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 436         panose-1:2 2 5 3 6 3 5 2 3 3;
 437         mso-font-charset:0;
 438         mso-generic-font-family:auto;
 439         mso-font-pitch:variable;
 440         mso-font-signature:3 0 0 0 1 0;}
 441 @font-face
 442         {font-family:"Bernard MT Condensed";
 443         panose-1:2 5 8 6 6 9 5 2 4 4;
 444         mso-font-charset:0;
 445         mso-generic-font-family:auto;
 446         mso-font-pitch:variable;
 447         mso-font-signature:3 0 0 0 1 0;}
 448 @font-face
 449         {font-family:"Big Caslon";
 450         panose-1:2 0 6 3 9 0 0 2 0 3;
 451         mso-font-charset:0;
 452         mso-generic-font-family:auto;
 453         mso-font-pitch:variable;
 454         mso-font-signature:3 0 0 0 1 0;}
 455 @font-face
 456         {font-family:"BlairMdITC TT-Medium";
 457         panose-1:0 0 5 0 0 0 0 0 0 0;
 458         mso-font-charset:0;
 459         mso-generic-font-family:auto;
 460         mso-font-pitch:variable;
 461         mso-font-signature:3 0 0 0 1 0;}
 462 @font-face
 463         {font-family:"Book Antiqua";
 464         panose-1:2 4 6 2 5 3 5 3 3 4;
 465         mso-font-charset:0;
 466         mso-generic-font-family:auto;
 467         mso-font-pitch:variable;
 468         mso-font-signature:3 0 0 0 1 0;}
 469 @font-face
 470         {font-family:"Bookman Old Style";
 471         panose-1:2 5 6 4 5 5 5 2 2 4;
 472         mso-font-charset:0;
 473         mso-generic-font-family:auto;
 474         mso-font-pitch:variable;
 475         mso-font-signature:3 0 0 0 1 0;}
 476 @font-face
 477         {font-family:"Bookshelf Symbol 7";
 478         panose-1:5 1 1 1 1 1 1 1 1 1;
 479         mso-font-charset:0;
 480         mso-generic-font-family:auto;
 481         mso-font-pitch:variable;
 482         mso-font-signature:3 0 0 0 1 0;}
 483 @font-face
 484         {font-family:"Bordeaux Roman Bold LET";
 485         panose-1:2 0 5 0 0 0 0 0 0 0;
 486         mso-font-charset:0;
 487         mso-generic-font-family:auto;
 488         mso-font-pitch:variable;
 489         mso-font-signature:3 0 0 0 1 0;}
 490 @font-face
 491         {font-family:Braggadocio;
 492         panose-1:4 3 11 7 13 11 2 2 4 3;
 493         mso-font-charset:0;
 494         mso-generic-font-family:auto;
 495         mso-font-pitch:variable;
 496         mso-font-signature:3 0 0 0 1 0;}
 497 @font-face
 498         {font-family:"Britannic Bold";
 499         panose-1:2 11 9 3 6 7 3 2 2 4;
 500         mso-font-charset:0;
 501         mso-generic-font-family:auto;
 502         mso-font-pitch:variable;
 503         mso-font-signature:3 0 0 0 1 0;}
 504 @font-face
 505         {font-family:"Brush Script MT Italic";
 506         panose-1:3 6 8 2 4 4 6 7 3 4;
 507         mso-font-charset:0;
 508         mso-generic-font-family:auto;
 509         mso-font-pitch:variable;
 510         mso-font-signature:3 0 0 0 1 0;}
 511 @font-face
 512         {font-family:"Calisto MT";
 513         panose-1:2 4 6 3 5 5 5 3 3 4;
 514         mso-font-charset:0;
 515         mso-generic-font-family:auto;
 516         mso-font-pitch:variable;
 517         mso-font-signature:3 0 0 0 1 0;}
 518 @font-face
 519         {font-family:Candara;
 520         panose-1:2 14 5 2 3 3 3 2 2 4;
 521         mso-font-charset:0;
 522         mso-generic-font-family:auto;
 523         mso-font-pitch:variable;
 524         mso-font-signature:3 0 0 0 1 0;}
 525 @font-face
 526         {font-family:"Century Gothic";
 527         panose-1:2 11 5 2 2 2 2 2 2 4;
 528         mso-font-charset:0;
 529         mso-generic-font-family:auto;
 530         mso-font-pitch:variable;
 531         mso-font-signature:3 0 0 0 1 0;}
 532 @font-face
 533         {font-family:Chalkboard;
 534         panose-1:3 5 6 2 4 2 2 2 2 5;
 535         mso-font-charset:0;
 536         mso-generic-font-family:auto;
 537         mso-font-pitch:variable;
 538         mso-font-signature:3 0 0 0 1 0;}
 539 @font-face
 540         {font-family:Chalkduster;
 541         panose-1:3 5 6 2 4 2 2 2 2 5;
 542         mso-font-charset:0;
 543         mso-generic-font-family:auto;
 544         mso-font-pitch:variable;
 545         mso-font-signature:3 0 0 0 1 0;}
 546 @font-face
 547         {font-family:Cochin;
 548         panose-1:2 0 6 3 2 0 0 2 0 3;
 549         mso-font-charset:0;
 550         mso-generic-font-family:auto;
 551         mso-font-pitch:variable;
 552         mso-font-signature:3 0 0 0 1 0;}
 553 @font-face
 554         {font-family:"Colonna MT";
 555         panose-1:4 2 8 5 6 2 2 3 2 3;
 556         mso-font-charset:0;
 557         mso-generic-font-family:auto;
 558         mso-font-pitch:variable;
 559         mso-font-signature:3 0 0 0 1 0;}
 560 @font-face
 561         {font-family:"Comic Sans MS";
 562         panose-1:3 15 7 2 3 3 2 2 2 4;
 563         mso-font-charset:0;
 564         mso-generic-font-family:auto;
 565         mso-font-pitch:variable;
 566         mso-font-signature:3 0 0 0 1 0;}
 567 @font-face
 568         {font-family:"Comic Sans MS Bold";
 569         panose-1:3 15 9 2 3 3 2 2 2 4;
 570         mso-font-charset:0;
 571         mso-generic-font-family:auto;
 572         mso-font-pitch:variable;
 573         mso-font-signature:3 0 0 0 1 0;}
 574 @font-face
 575         {font-family:Consolas;
 576         panose-1:2 11 6 9 2 2 4 3 2 4;
 577         mso-font-charset:0;
 578         mso-generic-font-family:auto;
 579         mso-font-pitch:variable;
 580         mso-font-signature:3 0 0 0 1 0;}
 581 @font-face
 582         {font-family:Constantia;
 583         panose-1:2 3 6 2 5 3 6 3 3 3;
 584         mso-font-charset:0;
 585         mso-generic-font-family:auto;
 586         mso-font-pitch:variable;
 587         mso-font-signature:3 0 0 0 1 0;}
 588 @font-face
 589         {font-family:"Cooper Black";
 590         panose-1:2 8 9 4 4 3 11 2 4 4;
 591         mso-font-charset:0;
 592         mso-generic-font-family:auto;
 593         mso-font-pitch:variable;
 594         mso-font-signature:3 0 0 0 1 0;}
 595 @font-face
 596         {font-family:Copperplate;
 597         panose-1:2 0 5 4 0 0 0 2 0 4;
 598         mso-font-charset:0;
 599         mso-generic-font-family:auto;
 600         mso-font-pitch:variable;
 601         mso-font-signature:3 0 0 0 1 0;}
 602 @font-face
 603         {font-family:"Copperplate Gothic Bold";
 604         panose-1:2 14 7 5 2 2 6 2 4 4;
 605         mso-font-charset:0;
 606         mso-generic-font-family:auto;
 607         mso-font-pitch:variable;
 608         mso-font-signature:3 0 0 0 1 0;}
 609 @font-face
 610         {font-family:"Copperplate Gothic Light";
 611         panose-1:2 14 5 7 2 2 6 2 4 4;
 612         mso-font-charset:0;
 613         mso-generic-font-family:auto;
 614         mso-font-pitch:variable;
 615         mso-font-signature:3 0 0 0 1 0;}
 616 @font-face
 617         {font-family:"Copperplate Light";
 618         panose-1:2 0 6 4 3 0 0 2 0 4;
 619         mso-font-charset:0;
 620         mso-generic-font-family:auto;
 621         mso-font-pitch:variable;
 622         mso-font-signature:3 0 0 0 1 0;}
 623 @font-face
 624         {font-family:Corbel;
 625         panose-1:2 11 5 3 2 2 4 2 2 4;
 626         mso-font-charset:0;
 627         mso-generic-font-family:auto;
 628         mso-font-pitch:variable;
 629         mso-font-signature:3 0 0 0 1 0;}
 630 @font-face
 631         {font-family:Cracked;
 632         panose-1:0 0 4 0 0 0 0 0 0 0;
 633         mso-font-charset:0;
 634         mso-generic-font-family:auto;
 635         mso-font-pitch:variable;
 636         mso-font-signature:3 0 0 0 1 0;}
 637 @font-face
 638         {font-family:"Curlz MT";
 639         panose-1:4 4 4 4 5 7 2 2 2 2;
 640         mso-font-charset:0;
 641         mso-generic-font-family:auto;
 642         mso-font-pitch:variable;
 643         mso-font-signature:3 0 0 0 1 0;}
 644 @font-face
 645         {font-family:Desdemona;
 646         panose-1:4 2 5 5 2 14 3 4 5 4;
 647         mso-font-charset:0;
 648         mso-generic-font-family:auto;
 649         mso-font-pitch:variable;
 650         mso-font-signature:3 0 0 0 1 0;}
 651 @font-face
 652         {font-family:Didot;
 653         panose-1:2 0 5 3 0 0 0 2 0 3;
 654         mso-font-charset:0;
 655         mso-generic-font-family:auto;
 656         mso-font-pitch:variable;
 657         mso-font-signature:3 0 0 0 1 0;}
 658 @font-face
 659         {font-family:"Edwardian Script ITC";
 660         panose-1:3 3 3 2 4 7 7 13 8 4;
 661         mso-font-charset:0;
 662         mso-generic-font-family:auto;
 663         mso-font-pitch:variable;
 664         mso-font-signature:3 0 0 0 1 0;}
 665 @font-face
 666         {font-family:"Engravers MT";
 667         panose-1:2 9 7 7 8 5 5 2 3 4;
 668         mso-font-charset:0;
 669         mso-generic-font-family:auto;
 670         mso-font-pitch:variable;
 671         mso-font-signature:3 0 0 0 1 0;}
 672 @font-face
 673         {font-family:"Euphemia UCAS";
 674         panose-1:2 11 5 3 4 1 2 2 1 4;
 675         mso-font-charset:0;
 676         mso-generic-font-family:auto;
 677         mso-font-pitch:variable;
 678         mso-font-signature:3 0 0 0 1 0;}
 679 @font-face
 680         {font-family:Eurostile;
 681         panose-1:2 11 5 4 2 2 2 5 2 4;
 682         mso-font-charset:0;
 683         mso-generic-font-family:auto;
 684         mso-font-pitch:variable;
 685         mso-font-signature:3 0 0 0 1 0;}
 686 @font-face
 687         {font-family:"Footlight MT Light";
 688         panose-1:2 4 6 2 6 3 10 2 3 4;
 689         mso-font-charset:0;
 690         mso-generic-font-family:auto;
 691         mso-font-pitch:variable;
 692         mso-font-signature:3 0 0 0 1 0;}
 693 @font-face
 694         {font-family:"Franklin Gothic Book";
 695         panose-1:2 11 5 3 2 1 2 2 2 4;
 696         mso-font-charset:0;
 697         mso-generic-font-family:auto;
 698         mso-font-pitch:variable;
 699         mso-font-signature:3 0 0 0 1 0;}
 700 @font-face
 701         {font-family:"Franklin Gothic Medium";
 702         panose-1:2 11 6 3 2 1 2 2 2 4;
 703         mso-font-charset:0;
 704         mso-generic-font-family:auto;
 705         mso-font-pitch:variable;
 706         mso-font-signature:3 0 0 0 1 0;}
 707 @font-face
 708         {font-family:Futura;
 709         panose-1:2 11 6 2 2 2 4 2 3 3;
 710         mso-font-charset:0;
 711         mso-generic-font-family:auto;
 712         mso-font-pitch:variable;
 713         mso-font-signature:3 0 0 0 1 0;}
 714 @font-face
 715         {font-family:"Futura Condensed";
 716         panose-1:2 11 5 6 2 2 4 3 2 4;
 717         mso-font-charset:0;
