
19828 <p class=MyNormal><span lang=AF>-Reconciliate sequences and template when
\r
19829 reading the template</span></p>
\r
19831 <p class=MyNormal><span lang=AF>-Add the server command lines to the checking
\r
19832 procedure</span></p>
\r
19834 <p class=MyNormal><span lang=AF><o:p> </o:p></span></p>
\r
19836 <p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p>
\r
19838 <p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p>
\r
19840 <p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p>
\r
19842 <p class=MsoBodyText><span lang=EN-US><o:p> </o:p></span></p>
\r
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