 718         mso-generic-font-family:auto;
 719         mso-font-pitch:variable;
 720         mso-font-signature:3 0 0 0 1 0;}
 721 @font-face
 722         {font-family:Garamond;
 723         panose-1:2 2 4 4 3 3 1 1 8 3;
 724         mso-font-charset:0;
 725         mso-generic-font-family:auto;
 726         mso-font-pitch:variable;
 727         mso-font-signature:3 0 0 0 1 0;}
 728 @font-face
 729         {font-family:Georgia;
 730         panose-1:2 4 5 2 5 4 5 2 3 3;
 731         mso-font-charset:0;
 732         mso-generic-font-family:auto;
 733         mso-font-pitch:variable;
 734         mso-font-signature:3 0 0 0 1 0;}
 735 @font-face
 736         {font-family:"Gill Sans";
 737         panose-1:2 11 5 2 2 1 4 2 2 3;
 738         mso-font-charset:0;
 739         mso-generic-font-family:auto;
 740         mso-font-pitch:variable;
 741         mso-font-signature:3 0 0 0 1 0;}
 742 @font-face
 743         {font-family:"Gill Sans Light";
 744         panose-1:2 11 3 2 2 1 4 2 2 3;
 745         mso-font-charset:0;
 746         mso-generic-font-family:auto;
 747         mso-font-pitch:variable;
 748         mso-font-signature:3 0 0 0 1 0;}
 749 @font-face
 750         {font-family:"Gill Sans MT";
 751         panose-1:2 11 5 2 2 1 4 2 2 3;
 752         mso-font-charset:0;
 753         mso-generic-font-family:auto;
 754         mso-font-pitch:variable;
 755         mso-font-signature:3 0 0 0 1 0;}
 756 @font-face
 757         {font-family:"Gill Sans Ultra Bold";
 758         panose-1:2 11 10 2 2 1 4 2 2 3;
 759         mso-font-charset:0;
 760         mso-generic-font-family:auto;
 761         mso-font-pitch:variable;
 762         mso-font-signature:3 0 0 0 1 0;}
 763 @font-face
 764         {font-family:"Gloucester MT Extra Condensed";
 765         panose-1:2 3 8 8 2 6 1 1 1 1;
 766         mso-font-charset:0;
 767         mso-generic-font-family:auto;
 768         mso-font-pitch:variable;
 769         mso-font-signature:3 0 0 0 1 0;}
 770 @font-face
 771         {font-family:"Goudy Old Style";
 772         panose-1:2 2 5 2 5 3 5 2 3 3;
 773         mso-font-charset:0;
 774         mso-generic-font-family:auto;
 775         mso-font-pitch:variable;
 776         mso-font-signature:3 0 0 0 1 0;}
 777 @font-face
 778         {font-family:Haettenschweiler;
 779         panose-1:2 11 7 6 4 9 2 6 2 4;
 780         mso-font-charset:0;
 781         mso-generic-font-family:auto;
 782         mso-font-pitch:variable;
 783         mso-font-signature:3 0 0 0 1 0;}
 784 @font-face
 785         {font-family:"Handwriting - Dakota";
 786         panose-1:2 0 4 0 0 0 0 0 0 0;
 787         mso-font-charset:0;
 788         mso-generic-font-family:auto;
 789         mso-font-pitch:variable;
 790         mso-font-signature:3 0 0 0 1 0;}
 791 @font-face
 792         {font-family:Harrington;
 793         panose-1:4 4 5 5 5 10 2 2 7 2;
 794         mso-font-charset:0;
 795         mso-generic-font-family:auto;
 796         mso-font-pitch:variable;
 797         mso-font-signature:3 0 0 0 1 0;}
 798 @font-face
 799         {font-family:"Helvetica Neue";
 800         panose-1:2 0 5 3 0 0 0 2 0 4;
 801         mso-font-charset:0;
 802         mso-generic-font-family:auto;
 803         mso-font-pitch:variable;
 804         mso-font-signature:3 0 0 0 1 0;}
 805 @font-face
 806         {font-family:"Helvetica Neue Black Condensed";
 807         panose-1:2 0 10 6 0 0 0 2 0 4;
 808         mso-font-charset:0;
 809         mso-generic-font-family:auto;
 810         mso-font-pitch:variable;
 811         mso-font-signature:3 0 0 0 1 0;}
 812 @font-face
 813         {font-family:"Helvetica Neue Bold Condensed";
 814         panose-1:2 0 8 6 0 0 0 2 0 4;
 815         mso-font-charset:0;
 816         mso-generic-font-family:auto;
 817         mso-font-pitch:variable;
 818         mso-font-signature:3 0 0 0 1 0;}
 819 @font-face
 820         {font-family:"Helvetica Neue Light";
 821         panose-1:2 0 4 3 0 0 0 2 0 4;
 822         mso-font-charset:0;
 823         mso-generic-font-family:auto;
 824         mso-font-pitch:variable;
 825         mso-font-signature:3 0 0 0 1 0;}
 826 @font-face
 827         {font-family:"Helvetica Neue Medium";
 828         panose-1:2 11 6 4 2 2 2 2 2 4;
 829         mso-font-charset:0;
 830         mso-generic-font-family:auto;
 831         mso-font-pitch:variable;
 832         mso-font-signature:3 0 0 0 1 0;}
 833 @font-face
 834         {font-family:"Helvetica Neue UltraLight";
 835         panose-1:2 0 2 6 0 0 0 2 0 4;
 836         mso-font-charset:0;
 837         mso-generic-font-family:auto;
 838         mso-font-pitch:variable;
 839         mso-font-signature:3 0 0 0 1 0;}
 840 @font-face
 841         {font-family:Herculanum;
 842         panose-1:2 0 5 5 0 0 0 2 0 4;
 843         mso-font-charset:0;
 844         mso-generic-font-family:auto;
 845         mso-font-pitch:variable;
 846         mso-font-signature:3 0 0 0 1 0;}
 847 @font-face
 848         {font-family:"Hoefler Text";
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 850         mso-font-charset:0;
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 857         mso-font-charset:2;
 858         mso-generic-font-family:auto;
 859         mso-font-pitch:variable;
 860         mso-font-signature:0 0 65536 0 -2147483648 0;}
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 862         {font-family:"Imprint MT Shadow";
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 864         mso-font-charset:0;
 865         mso-generic-font-family:auto;
 866         mso-font-pitch:variable;
 867         mso-font-signature:3 0 0 0 1 0;}
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 869         {font-family:InaiMathi;
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 871         mso-font-charset:0;
 872         mso-generic-font-family:auto;
 873         mso-font-pitch:variable;
 874         mso-font-signature:3 0 0 0 1 0;}
 875 @font-face
 876         {font-family:"Kino MT";
 877         panose-1:4 3 7 5 13 12 2 2 7 3;
 878         mso-font-charset:0;
 879         mso-generic-font-family:auto;
 880         mso-font-pitch:variable;
 881         mso-font-signature:3 0 0 0 1 0;}
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 883         {font-family:Krungthep;
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 885         mso-font-charset:0;
 886         mso-generic-font-family:auto;
 887         mso-font-pitch:variable;
 888         mso-font-signature:3 0 0 0 1 0;}
 889 @font-face
 890         {font-family:KufiStandardGK;
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 892         mso-font-charset:0;
 893         mso-generic-font-family:auto;
 894         mso-font-pitch:variable;
 895         mso-font-signature:3 0 0 0 1 0;}
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 897         {font-family:"Lucida Blackletter";
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 899         mso-font-charset:0;
 900         mso-generic-font-family:auto;
 901         mso-font-pitch:variable;
 902         mso-font-signature:3 0 0 0 1 0;}
 903 @font-face
 904         {font-family:"Lucida Bright";
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 906         mso-font-charset:0;
 907         mso-generic-font-family:auto;
 908         mso-font-pitch:variable;
 909         mso-font-signature:3 0 0 0 1 0;}
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 911         {font-family:"Lucida Calligraphy";
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 913         mso-font-charset:0;
 914         mso-generic-font-family:auto;
 915         mso-font-pitch:variable;
 916         mso-font-signature:3 0 0 0 1 0;}
 917 @font-face
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 920         mso-font-charset:0;
 921         mso-generic-font-family:auto;
 922         mso-font-pitch:variable;
 923         mso-font-signature:3 0 0 0 1 0;}
 924 @font-face
 925         {font-family:"Lucida Fax";
 926         panose-1:2 6 6 2 5 5 5 2 2 4;
 927         mso-font-charset:0;
 928         mso-generic-font-family:auto;
 929         mso-font-pitch:variable;
 930         mso-font-signature:3 0 0 0 1 0;}
 931 @font-face
 932         {font-family:"Lucida Grande";
 933         mso-font-charset:0;
 934         mso-generic-font-family:auto;
 935         mso-font-pitch:variable;
 936         mso-font-signature:3 0 0 0 1 0;}
 937 @font-face
 938         {font-family:"Lucida Handwriting";
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 940         mso-font-charset:0;
 941         mso-generic-font-family:auto;
 942         mso-font-pitch:variable;
 943         mso-font-signature:3 0 0 0 1 0;}
 944 @font-face
 945         {font-family:"Lucida Sans";
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 947         mso-font-charset:0;
 948         mso-generic-font-family:auto;
 949         mso-font-pitch:variable;
 950         mso-font-signature:3 0 0 0 1 0;}
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 952         {font-family:"Lucida Sans Typewriter";
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 954         mso-font-charset:0;
 955         mso-generic-font-family:auto;
 956         mso-font-pitch:variable;
 957         mso-font-signature:3 0 0 0 1 0;}
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 959         {font-family:"Lucida Sans Unicode";
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 961         mso-font-charset:0;
 962         mso-generic-font-family:auto;
 963         mso-font-pitch:variable;
 964         mso-font-signature:3 0 0 0 1 0;}
 965 @font-face
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 968         mso-font-charset:0;
 969         mso-generic-font-family:auto;
 970         mso-font-pitch:variable;
 971         mso-font-signature:3 0 0 0 1 0;}
 972 @font-face
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 976         mso-generic-font-family:auto;
 977         mso-font-pitch:variable;
 978         mso-font-signature:3 0 0 0 1 0;}
 979 @font-face
 980         {font-family:"Matura MT Script Capitals";
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 982         mso-font-charset:0;
 983         mso-generic-font-family:auto;
 984         mso-font-pitch:variable;
 985         mso-font-signature:3 0 0 0 1 0;}
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 990         mso-generic-font-family:auto;
 991         mso-font-pitch:variable;
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 994         {font-family:"Menlo Bold Italic";
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 996         mso-font-charset:0;
 997         mso-generic-font-family:auto;
 998         mso-font-pitch:variable;
 999         mso-font-signature:3 0 0 0 1 0;}
1000 @font-face
1001         {font-family:"Menlo Italic";
1002         panose-1:2 11 6 9 3 3 4 11 2 4;
1003         mso-font-charset:0;
1004         mso-generic-font-family:auto;
1005         mso-font-pitch:variable;
1006         mso-font-signature:3 0 0 0 1 0;}
1007 @font-face
1008         {font-family:"Menlo Regular";
1009         panose-1:2 11 6 9 3 8 4 2 2 4;
1010         mso-font-charset:0;
1011         mso-generic-font-family:auto;
1012         mso-font-pitch:variable;
1013         mso-font-signature:3 0 0 0 1 0;}
1014 @font-face
1015         {font-family:"Microsoft Sans Serif";
1016         panose-1:2 11 6 4 2 2 2 2 2 4;
1017         mso-font-charset:0;
1018         mso-generic-font-family:auto;
1019         mso-font-pitch:variable;
1020         mso-font-signature:3 0 0 0 1 0;}
1021 @font-face
1022         {font-family:Mistral;
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1024         mso-font-charset:0;
1025         mso-generic-font-family:auto;
1026         mso-font-pitch:variable;
1027         mso-font-signature:3 0 0 0 1 0;}
1028 @font-face
1029         {font-family:"Modern No\. 20";
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1031         mso-font-charset:0;
1032         mso-generic-font-family:auto;
1033         mso-font-pitch:variable;
1034         mso-font-signature:3 0 0 0 1 0;}
1035 @font-face
1036         {font-family:Monaco;
1037         panose-1:2 0 5 0 0 0 0 0 0 0;
1038         mso-font-charset:0;
1039         mso-generic-font-family:auto;
1040         mso-font-pitch:variable;
1041         mso-font-signature:3 0 0 0 1 0;}
1042 @font-face
1043         {font-family:"Monotype Corsiva";
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1045         mso-font-charset:0;
1046         mso-generic-font-family:auto;
1047         mso-font-pitch:variable;
1048         mso-font-signature:3 0 0 0 1 0;}
1049 @font-face
1050         {font-family:"Monotype Sorts";
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1052         mso-font-charset:2;
1053         mso-generic-font-family:auto;
1054         mso-font-pitch:variable;
1055         mso-font-signature:0 0 65536 0 -2147483648 0;}
1056 @font-face
1057         {font-family:"MS Reference Sans Serif";
1058         panose-1:2 11 6 4 3 5 4 4 2 4;
1059         mso-font-charset:0;
1060         mso-generic-font-family:auto;
1061         mso-font-pitch:variable;
1062         mso-font-signature:3 0 0 0 1 0;}
1063 @font-face
1064         {font-family:"MS Reference Specialty";
1065         panose-1:5 0 5 0 0 0 0 0 0 0;
1066         mso-font-charset:0;
1067         mso-generic-font-family:auto;
1068         mso-font-pitch:variable;
1069         mso-font-signature:3 0 0 0 1 0;}
1070 @font-face
1071         {font-family:"MT Extra";
1072         panose-1:5 5 1 2 1 2 5 2 2 2;
1073         mso-font-charset:2;
1074         mso-generic-font-family:auto;
1075         mso-font-pitch:variable;
1076         mso-font-signature:0 0 65536 0 -2147483648 0;}
1077 @font-face
1078         {font-family:"News Gothic MT";
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1080         mso-font-charset:0;
1081         mso-generic-font-family:auto;
1082         mso-font-pitch:variable;
1083         mso-font-signature:3 0 0 0 1 0;}
1084 @font-face
1085         {font-family:Onyx;
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1087         mso-font-charset:0;
1088         mso-generic-font-family:auto;
1089         mso-font-pitch:variable;
1090         mso-font-signature:3 0 0 0 1 0;}
1091 @font-face
1092         {font-family:Optima;
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1094         mso-font-charset:0;
1095         mso-generic-font-family:auto;
1096         mso-font-pitch:variable;
1097         mso-font-signature:3 0 0 0 1 0;}
1098 @font-face
1099         {font-family:"Optima ExtraBlack";
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1101         mso-font-charset:0;
1102         mso-generic-font-family:auto;
1103         mso-font-pitch:variable;
1104         mso-font-signature:3 0 0 0 1 0;}
1105 @font-face
1106         {font-family:Palatino;
1107         panose-1:2 0 5 0 0 0 0 0 0 0;
1108         mso-font-charset:0;
1109         mso-generic-font-family:auto;
1110         mso-font-pitch:variable;
1111         mso-font-signature:3 0 0 0 1 0;}
1112 @font-face
1113         {font-family:Papyrus;
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1115         mso-font-charset:0;
1116         mso-generic-font-family:auto;
1117         mso-font-pitch:variable;
1118         mso-font-signature:3 0 0 0 1 0;}
1119 @font-face
1120         {font-family:"Papyrus Condensed";
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1122         mso-font-charset:0;
1123         mso-generic-font-family:auto;
1124         mso-font-pitch:variable;
1125         mso-font-signature:3 0 0 0 1 0;}
1126 @font-face
1127         {font-family:Perpetua;
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1129         mso-font-charset:0;
1130         mso-generic-font-family:auto;
1131         mso-font-pitch:variable;
1132         mso-font-signature:3 0 0 0 1 0;}
1133 @font-face
1134         {font-family:"Perpetua Titling MT";
1135         panose-1:2 2 5 2 6 5 5 2 8 4;
1136         mso-font-charset:0;
1137         mso-generic-font-family:auto;
1138         mso-font-pitch:variable;
1139         mso-font-signature:3 0 0 0 1 0;}
1140 @font-face
1141         {font-family:"Plantagenet Cherokee";
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1143         mso-font-charset:0;
1144         mso-generic-font-family:auto;
1145         mso-font-pitch:variable;
1146         mso-font-signature:3 0 0 0 1 0;}
1147 @font-face
1148         {font-family:Playbill;
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1150         mso-font-charset:0;
1151         mso-generic-font-family:auto;
1152         mso-font-pitch:variable;
1153         mso-font-signature:3 0 0 0 1 0;}
1154 @font-face
1155         {font-family:"PortagoITC TT";
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1157         mso-font-charset:0;
1158         mso-generic-font-family:auto;
1159         mso-font-pitch:variable;
1160         mso-font-signature:3 0 0 0 1 0;}
1161 @font-face
1162         {font-family:Rockwell;
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1164         mso-font-charset:0;
1165         mso-generic-font-family:auto;
1166         mso-font-pitch:variable;
1167         mso-font-signature:3 0 0 0 1 0;}
1168 @font-face
1169         {font-family:"Rockwell Extra Bold";
1170         panose-1:2 6 9 3 4 5 5 2 4 3;
1171         mso-font-charset:0;
1172         mso-generic-font-family:auto;
1173         mso-font-pitch:variable;
1174         mso-font-signature:3 0 0 0 1 0;}
1175 @font-face
1176         {font-family:Sathu;
1177         panose-1:0 0 4 0 0 0 0 0 0 0;
1178         mso-font-charset:0;
1179         mso-generic-font-family:auto;
1180         mso-font-pitch:variable;
1181         mso-font-signature:3 0 0 0 1 0;}
1182 @font-face
1183         {font-family:Silom;
1184         panose-1:0 0 4 0 0 0 0 0 0 0;
1185         mso-font-charset:0;
1186         mso-generic-font-family:auto;
1187         mso-font-pitch:variable;
1188         mso-font-signature:3 0 0 0 1 0;}
1189 @font-face
1190         {font-family:Skia;
1191         panose-1:2 13 5 2 2 2 4 2 2 4;
1192         mso-font-charset:0;
1193         mso-generic-font-family:auto;
1194         mso-font-pitch:variable;
1195         mso-font-signature:3 0 0 0 1 0;}
1196 @font-face
1197         {font-family:Stencil;
1198         panose-1:4 4 9 5 13 8 2 2 4 4;
1199         mso-font-charset:0;
1200         mso-generic-font-family:auto;
1201         mso-font-pitch:variable;
1202         mso-font-signature:3 0 0 0 1 0;}
1203 @font-face
1204         {font-family:"Tahoma Bold";
1205         panose-1:2 11 8 4 3 5 4 4 2 4;
1206         mso-font-charset:0;
1207         mso-generic-font-family:auto;
1208         mso-font-pitch:variable;
1209         mso-font-signature:3 0 0 0 1 0;}
1210 @font-face
1211         {font-family:Thonburi;
1212         panose-1:0 0 4 0 0 0 0 0 0 0;
1213         mso-font-charset:0;
1214         mso-generic-font-family:auto;
1215         mso-font-pitch:variable;
1216         mso-font-signature:3 0 0 0 1 0;}
1217 @font-face
1218         {font-family:"Times New Roman Bold Italic";
1219         panose-1:2 2 7 3 6 5 5 9 3 4;
1220         mso-font-charset:0;
1221         mso-generic-font-family:auto;
1222         mso-font-pitch:variable;
1223         mso-font-signature:3 0 0 0 1 0;}
1224 @font-face
1225         {font-family:"Trebuchet MS Bold";
1226         panose-1:2 11 7 3 2 2 2 2 2 4;
1227         mso-font-charset:0;
1228         mso-generic-font-family:auto;
1229         mso-font-pitch:variable;
1230         mso-font-signature:3 0 0 0 1 0;}
1231 @font-face
1232         {font-family:"Trebuchet MS Bold Italic";
1233         panose-1:2 11 7 3 2 2 2 9 2 4;
1234         mso-font-charset:0;
1235         mso-generic-font-family:auto;
1236         mso-font-pitch:variable;
1237         mso-font-signature:3 0 0 0 1 0;}
1238 @font-face
1239         {font-family:"Trebuchet MS Italic";
1240         panose-1:2 11 6 3 2 2 2 9 2 4;
1241         mso-font-charset:0;
1242         mso-generic-font-family:auto;
1243         mso-font-pitch:variable;
1244         mso-font-signature:3 0 0 0 1 0;}
1245 @font-face
1246         {font-family:"Tw Cen MT";
1247         panose-1:2 11 6 2 2 1 4 2 6 3;
1248         mso-font-charset:0;
1249         mso-generic-font-family:auto;
1250         mso-font-pitch:variable;
1251         mso-font-signature:3 0 0 0 1 0;}
1252 @font-face
1253         {font-family:Webdings;
1254         panose-1:5 3 1 2 1 5 9 6 7 3;
1255         mso-font-charset:2;
1256         mso-generic-font-family:auto;
1257         mso-font-pitch:variable;
1258         mso-font-signature:0 0 65536 0 -2147483648 0;}
1259 @font-face
1260         {font-family:"Wide Latin";
1261         panose-1:2 10 10 7 5 5 5 2 4 4;
1262         mso-font-charset:0;
1263         mso-generic-font-family:auto;
1264         mso-font-pitch:variable;
1265         mso-font-signature:3 0 0 0 1 0;}
1266 @font-face
1267         {font-family:"Wingdings 3";
1268         panose-1:5 4 1 2 1 8 7 7 7 7;
1269         mso-font-charset:2;
1270         mso-generic-font-family:auto;
1271         mso-font-pitch:variable;
1272         mso-font-signature:0 0 65536 0 -2147483648 0;}
1273 @font-face
1274         {font-family:"Zapf Dingbats";
1275         panose-1:5 2 1 2 1 7 4 2 6 9;
1276         mso-font-charset:2;
1277         mso-generic-font-family:auto;
1278         mso-font-pitch:variable;
1279         mso-font-signature:0 0 65536 0 -2147483648 0;}
1280 @font-face
1281         {font-family:Zapfino;
1282         panose-1:3 3 3 0 4 7 7 7 12 3;
1283         mso-font-charset:0;
1284         mso-generic-font-family:auto;
1285         mso-font-pitch:variable;
1286         mso-font-signature:3 0 0 0 1 0;}
1287 @font-face
1288         {font-family:"Lucida Grande CE";
1289         panose-1:2 11 6 0 4 5 2 2 2 4;
1290         mso-font-charset:88;
1291         mso-generic-font-family:auto;
1292         mso-font-pitch:variable;
1293         mso-font-signature:5 0 0 0 2 0;}
1294 @font-face
1295         {font-family:"Charcoal CY";
1296         panose-1:0 0 4 0 0 0 0 0 0 0;
1297         mso-font-charset:89;
1298         mso-generic-font-family:auto;
1299         mso-font-pitch:variable;
1300         mso-font-signature:513 0 0 0 4 0;}
1301 @font-face
1302         {font-family:"Geneva CY";
1303         panose-1:0 0 4 0 0 0 0 0 0 0;
1304         mso-font-charset:89;
1305         mso-generic-font-family:auto;
1306         mso-font-pitch:variable;
1307         mso-font-signature:513 0 0 0 4 0;}
1308 @font-face
1309         {font-family:"Helvetica CY";
1310         panose-1:0 0 4 0 0 0 0 0 0 0;
1311         mso-font-charset:89;
1312         mso-generic-font-family:auto;
1313         mso-font-pitch:variable;
1314         mso-font-signature:513 0 0 0 4 0;}
1315 @font-face
1316         {font-family:"Lucida Grande CY";
1317         panose-1:2 11 6 0 4 5 2 2 2 4;
1318         mso-font-charset:89;
1319         mso-generic-font-family:auto;
1320         mso-font-pitch:variable;
1321         mso-font-signature:513 0 0 0 4 0;}
1322 @font-face
1323         {font-family:"Apple LiGothic Medium";
1324         panose-1:2 0 5 0 0 0 0 0 0 0;
1325         mso-font-charset:81;
1326         mso-generic-font-family:auto;
1327         mso-font-pitch:variable;
1328         mso-font-signature:1 0 16778248 0 1048576 0;}
1329 @font-face
1330         {font-family:"Apple LiSung Light";
1331         panose-1:2 0 5 0 0 0 0 0 0 0;
1332         mso-font-charset:81;
1333         mso-generic-font-family:auto;
1334         mso-font-pitch:variable;
1335         mso-font-signature:1 0 16778248 0 1048576 0;}
1336 @font-face
1337         {font-family:BiauKai;
1338         panose-1:2 1 6 1 0 1 1 1 1 1;
1339         mso-font-charset:81;
1340         mso-generic-font-family:auto;
1341         mso-font-pitch:variable;
1342         mso-font-signature:1 0 16778248 0 1048576 0;}
1343 @font-face
1344         {font-family:"Heiti TC Light";
1345         panose-1:2 0 0 0 0 0 0 0 0 0;
1346         mso-font-charset:81;
1347         mso-generic-font-family:auto;
1348         mso-font-pitch:variable;
1349         mso-font-signature:1 0 16778248 0 1048576 0;}
1350 @font-face
1351         {font-family:"Heiti TC Medium";
1352         panose-1:0 0 0 0 0 0 0 0 0 0;
1353         mso-font-charset:81;
1354         mso-generic-font-family:auto;
1355         mso-font-pitch:variable;
1356         mso-font-signature:1 0 16778248 0 1048576 0;}
1357 @font-face
1358         {font-family:"\5137\5B8B Pro";
1359         mso-font-charset:81;
1360         mso-generic-font-family:auto;
1361         mso-font-pitch:variable;
1362         mso-font-signature:1 0 16778248 0 1048576 0;}
1363 @font-face
1364         {font-family:"\5137\9ED1 Pro";
1365         mso-font-charset:81;
1366         mso-generic-font-family:auto;
1367         mso-font-pitch:variable;
1368         mso-font-signature:1 0 16778248 0 1048576 0;}
1369 @font-face
1370         {font-family:"GB18030 Bitmap";
1371         mso-font-charset:80;
1372         mso-generic-font-family:auto;
1373         mso-font-pitch:variable;
1374         mso-font-signature:1 0 16778254 0 262144 0;}
1375 @font-face
1376         {font-family:Hei;
1377         panose-1:2 0 5 0 0 0 0 0 0 0;
1378         mso-font-charset:80;
1379         mso-generic-font-family:auto;
1380         mso-font-pitch:variable;
1381         mso-font-signature:1 0 16778254 0 262144 0;}
1382 @font-face
1383         {font-family:"Heiti SC Light";
1384         panose-1:2 0 0 0 0 0 0 0 0 0;
1385         mso-font-charset:80;
1386         mso-generic-font-family:auto;
1387         mso-font-pitch:variable;
1388         mso-font-signature:1 0 16778254 0 262144 0;}
1389 @font-face
1390         {font-family:"Heiti SC Medium";
1391         panose-1:0 0 0 0 0 0 0 0 0 0;
1392         mso-font-charset:80;
1393         mso-generic-font-family:auto;
1394         mso-font-pitch:variable;
1395         mso-font-signature:1 0 16778254 0 262144 0;}
1396 @font-face
1397         {font-family:"Hiragino Sans GB W3";
1398         panose-1:2 11 3 0 0 0 0 0 0 0;
1399         mso-font-charset:80;
1400         mso-generic-font-family:auto;
1401         mso-font-pitch:variable;
1402         mso-font-signature:1 0 16778254 0 262144 0;}
1403 @font-face
1404         {font-family:"Hiragino Sans GB W6";
1405         panose-1:2 11 6 0 0 0 0 0 0 0;
1406         mso-font-charset:80;
1407         mso-generic-font-family:auto;
1408         mso-font-pitch:variable;
1409         mso-font-signature:1 0 16778254 0 262144 0;}
1410 @font-face
1411         {font-family:Kai;
1412         panose-1:2 0 5 0 0 0 0 0 0 0;
1413         mso-font-charset:80;
1414         mso-generic-font-family:auto;
1415         mso-font-pitch:variable;
1416         mso-font-signature:1 0 16778254 0 262144 0;}
1417 @font-face
1418         {font-family:\534E\6587\4EFF\5B8B;
1419         mso-font-charset:80;
1420         mso-generic-font-family:auto;
1421         mso-font-pitch:variable;
1422         mso-font-signature:1 0 16778254 0 262144 0;}
1423 @font-face
1424         {font-family:\534E\6587\9ED1\4F53;
1425         mso-font-charset:80;
1426         mso-generic-font-family:auto;
1427         mso-font-pitch:variable;
1428         mso-font-signature:1 0 16778254 0 262144 0;}
1429 @font-face
1430         {font-family:\534E\6587\6977\4F53;
1431         mso-font-charset:80;
1432         mso-generic-font-family:auto;
1433         mso-font-pitch:variable;
1434         mso-font-signature:1 0 16778254 0 262144 0;}
1435 @font-face
1436         {font-family:\534E\6587\5B8B\4F53;
1437         mso-font-charset:80;
1438         mso-generic-font-family:auto;
1439         mso-font-pitch:variable;
1440         mso-font-signature:1 0 16778254 0 262144 0;}
1441 @font-face
1442         {font-family:\534E\6587\7EC6\9ED1;
1443         mso-font-charset:80;
1444         mso-generic-font-family:auto;
1445         mso-font-pitch:variable;
1446         mso-font-signature:1 0 16778254 0 262144 0;}
1447 @font-face
1448         {font-family:"MS PGothic";
1449         mso-font-charset:78;
1450         mso-generic-font-family:auto;
1451         mso-font-pitch:variable;
1452         mso-font-signature:1 0 16778247 0 131072 0;}
1453 @font-face
1454         {font-family:"MS PMincho";
1455         mso-font-charset:78;
1456         mso-generic-font-family:auto;
1457         mso-font-pitch:variable;
1458         mso-font-signature:1 0 16778247 0 131072 0;}
1459 @font-face
1460         {font-family:Osaka;
1461         panose-1:2 11 6 0 0 0 0 0 0 0;
1462         mso-font-charset:78;
1463         mso-generic-font-family:auto;
1464         mso-font-pitch:variable;
1465         mso-font-signature:1 0 16778247 0 131072 0;}
1466 @font-face
1467         {font-family:Osaka\2212\7B49\5E45;
1468         mso-font-charset:78;
1469         mso-generic-font-family:auto;
1470         mso-font-pitch:variable;
1471         mso-font-signature:1 0 16778247 0 131072 0;}
1472 @font-face
1473         {font-family:"\30D2\30E9\30AE\30CE\89D2\30B4 Pro W3";
1474         mso-font-charset:78;
1475         mso-generic-font-family:auto;
1476         mso-font-pitch:variable;
1477         mso-font-signature:1 0 16778247 0 131072 0;}
1478 @font-face
1479         {font-family:"\30D2\30E9\30AE\30CE\89D2\30B4 Pro W6";
1480         mso-font-charset:78;
1481         mso-generic-font-family:auto;
1482         mso-font-pitch:variable;
1483         mso-font-signature:1 0 16778247 0 131072 0;}
1484 @font-face
1485         {font-family:"\30D2\30E9\30AE\30CE\89D2\30B4 ProN W3";
1486         mso-font-charset:78;
1487         mso-generic-font-family:auto;
1488         mso-font-pitch:variable;
1489         mso-font-signature:1 0 16778247 0 131072 0;}
1490 @font-face
1491         {font-family:"\30D2\30E9\30AE\30CE\89D2\30B4 ProN W6";
1492         mso-font-charset:78;
1493         mso-generic-font-family:auto;
1494         mso-font-pitch:variable;
1495         mso-font-signature:1 0 16778247 0 131072 0;}
1496 @font-face
1497         {font-family:"\30D2\30E9\30AE\30CE\89D2\30B4 Std W8";
1498         mso-font-charset:78;
1499         mso-generic-font-family:auto;
1500         mso-font-pitch:variable;
1501         mso-font-signature:1 0 16778247 0 131072 0;}
1502 @font-face
1503         {font-family:"\30D2\30E9\30AE\30CE\89D2\30B4 StdN W8";
1504         mso-font-charset:78;
1505         mso-generic-font-family:auto;
1506         mso-font-pitch:variable;
1507         mso-font-signature:1 0 16778247 0 131072 0;}
1508 @font-face
1509         {font-family:"\30D2\30E9\30AE\30CE\4E38\30B4 Pro W4";
1510         mso-font-charset:78;
1511         mso-generic-font-family:auto;
1512         mso-font-pitch:variable;
1513         mso-font-signature:1 0 16778247 0 131072 0;}
1514 @font-face
1515         {font-family:"\30D2\30E9\30AE\30CE\4E38\30B4 ProN W4";
1516         mso-font-charset:78;
1517         mso-generic-font-family:auto;
1518         mso-font-pitch:variable;
1519         mso-font-signature:1 0 16778247 0 131072 0;}
1520 @font-face
1521         {font-family:"\30D2\30E9\30AE\30CE\660E\671D Pro W3";
1522         mso-font-charset:78;
1523         mso-generic-font-family:auto;
1524         mso-font-pitch:variable;
1525         mso-font-signature:1 0 16778247 0 131072 0;}
1526 @font-face
1527         {font-family:"\30D2\30E9\30AE\30CE\660E\671D Pro W6";
1528         mso-font-charset:78;
1529         mso-generic-font-family:auto;
1530         mso-font-pitch:variable;
1531         mso-font-signature:1 0 16778247 0 131072 0;}
1532 @font-face
1533         {font-family:"\30D2\30E9\30AE\30CE\660E\671D ProN W3";
1534         mso-font-charset:78;
1535         mso-generic-font-family:auto;
1536         mso-font-pitch:variable;
1537         mso-font-signature:1 0 16778247 0 131072 0;}
1538 @font-face
1539         {font-family:"\30D2\30E9\30AE\30CE\660E\671D ProN W6";
1540         mso-font-charset:78;
1541         mso-generic-font-family:auto;
1542         mso-font-pitch:variable;
1543         mso-font-signature:1 0 16778247 0 131072 0;}
1544 @font-face
1545         {font-family:\30E1\30A4\30EA\30AA;
1546         mso-font-charset:78;
1547         mso-generic-font-family:auto;
1548         mso-font-pitch:variable;
1549         mso-font-signature:1 0 16778247 0 131072 0;}
1550 @font-face
1551         {font-family:AppleGothic;
1552         panose-1:2 0 5 0 0 0 0 0 0 0;
1553         mso-font-charset:79;
1554         mso-generic-font-family:auto;
1555         mso-font-pitch:variable;
1556         mso-font-signature:1 0 16786438 0 524288 0;}
1557 @font-face
1558         {font-family:AppleMyungjo;
1559         panose-1:2 0 5 0 0 0 0 0 0 0;
1560         mso-font-charset:79;
1561         mso-generic-font-family:auto;
1562         mso-font-pitch:variable;
1563         mso-font-signature:1 0 16786438 0 524288 0;}
1564 @font-face
1565         {font-family:PC\BA85\C870;
1566         mso-font-charset:79;
1567         mso-generic-font-family:auto;
1568         mso-font-pitch:variable;
1569         mso-font-signature:1 0 16786438 0 524288 0;}
1570 @font-face
1571         {font-family:\AD74\B9BC;
1572         mso-font-charset:79;
1573         mso-generic-font-family:auto;
1574         mso-font-pitch:variable;
1575         mso-font-signature:1 0 16786438 0 524288 0;}
1576 @font-face
1577         {font-family:"FE Modern font face";
1578         mso-font-charset:79;
1579         mso-generic-font-family:auto;
1580         mso-font-pitch:variable;
1581         mso-font-signature:1 0 16786438 0 524288 0;}
1582 @font-face
1583         {font-family:\D544\AE30\CCB4;
1584         mso-font-charset:79;
1585         mso-generic-font-family:auto;
1586         mso-font-pitch:variable;
1587         mso-font-signature:1 0 16786438 0 524288 0;}
1588 @font-face
1589         {font-family:\D5E4\B4DC\B77C\C778A;
1590         mso-font-charset:79;
1591         mso-generic-font-family:auto;
1592         mso-font-pitch:variable;
1593         mso-font-signature:1 0 16786438 0 524288 0;}
1594 @font-face
1595         {font-family:starbats;
1596         mso-font-charset:2;
1597         mso-generic-font-family:auto;
1598         mso-font-pitch:variable;
1599         mso-font-signature:0 0 0 0 0 0;}
1600 @font-face
1601         {font-family:Minion-Bold;
1602         panose-1:0 0 0 0 0 0 0 0 0 0;
1603         mso-font-alt:Cambria;
1604         mso-font-charset:77;
1605         mso-generic-font-family:roman;
1606         mso-font-format:other;
1607         mso-font-pitch:auto;
1608         mso-font-signature:3 0 0 0 1 0;}
1609 @font-face
1610         {font-family:Minion-Regular;
1611         panose-1:0 0 0 0 0 0 0 0 0 0;
1612         mso-font-charset:77;
1613         mso-generic-font-family:roman;
1614         mso-font-format:other;
1615         mso-font-pitch:auto;
1616         mso-font-signature:3 0 0 0 1 0;}
1617 @font-face
1618         {font-family:Minion-Italic;
1619         panose-1:0 0 0 0 0 0 0 0 0 0;
1620         mso-font-charset:77;
1621         mso-generic-font-family:roman;
1622         mso-font-format:other;
1623         mso-font-pitch:auto;
1624         mso-font-signature:3 0 0 0 1 0;}
1625 @font-face
1626         {font-family:OfficinaSerif-Bold;
1627         panose-1:0 0 0 0 0 0 0 0 0 0;
1628         mso-font-charset:77;
1629         mso-generic-font-family:roman;
1630         mso-font-format:other;
1631         mso-font-pitch:auto;
1632         mso-font-signature:3 0 0 0 1 0;}
1633 @font-face
1634         {font-family:Minion-Semibold;
1635         panose-1:0 0 0 0 0 0 0 0 0 0;
1636         mso-font-charset:77;
1637         mso-generic-font-family:roman;
1638         mso-font-format:other;
1639         mso-font-pitch:auto;
1640         mso-font-signature:3 0 0 0 1 0;}
1641 @font-face
1642         {font-family:OfficinaSans-Book;
1643         panose-1:0 0 0 0 0 0 0 0 0 0;
1644         mso-font-charset:77;
1645         mso-generic-font-family:swiss;
1646         mso-font-format:other;
1647         mso-font-pitch:auto;
1648         mso-font-signature:3 0 0 0 1 0;}
1649 @font-face
1650         {font-family:OfficinaSans-Bold;
1651         panose-1:0 0 0 0 0 0 0 0 0 0;
1652         mso-font-charset:77;
1653         mso-generic-font-family:swiss;
1654         mso-font-format:other;
1655         mso-font-pitch:auto;
1656         mso-font-signature:3 0 0 0 1 0;}
1657 @font-face
1658         {font-family:Helvetica-Bold;
1659         panose-1:0 0 0 0 0 0 0 0 0 0;
1660         mso-font-charset:77;
1661         mso-generic-font-family:swiss;
1662         mso-font-format:other;
1663         mso-font-pitch:auto;
1664         mso-font-signature:3 0 0 0 1 0;}
1665 @font-face
1666         {font-family:OfficinaSerif-Book;
1667         panose-1:0 0 0 0 0 0 0 0 0 0;
1668         mso-font-charset:77;
1669         mso-generic-font-family:roman;
1670         mso-font-format:other;
1671         mso-font-pitch:auto;
1672         mso-font-signature:3 0 0 0 1 0;}
1673  /* Style Definitions */
1674 p.MsoNormal, li.MsoNormal, div.MsoNormal
1675         {mso-style-parent:"";
1676         margin:0cm;
1677         margin-bottom:.0001pt;
1678         mso-pagination:widow-orphan;
1679         font-size:8.0pt;
1680         mso-bidi-font-size:10.0pt;
1681         font-family:Garamond;
1682         mso-fareast-font-family:"Times New Roman";
1683         mso-bidi-font-family:"Times New Roman";}
1684 h1
1685         {mso-style-link:"Heading 1 Char";
1686         mso-style-next:"Body Text";
1687         margin-top:12.0pt;
1688         margin-right:0cm;
1689         margin-bottom:6.0pt;
1690         margin-left:0cm;
1691         mso-pagination:widow-orphan;
1692         page-break-after:avoid;
1693         mso-outline-level:1;
1694         font-size:16.0pt;
1695         mso-bidi-font-size:10.0pt;
1696         font-family:"Arial Black";
1697         color:gray;
1698         letter-spacing:-1.25pt;
1699         mso-font-kerning:14.0pt;
1700         font-weight:normal;}
1701 h2
1702         {mso-style-update:auto;
1703         mso-style-parent:"Heading 1";
1704         mso-style-next:"Body Text";
1705         margin-top:12.0pt;
1706         margin-right:0cm;
1707         margin-bottom:6.0pt;
1708         margin-left:0cm;
1709         mso-line-height-alt:12.0pt;
1710         mso-pagination:widow-orphan;
1711         page-break-after:avoid;
1712         mso-outline-level:2;
1713         font-size:16.0pt;
1714         mso-bidi-font-size:10.0pt;
1715         font-family:"Arial Black";
1716         color:gray;
1717         letter-spacing:-.5pt;
1718         mso-font-kerning:14.0pt;
1719         font-weight:normal;}
1720 h3
1721         {mso-style-update:auto;
1722         mso-style-next:Normal;
1723         margin-top:6.0pt;
1724         margin-right:0cm;
1725         margin-bottom:6.0pt;
1726         margin-left:18.0pt;
1727         text-align:justify;
1728         mso-pagination:none;
1729         page-break-after:avoid;
1730         mso-outline-level:3;
1731         mso-hyphenate:none;
1732         mso-layout-grid-align:none;
1733         punctuation-wrap:simple;
1734         text-autospace:none;
1735         font-size:14.0pt;
1736         mso-bidi-font-size:10.0pt;
1737         font-family:"Arial Black";
1738         mso-hansi-font-family:Symbol;
1739         font-weight:normal;}
1740 h4
1741         {mso-style-update:auto;
1742         mso-style-parent:MyNormal;
1743         mso-style-next:Normal;
1744         margin-top:2.0pt;
1745         margin-right:0cm;
1746         margin-bottom:12.0pt;
1747         margin-left:1.0cm;
1748         mso-pagination:none;
1749         page-break-after:avoid;
1750         mso-outline-level:4;
1751         mso-hyphenate:none;
1752         mso-layout-grid-align:none;
1753         punctuation-wrap:simple;
1754         text-autospace:none;
1755         font-size:11.0pt;
1756         font-family:"Times New Roman";
1757         mso-bidi-font-family:"Courier New";
1758         text-transform:uppercase;
1759         letter-spacing:1.5pt;
1760         mso-ansi-language:AF;
1761         font-weight:normal;}
1762 h5
1763         {mso-style-next:"Body Text";
1764         margin-top:2.0pt;
1765         margin-right:0cm;
1766         margin-bottom:12.0pt;
1767         margin-left:0cm;
1768         mso-pagination:widow-orphan;
1769         page-break-after:avoid;
1770         mso-outline-level:5;
1771         mso-element:frame;
1772         mso-element-frame-width:90.0pt;
1773         mso-element-wrap:around;
1774         mso-element-anchor-vertical:paragraph;
1775         mso-element-anchor-horizontal:page;
1776         mso-element-left:60.05pt;
1777         mso-element-top:.05pt;
1778         mso-height-rule:exactly;
1779         font-size:9.0pt;
1780         mso-bidi-font-size:10.0pt;
1781         font-family:"Arial Black";
1782         letter-spacing:-.25pt;
1783         font-weight:normal;}
1784 h6
1785         {mso-style-next:"Body Text";
1786         margin:0cm;
1787         margin-bottom:.0001pt;
1788         mso-pagination:widow-orphan;
1789         page-break-after:avoid;
1790         mso-outline-level:6;
1791         mso-element:frame;
1792         mso-element-frame-width:90.0pt;
1793         mso-element-wrap:around;
1794         mso-element-anchor-vertical:paragraph;
1795         mso-element-anchor-horizontal:page;
1796         mso-element-left:60.05pt;
1797         mso-element-top:.05pt;
1798         mso-height-rule:exactly;
1799         font-size:8.0pt;
1800         mso-bidi-font-size:10.0pt;
1801         font-family:Garamond;
1802         font-weight:normal;}
1803 p.MsoHeading7, li.MsoHeading7, div.MsoHeading7
1804         {mso-style-next:"Body Text";
1805         margin-top:3.0pt;
1806         margin-right:0cm;
1807         margin-bottom:0cm;
1808         margin-left:0cm;
1809         margin-bottom:.0001pt;
1810         mso-pagination:widow-orphan;
1811         mso-outline-level:7;
1812         background:#F2F2F2;
1813         mso-shading:windowtext;
1814         mso-pattern:gray-5 auto;
1815         border:none;
1816         mso-border-alt:solid white .75pt;
1817         padding:0cm;
1818         mso-padding-alt:12.0pt 12.0pt 12.0pt 12.0pt;
1819         mso-element:frame;
1820         mso-element-frame-width:189.0pt;
1821         mso-element-frame-hspace:12.0pt;
1822         mso-element-wrap:around;
1823         mso-element-anchor-vertical:paragraph;
1824         mso-element-anchor-horizontal:page;
1825         mso-element-left:74.45pt;
1826         mso-element-top:.05pt;
1827         mso-height-rule:exactly;
1828         font-size:14.0pt;
1829         mso-bidi-font-size:10.0pt;
1830         font-family:Garamond;
1831         mso-fareast-font-family:"Times New Roman";
1832         mso-bidi-font-family:"Times New Roman";
1833         letter-spacing:-.25pt;
1834         font-style:italic;
1835         mso-bidi-font-style:normal;}
1836 p.MsoHeading8, li.MsoHeading8, div.MsoHeading8
1837         {mso-style-next:"Body Text";
1838         margin-top:3.0pt;
1839         margin-right:0cm;
1840         margin-bottom:0cm;
1841         margin-left:0cm;
1842         margin-bottom:.0001pt;
1843         text-align:center;
1844         line-height:16.0pt;
1845         mso-line-height-rule:exactly;
1846         mso-pagination:widow-orphan;
1847         page-break-after:avoid;
1848         mso-outline-level:8;
1849         border:none;
1850         mso-border-top-alt:solid windowtext 3.0pt;
1851         mso-border-bottom-alt:solid windowtext .75pt;
1852         padding:0cm;
1853         mso-padding-alt:0cm 0cm 0cm 0cm;
1854         mso-element:frame;
1855         mso-element-frame-width:93.0pt;
1856         mso-element-wrap:around;
1857         mso-element-anchor-vertical:paragraph;
1858         mso-element-anchor-horizontal:page;
1859         mso-element-left:60.05pt;
1860         mso-element-top:.05pt;
1861         mso-height-rule:exactly;
1862         font-size:7.0pt;
1863         mso-bidi-font-size:10.0pt;
1864         font-family:"Arial Black";
1865         mso-fareast-font-family:"Times New Roman";
1866         mso-bidi-font-family:"Times New Roman";
1867         text-transform:uppercase;
1868         letter-spacing:3.0pt;}
1869 p.MsoHeading9, li.MsoHeading9, div.MsoHeading9
1870         {mso-style-next:"Body Text";
1871         margin-top:4.0pt;
1872         margin-right:0cm;
1873         margin-bottom:3.0pt;
1874         margin-left:0cm;
1875         mso-pagination:widow-orphan;
1876         page-break-after:avoid;
1877         mso-outline-level:9;
1878         font-size:8.0pt;
1879         mso-bidi-font-size:10.0pt;
1880         font-family:Garamond;
1881         mso-fareast-font-family:"Times New Roman";
1882         mso-bidi-font-family:"Times New Roman";
1883         mso-font-kerning:14.0pt;
1884         font-weight:bold;
1885         mso-bidi-font-weight:normal;
1886         font-style:italic;
1887         mso-bidi-font-style:normal;}
1888 p.MsoIndex1, li.MsoIndex1, div.MsoIndex1
1889         {mso-style-update:auto;
1890         mso-style-noshow:yes;
1891         mso-style-next:Normal;
1892         margin-top:0cm;
1893         margin-right:0cm;
1894         margin-bottom:0cm;
1895         margin-left:8.0pt;
1896         margin-bottom:.0001pt;
1897         text-indent:-8.0pt;
1898         mso-pagination:widow-orphan;
1899         font-size:8.0pt;
1900         mso-bidi-font-size:10.0pt;
1901         font-family:Garamond;
1902         mso-fareast-font-family:"Times New Roman";
1903         mso-bidi-font-family:"Times New Roman";}
1904 p.MsoToc1, li.MsoToc1, div.MsoToc1
1905         {mso-style-noshow:yes;
1906         margin-top:6.0pt;
1907         margin-right:0cm;
1908         margin-bottom:0cm;
1909         margin-left:0cm;
1910         margin-bottom:.0001pt;
1911         mso-pagination:widow-orphan;
1912         font-size:12.0pt;
1913         font-family:Cambria;
1914         mso-ascii-font-family:Cambria;
1915         mso-ascii-theme-font:minor-latin;
1916         mso-fareast-font-family:"Times New Roman";
1917         mso-hansi-font-family:Cambria;
1918         mso-hansi-theme-font:minor-latin;
1919         mso-bidi-font-family:"Times New Roman";
1920         font-weight:bold;
1921         mso-bidi-font-weight:normal;}
1922 p.MsoToc2, li.MsoToc2, div.MsoToc2
1923         {mso-style-noshow:yes;
1924         mso-style-parent:"TOC 1";
1925         margin-top:0cm;
1926         margin-right:0cm;
1927         margin-bottom:0cm;
1928         margin-left:8.0pt;
1929         margin-bottom:.0001pt;
1930         mso-pagination:widow-orphan;
1931         font-size:11.0pt;
1932         font-family:Cambria;
1933         mso-ascii-font-family:Cambria;
1934         mso-ascii-theme-font:minor-latin;
1935         mso-fareast-font-family:"Times New Roman";
1936         mso-hansi-font-family:Cambria;
1937         mso-hansi-theme-font:minor-latin;
1938         mso-bidi-font-family:"Times New Roman";
1939         font-weight:bold;
1940         mso-bidi-font-weight:normal;}
1941 p.MsoToc3, li.MsoToc3, div.MsoToc3
1942         {mso-style-noshow:yes;
1943         mso-style-next:Normal;
1944         margin-top:0cm;
1945         margin-right:0cm;
1946         margin-bottom:0cm;
1947         margin-left:16.0pt;
1948         margin-bottom:.0001pt;
1949         mso-pagination:widow-orphan;
1950         font-size:11.0pt;
1951         font-family:Cambria;
1952         mso-ascii-font-family:Cambria;
1953         mso-ascii-theme-font:minor-latin;
1954         mso-fareast-font-family:"Times New Roman";
1955         mso-hansi-font-family:Cambria;
1956         mso-hansi-theme-font:minor-latin;
1957         mso-bidi-font-family:"Times New Roman";}
1958 p.MsoToc4, li.MsoToc4, div.MsoToc4
1959         {mso-style-noshow:yes;
1960         mso-style-next:Normal;
1961         margin-top:0cm;
1962         margin-right:0cm;
1963         margin-bottom:0cm;
1964         margin-left:24.0pt;
1965         margin-bottom:.0001pt;
1966         mso-pagination:widow-orphan;
1967         font-size:10.0pt;
1968         font-family:Cambria;
1969         mso-ascii-font-family:Cambria;
1970         mso-ascii-theme-font:minor-latin;
1971         mso-fareast-font-family:"Times New Roman";
1972         mso-hansi-font-family:Cambria;
1973         mso-hansi-theme-font:minor-latin;
1974         mso-bidi-font-family:"Times New Roman";}
1975 p.MsoToc5, li.MsoToc5, div.MsoToc5
1976         {mso-style-update:auto;
1977         mso-style-noshow:yes;
1978         mso-style-next:Normal;
1979         margin-top:0cm;
1980         margin-right:0cm;
1981         margin-bottom:0cm;
1982         margin-left:32.0pt;
1983         margin-bottom:.0001pt;
1984         mso-pagination:widow-orphan;
1985         font-size:10.0pt;
1986         font-family:Cambria;
1987         mso-ascii-font-family:Cambria;
1988         mso-ascii-theme-font:minor-latin;
1989         mso-fareast-font-family:"Times New Roman";
1990         mso-hansi-font-family:Cambria;
1991         mso-hansi-theme-font:minor-latin;
1992         mso-bidi-font-family:"Times New Roman";}
1993 p.MsoToc6, li.MsoToc6, div.MsoToc6
1994         {mso-style-update:auto;
1995         mso-style-noshow:yes;
1996         mso-style-next:Normal;
1997         margin-top:0cm;
1998         margin-right:0cm;
1999         margin-bottom:0cm;
2000         margin-left:40.0pt;
2001         margin-bottom:.0001pt;
2002         mso-pagination:widow-orphan;
2003         font-size:10.0pt;
2004         font-family:Cambria;
2005         mso-ascii-font-family:Cambria;
2006         mso-ascii-theme-font:minor-latin;
2007         mso-fareast-font-family:"Times New Roman";
2008         mso-hansi-font-family:Cambria;
2009         mso-hansi-theme-font:minor-latin;
2010         mso-bidi-font-family:"Times New Roman";}
2011 p.MsoToc7, li.MsoToc7, div.MsoToc7
2012         {mso-style-update:auto;
2013         mso-style-noshow:yes;
2014         mso-style-next:Normal;
2015         margin-top:0cm;
2016         margin-right:0cm;
2017         margin-bottom:0cm;
2018         margin-left:48.0pt;
2019         margin-bottom:.0001pt;
2020         mso-pagination:widow-orphan;
2021         font-size:10.0pt;
2022         font-family:Cambria;
2023         mso-ascii-font-family:Cambria;
2024         mso-ascii-theme-font:minor-latin;
2025         mso-fareast-font-family:"Times New Roman";
2026         mso-hansi-font-family:Cambria;
2027         mso-hansi-theme-font:minor-latin;
2028         mso-bidi-font-family:"Times New Roman";}
2029 p.MsoToc8, li.MsoToc8, div.MsoToc8
2030         {mso-style-update:auto;
2031         mso-style-noshow:yes;
2032         mso-style-next:Normal;
2033         margin-top:0cm;
2034         margin-right:0cm;
2035         margin-bottom:0cm;
2036         margin-left:56.0pt;
2037         margin-bottom:.0001pt;
2038         mso-pagination:widow-orphan;
2039         font-size:10.0pt;
2040         font-family:Cambria;
2041         mso-ascii-font-family:Cambria;
2042         mso-ascii-theme-font:minor-latin;
2043         mso-fareast-font-family:"Times New Roman";
2044         mso-hansi-font-family:Cambria;
2045         mso-hansi-theme-font:minor-latin;
2046         mso-bidi-font-family:"Times New Roman";}
2047 p.MsoToc9, li.MsoToc9, div.MsoToc9
2048         {mso-style-update:auto;
2049         mso-style-noshow:yes;
2050         mso-style-next:Normal;
2051         margin-top:0cm;
2052         margin-right:0cm;
2053         margin-bottom:0cm;
2054         margin-left:64.0pt;
2055         margin-bottom:.0001pt;
2056         mso-pagination:widow-orphan;
2057         font-size:10.0pt;
2058         font-family:Cambria;
2059         mso-ascii-font-family:Cambria;
2060         mso-ascii-theme-font:minor-latin;
2061         mso-fareast-font-family:"Times New Roman";
2062         mso-hansi-font-family:Cambria;
2063         mso-hansi-theme-font:minor-latin;
2064         mso-bidi-font-family:"Times New Roman";}
2065 p.MsoHeader, li.MsoHeader, div.MsoHeader
2066         {margin:0cm;
2067         margin-bottom:.0001pt;
2068         mso-pagination:widow-orphan lines-together;
2069         tab-stops:center 216.0pt right 432.0pt;
2070         font-size:7.0pt;
2071         mso-bidi-font-size:10.0pt;
2072         font-family:"Arial Black";
2073         mso-fareast-font-family:"Times New Roman";
2074         mso-bidi-font-family:"Times New Roman";
2075         text-transform:uppercase;
2076         letter-spacing:3.0pt;}
2077 p.MsoFooter, li.MsoFooter, div.MsoFooter
2078         {margin:0cm;
2079         margin-bottom:.0001pt;
2080         text-align:center;
2081         mso-pagination:widow-orphan lines-together;
2082         tab-stops:center 216.0pt right 432.0pt;
2083         border:none;
2084         mso-border-top-alt:solid windowtext .75pt;
2085         padding:0cm;
2086         mso-padding-alt:3.0pt 0cm 0cm 0cm;
2087         font-size:8.0pt;
2088         mso-bidi-font-size:10.0pt;
2089         font-family:"Arial Black";
2090         mso-fareast-font-family:"Times New Roman";
2091         mso-bidi-font-family:"Times New Roman";}
2092 p.MsoCaption, li.MsoCaption, div.MsoCaption
2093         {mso-style-next:"Body Text";
2094         margin-top:0cm;
2095         margin-right:0cm;
2096         margin-bottom:12.0pt;
2097         margin-left:0cm;
2098         mso-pagination:widow-orphan;
2099         font-size:8.0pt;
2100         mso-bidi-font-size:10.0pt;
2101         font-family:Garamond;
2102         mso-fareast-font-family:"Times New Roman";
2103         mso-bidi-font-family:"Times New Roman";
2104         letter-spacing:-.25pt;}
2105 span.MsoCommentReference
2106         {mso-style-noshow:yes;
2107         mso-style-parent:"";
2108         mso-ansi-font-size:8.0pt;}
2109 span.MsoLineNumber
2110         {mso-style-parent:"";
2111         mso-ansi-font-size:9.0pt;
2112         font-family:Arial;
2113         mso-ascii-font-family:Arial;
2114         mso-hansi-font-family:Arial;
2115         mso-bidi-font-family:Arial;}
2116 span.MsoPageNumber
2117         {mso-style-parent:"";
2118         font-weight:bold;
2119         mso-bidi-font-weight:normal;}
2120 p.MsoList, li.MsoList, div.MsoList
2121         {mso-style-parent:"Body Text";
2122         mso-style-link:"List Char";
2123         margin-top:0cm;
2124         margin-right:0cm;
2125         margin-bottom:12.0pt;
2126         margin-left:18.0pt;
2127         text-align:justify;
2128         mso-pagination:widow-orphan;
2129         tab-stops:36.0pt;
2130         font-size:12.0pt;
2131         mso-bidi-font-size:10.0pt;
2132         font-family:Garamond;
2133         mso-fareast-font-family:"Times New Roman";
2134         mso-bidi-font-family:"Times New Roman";
2135         letter-spacing:-.25pt;}
2136 p.MsoListBullet, li.MsoListBullet, div.MsoListBullet
2137         {mso-style-parent:List;
2138         margin-top:0cm;
2139         margin-right:0cm;
2140         margin-bottom:12.0pt;
2141         margin-left:18.0pt;
2142         text-align:justify;
2143         text-indent:0cm;
2144         mso-pagination:widow-orphan;
2145         mso-list:l25 level1 lfo5;
2146         font-size:12.0pt;
2147         mso-bidi-font-size:10.0pt;
2148         font-family:Garamond;
2149         mso-fareast-font-family:"Times New Roman";
2150         mso-bidi-font-family:"Times New Roman";
2151         letter-spacing:-.25pt;}
2152 p.MsoListNumber, li.MsoListNumber, div.MsoListNumber
2153         {mso-style-parent:List;
2154         margin-top:0cm;
2155         margin-right:18.0pt;
2156         margin-bottom:12.0pt;
2157         margin-left:36.0pt;
2158         text-align:justify;
2159         text-indent:-18.0pt;
2160         mso-pagination:widow-orphan;
2161         mso-list:l8 level1 lfo7;
2162         font-size:12.0pt;
2163         mso-bidi-font-size:10.0pt;
2164         font-family:Garamond;
2165         mso-fareast-font-family:"Times New Roman";
2166         mso-bidi-font-family:"Times New Roman";
2167         letter-spacing:-.25pt;}
2168 p.MsoList2, li.MsoList2, div.MsoList2
2169         {mso-style-parent:List;
2170         margin-top:0cm;
2171         margin-right:0cm;
2172         margin-bottom:12.0pt;
2173         margin-left:54.0pt;
2174         text-align:justify;
2175         mso-pagination:widow-orphan;
2176         tab-stops:54.0pt;
2177         font-size:12.0pt;
2178         mso-bidi-font-size:10.0pt;
2179         font-family:Garamond;
2180         mso-fareast-font-family:"Times New Roman";
2181         mso-bidi-font-family:"Times New Roman";
2182         letter-spacing:-.25pt;}
2183 p.MsoList3, li.MsoList3, div.MsoList3
2184         {mso-style-parent:List;
2185         margin-top:0cm;
2186         margin-right:0cm;
2187         margin-bottom:12.0pt;
2188         margin-left:72.0pt;
2189         text-align:justify;
2190         mso-pagination:widow-orphan;
2191         tab-stops:72.0pt;
2192         font-size:12.0pt;
2193         mso-bidi-font-size:10.0pt;
2194         font-family:Garamond;
2195         mso-fareast-font-family:"Times New Roman";
2196         mso-bidi-font-family:"Times New Roman";
2197         letter-spacing:-.25pt;}
2198 p.MsoList4, li.MsoList4, div.MsoList4
2199         {mso-style-parent:List;
2200         margin-top:0cm;
2201         margin-right:0cm;
2202         margin-bottom:12.0pt;
2203         margin-left:90.0pt;
2204         text-align:justify;
2205         mso-pagination:widow-orphan;
2206         tab-stops:90.0pt;
2207         font-size:12.0pt;
2208         mso-bidi-font-size:10.0pt;
2209         font-family:Garamond;
2210         mso-fareast-font-family:"Times New Roman";
2211         mso-bidi-font-family:"Times New Roman";
2212         letter-spacing:-.25pt;}
2213 p.MsoList5, li.MsoList5, div.MsoList5
2214         {mso-style-parent:List;
2215         margin-top:0cm;
2216         margin-right:0cm;
2217         margin-bottom:12.0pt;
2218         margin-left:108.0pt;
2219         text-align:justify;
2220         mso-pagination:widow-orphan;
2221         tab-stops:108.0pt;
2222         font-size:12.0pt;
2223         mso-bidi-font-size:10.0pt;
2224         font-family:Garamond;
2225         mso-fareast-font-family:"Times New Roman";
2226         mso-bidi-font-family:"Times New Roman";
2227         letter-spacing:-.25pt;}
2228 p.MsoListBullet2, li.MsoListBullet2, div.MsoListBullet2
2229         {mso-style-parent:"List Bullet";
2230         margin-top:0cm;
2231         margin-right:0cm;
2232         margin-bottom:12.0pt;
2233         margin-left:54.0pt;
2234         text-align:justify;
2235         text-indent:0cm;
2236         mso-pagination:widow-orphan;
2237         mso-list:l7 level1 lfo8;
2238         font-size:12.0pt;
2239         mso-bidi-font-size:10.0pt;
2240         font-family:Garamond;
2241         mso-fareast-font-family:"Times New Roman";
2242         mso-bidi-font-family:"Times New Roman";
2243         letter-spacing:-.25pt;}
2244 p.MsoListBullet3, li.MsoListBullet3, div.MsoListBullet3
2245         {mso-style-parent:"List Bullet";
2246         margin-top:0cm;
2247         margin-right:0cm;
2248         margin-bottom:12.0pt;
2249         margin-left:72.0pt;
2250         text-align:justify;
2251         text-indent:0cm;
2252         mso-pagination:widow-orphan;
2253         mso-list:l6 level1 lfo9;
2254         font-size:12.0pt;
2255         mso-bidi-font-size:10.0pt;
2256         font-family:Garamond;
2257         mso-fareast-font-family:"Times New Roman";
2258         mso-bidi-font-family:"Times New Roman";
2259         letter-spacing:-.25pt;}
2260 p.MsoListBullet4, li.MsoListBullet4, div.MsoListBullet4
2261         {mso-style-parent:"List Bullet";
2262         margin-top:0cm;
2263         margin-right:0cm;
2264         margin-bottom:12.0pt;
2265         margin-left:90.0pt;
2266         text-align:justify;
2267         text-indent:0cm;
2268         mso-pagination:widow-orphan;
2269         mso-list:l5 level1 lfo10;
2270         font-size:12.0pt;
2271         mso-bidi-font-size:10.0pt;
2272         font-family:Garamond;
2273         mso-fareast-font-family:"Times New Roman";
2274         mso-bidi-font-family:"Times New Roman";
2275         letter-spacing:-.25pt;}
2276 p.MsoListBullet5, li.MsoListBullet5, div.MsoListBullet5
2277         {margin-top:0cm;
2278         margin-right:18.0pt;
2279         margin-bottom:0cm;
2280         margin-left:18.0pt;
2281         margin-bottom:.0001pt;
2282         text-indent:-18.0pt;
2283         line-height:16.0pt;
2284         mso-line-height-rule:exactly;
2285         mso-pagination:widow-orphan;
2286         mso-list:l22 level1 lfo12;
2287         tab-stops:list 18.0pt;
2288         border:none;
2289         mso-border-bottom-alt:solid windowtext .75pt;
2290         padding:0cm;
2291         mso-padding-alt:0cm 0cm 0cm 0cm;
2292         mso-element:frame;
2293         mso-element-frame-width:93.0pt;
2294         mso-element-wrap:around;
2295         mso-element-anchor-vertical:paragraph;
2296         mso-element-anchor-horizontal:page;
2297         mso-element-left:60.05pt;
2298         mso-element-top:.05pt;
2299         mso-height-rule:exactly;
2300         font-size:9.0pt;
2301         mso-bidi-font-size:10.0pt;
2302         font-family:Garamond;
2303         mso-fareast-font-family:"Times New Roman";
2304         mso-bidi-font-family:"Times New Roman";}
2305 p.MsoListNumber2, li.MsoListNumber2, div.MsoListNumber2
2306         {mso-style-parent:"List Number";
2307         margin-top:0cm;
2308         margin-right:18.0pt;
2309         margin-bottom:12.0pt;
2310         margin-left:54.0pt;
2311         text-align:justify;
2312         text-indent:-18.0pt;
2313         mso-pagination:widow-orphan;
2314         mso-list:l3 level1 lfo14;
2315         font-size:12.0pt;
2316         mso-bidi-font-size:10.0pt;
2317         font-family:Garamond;
2318         mso-fareast-font-family:"Times New Roman";
2319         mso-bidi-font-family:"Times New Roman";
2320         letter-spacing:-.25pt;}
2321 p.MsoListNumber3, li.MsoListNumber3, div.MsoListNumber3
2322         {mso-style-parent:"List Number";
2323         margin-top:0cm;
2324         margin-right:18.0pt;
2325         margin-bottom:12.0pt;
2326         margin-left:72.0pt;
2327         text-align:justify;
2328         text-indent:-18.0pt;
2329         mso-pagination:widow-orphan;
2330         mso-list:l2 level1 lfo15;
2331         font-size:12.0pt;
2332         mso-bidi-font-size:10.0pt;
2333         font-family:Garamond;
2334         mso-fareast-font-family:"Times New Roman";
2335         mso-bidi-font-family:"Times New Roman";
2336         letter-spacing:-.25pt;}
2337 p.MsoListNumber4, li.MsoListNumber4, div.MsoListNumber4
2338         {mso-style-parent:"List Number";
2339         margin-top:0cm;
2340         margin-right:18.0pt;
2341         margin-bottom:12.0pt;
2342         margin-left:90.0pt;
2343         text-align:justify;
2344         text-indent:-18.0pt;
2345         mso-pagination:widow-orphan;
2346         mso-list:l1 level1 lfo16;
2347         font-size:12.0pt;
2348         mso-bidi-font-size:10.0pt;
2349         font-family:Garamond;
2350         mso-fareast-font-family:"Times New Roman";
2351         mso-bidi-font-family:"Times New Roman";
2352         letter-spacing:-.25pt;}
2353 p.MsoListNumber5, li.MsoListNumber5, div.MsoListNumber5
2354         {mso-style-parent:"List Number";
2355         margin-top:0cm;
2356         margin-right:18.0pt;
2357         margin-bottom:12.0pt;
2358         margin-left:108.0pt;
2359         text-align:justify;
2360         text-indent:-18.0pt;
2361         mso-pagination:widow-orphan;
2362         mso-list:l0 level1 lfo17;
2363         font-size:12.0pt;
2364         mso-bidi-font-size:10.0pt;
2365         font-family:Garamond;
2366         mso-fareast-font-family:"Times New Roman";
2367         mso-bidi-font-family:"Times New Roman";
2368         letter-spacing:-.25pt;}
2369 p.MsoTitle, li.MsoTitle, div.MsoTitle
2370         {mso-style-parent:"Heading Base";
2371         margin-top:5.0pt;
2372         margin-right:0cm;
2373         margin-bottom:180.0pt;
2374         margin-left:0cm;
2375         text-align:center;
2376         line-height:30.0pt;
2377         mso-line-height-rule:exactly;
2378         mso-pagination:widow-orphan;
2379         page-break-after:avoid;
2380         border:none;
2381         mso-border-bottom-alt:solid gray .75pt;
2382         padding:0cm;
2383         mso-padding-alt:0cm 0cm 14.0pt 0cm;
2384         font-size:24.0pt;
2385         mso-bidi-font-size:10.0pt;
2386         font-family:"Arial Black";
2387         mso-fareast-font-family:"Times New Roman";
2388         mso-bidi-font-family:"Times New Roman";
2389         color:gray;
2390         letter-spacing:-1.75pt;
2391         mso-font-kerning:14.0pt;}
2392 p.MsoBodyText, li.MsoBodyText, div.MsoBodyText
2393         {margin-top:0cm;
2394         margin-right:0cm;
2395         margin-bottom:12.0pt;
2396         margin-left:0cm;
2397         text-align:justify;
2398         mso-pagination:widow-orphan;
2399         font-size:12.0pt;
2400         mso-bidi-font-size:10.0pt;
2401         font-family:Garamond;
2402         mso-fareast-font-family:"Times New Roman";
2403         mso-bidi-font-family:"Times New Roman";
2404         letter-spacing:-.25pt;}
2405 p.MsoBodyTextIndent, li.MsoBodyTextIndent, div.MsoBodyTextIndent
2406         {mso-style-parent:"Body Text";
2407         margin-top:0cm;
2408         margin-right:0cm;
2409         margin-bottom:12.0pt;
2410         margin-left:0cm;
2411         text-align:justify;
2412         text-indent:18.0pt;
2413         mso-pagination:widow-orphan;
2414         font-size:12.0pt;
2415         mso-bidi-font-size:10.0pt;
2416         font-family:Garamond;
2417         mso-fareast-font-family:"Times New Roman";
2418         mso-bidi-font-family:"Times New Roman";
2419         letter-spacing:-.25pt;}
2420 p.MsoListContinue, li.MsoListContinue, div.MsoListContinue
2421         {mso-style-parent:List;
2422         margin-top:0cm;
2423         margin-right:0cm;
2424         margin-bottom:8.0pt;
2425         margin-left:18.0pt;
2426         text-align:justify;
2427         mso-pagination:widow-orphan;
2428         font-size:12.0pt;
2429         mso-bidi-font-size:10.0pt;
2430         font-family:Garamond;
2431         mso-fareast-font-family:"Times New Roman";
2432         mso-bidi-font-family:"Times New Roman";
2433         letter-spacing:-.25pt;}
2434 p.MsoListContinue2, li.MsoListContinue2, div.MsoListContinue2
2435         {mso-style-parent:"List Continue";
2436         margin-top:0cm;
2437         margin-right:0cm;
2438         margin-bottom:8.0pt;
2439         margin-left:54.0pt;
2440         text-align:justify;
2441         mso-pagination:widow-orphan;
2442         font-size:12.0pt;
2443         mso-bidi-font-size:10.0pt;
2444         font-family:Garamond;
2445         mso-fareast-font-family:"Times New Roman";
2446         mso-bidi-font-family:"Times New Roman";
2447         letter-spacing:-.25pt;}
2448 p.MsoListContinue3, li.MsoListContinue3, div.MsoListContinue3
2449         {mso-style-parent:"List Continue";
2450         margin-top:0cm;
2451         margin-right:0cm;
2452         margin-bottom:8.0pt;
2453         margin-left:72.0pt;
2454         text-align:justify;
2455         mso-pagination:widow-orphan;
2456         font-size:12.0pt;
2457         mso-bidi-font-size:10.0pt;
2458         font-family:Garamond;
2459         mso-fareast-font-family:"Times New Roman";
2460         mso-bidi-font-family:"Times New Roman";
2461         letter-spacing:-.25pt;}
2462 p.MsoListContinue4, li.MsoListContinue4, div.MsoListContinue4
2463         {mso-style-parent:"List Continue";
2464         margin-top:0cm;
2465         margin-right:0cm;
2466         margin-bottom:8.0pt;
2467         margin-left:90.0pt;
2468         text-align:justify;
2469         mso-pagination:widow-orphan;
2470         font-size:12.0pt;
2471         mso-bidi-font-size:10.0pt;
2472         font-family:Garamond;
2473         mso-fareast-font-family:"Times New Roman";
2474         mso-bidi-font-family:"Times New Roman";
2475         letter-spacing:-.25pt;}
2476 p.MsoListContinue5, li.MsoListContinue5, div.MsoListContinue5
2477         {mso-style-parent:"List Continue";
2478         margin-top:0cm;
2479         margin-right:0cm;
2480         margin-bottom:8.0pt;
2481         margin-left:108.0pt;
2482         text-align:justify;
2483         mso-pagination:widow-orphan;
2484         font-size:12.0pt;
2485         mso-bidi-font-size:10.0pt;
2486         font-family:Garamond;
2487         mso-fareast-font-family:"Times New Roman";
2488         mso-bidi-font-family:"Times New Roman";
2489         letter-spacing:-.25pt;}
2490 p.MsoSubtitle, li.MsoSubtitle, div.MsoSubtitle
2491         {mso-style-parent:Title;
2492         mso-style-next:"Body Text";
2493         margin-top:97.0pt;
2494         margin-right:0cm;
2495         margin-bottom:0cm;
2496         margin-left:0cm;
2497         margin-bottom:.0001pt;
2498         text-align:center;
2499         line-height:10.0pt;
2500         mso-pagination:widow-orphan;
2501         page-break-after:avoid;
2502         border:none;
2503         mso-border-bottom-alt:solid gray .75pt;
2504         padding:0cm;
2505         mso-padding-alt:0cm 0cm 14.0pt 0cm;
2506         font-size:9.0pt;
2507         mso-bidi-font-size:10.0pt;
2508         font-family:Garamond;
2509         mso-fareast-font-family:"Times New Roman";
2510         mso-bidi-font-family:"Times New Roman";
2511         color:gray;
2512         text-transform:uppercase;
2513         letter-spacing:1.5pt;
2514         mso-font-kerning:14.0pt;
2515         mso-bidi-font-weight:bold;}
2516 p.MsoDate, li.MsoDate, div.MsoDate
2517         {mso-style-parent:"Body Text";
2518         margin-top:24.0pt;
2519         margin-right:0cm;
2520         margin-bottom:8.0pt;
2521         margin-left:0cm;
2522         text-align:center;
2523         mso-pagination:widow-orphan;
2524         font-size:10.0pt;
2525         font-family:"Times New Roman";
2526         mso-fareast-font-family:"Times New Roman";
2527         mso-bidi-font-family:"Times New Roman";
2528         font-weight:bold;
2529         mso-bidi-font-weight:normal;}
2530 a:link, span.MsoHyperlink
2531         {color:blue;
2532         text-decoration:underline;
2533         text-underline:single;}
2534 a:visited, span.MsoHyperlinkFollowed
2535         {color:purple;
2536         text-decoration:underline;
2537         text-underline:single;}
2538 em
2539         {mso-style-parent:"";
2540         mso-ansi-font-size:9.0pt;
2541         font-family:"Arial Black";
2542         mso-ascii-font-family:"Arial Black";
2543         mso-hansi-font-family:"Arial Black";
2544         font-style:normal;}
2545 p.MsoPlainText, li.MsoPlainText, div.MsoPlainText
2546         {margin:0cm;
2547         margin-bottom:.0001pt;
2548         mso-pagination:widow-orphan;
2549         font-size:10.0pt;
2550         font-family:"Courier New";
2551         mso-fareast-font-family:"Times New Roman";
2552         mso-bidi-font-family:"Courier New";
2553         mso-ansi-language:FR;
2554         mso-fareast-language:FR;}
2555 code
2556         {mso-bidi-font-size:10.0pt;
2557         font-family:"Courier New";
2558         mso-ascii-font-family:"Courier New";
2559         mso-fareast-font-family:"MS Mincho";
2560         mso-hansi-font-family:"Courier New";
2561         mso-bidi-font-family:"Courier New";}
2562 span.Heading1Char
2563         {mso-style-name:"Heading 1 Char";
2564         mso-style-locked:yes;
2565         mso-style-link:"Heading 1";
2566         mso-ansi-font-size:16.0pt;
2567         font-family:"Arial Black";
2568         mso-ascii-font-family:"Arial Black";
2569         mso-hansi-font-family:"Arial Black";
2570         color:gray;
2571         letter-spacing:-1.25pt;
2572         mso-font-kerning:14.0pt;
2573         mso-ansi-language:EN-US;
2574         mso-fareast-language:EN-US;}
2575 p.MyNormal, li.MyNormal, div.MyNormal
2576         {mso-style-name:MyNormal;
2577         mso-style-update:auto;
2578         mso-style-link:"MyNormal Char";
2579         margin-top:2.0pt;
2580         margin-right:0cm;
2581         margin-bottom:6.0pt;
2582         margin-left:42.55pt;
2583         text-align:justify;
2584         mso-pagination:none;
2585         mso-hyphenate:none;
2586         mso-layout-grid-align:none;
2587         punctuation-wrap:simple;
2588         text-autospace:none;
2589         font-size:11.0pt;
2590         font-family:"Times New Roman";
2591         mso-fareast-font-family:"Times New Roman";
2592         mso-bidi-font-family:"Courier New";
2593         mso-ansi-language:AF;}
2594 span.MyNormalChar
2595         {mso-style-name:"MyNormal Char";
2596         mso-style-locked:yes;
2597         mso-style-parent:"example Char";
2598         mso-style-link:MyNormal;
2599         mso-ansi-font-size:11.0pt;
2600         mso-bidi-font-size:11.0pt;
2601         font-family:"Courier New";
2602         mso-ascii-font-family:"Courier New";
2603         mso-hansi-font-family:"Courier New";
2604         mso-bidi-font-family:"Courier New";
2605         mso-ansi-language:AF;
2606         mso-fareast-language:EN-US;}
2607 span.exampleChar
2608         {mso-style-name:"example Char";
2609         mso-style-locked:yes;
2610         mso-style-link:example;
2611         mso-ansi-font-size:8.0pt;
2612         font-family:"Courier New";
2613         mso-ascii-font-family:"Courier New";
2614         mso-hansi-font-family:"Courier New";
2615         mso-bidi-font-family:"Courier New";
2616         mso-ansi-language:EN-US;
2617         mso-fareast-language:EN-US;}
2618 p.example, li.example, div.example
2619         {mso-style-name:example;
2620         mso-style-update:auto;
2621         mso-style-link:"example Char";
2622         margin-top:6.0pt;
2623         margin-right:0cm;
2624         margin-bottom:6.0pt;
2625         margin-left:0cm;
2626         text-indent:36.0pt;
2627         mso-pagination:none;
2628         mso-hyphenate:none;
2629         mso-layout-grid-align:none;
2630         punctuation-wrap:simple;
2631         text-autospace:none;
2632         font-size:8.0pt;
2633         mso-bidi-font-size:10.0pt;
2634         font-family:"Courier New";
2635         mso-fareast-font-family:"Times New Roman";
2636         mso-bidi-font-family:"Courier New";}
2637 p.FAQ, li.FAQ, div.FAQ
2638         {mso-style-name:FAQ;
2639         mso-style-update:auto;
2640         mso-style-parent:MyNormal;
2641         margin-top:12.0pt;
2642         margin-right:0cm;
2643         margin-bottom:6.0pt;
2644         margin-left:1.0cm;
2645         text-align:justify;
2646         mso-pagination:none;
2647         mso-hyphenate:none;
2648         mso-layout-grid-align:none;
2649         punctuation-wrap:simple;
2650         text-autospace:none;
2651         font-size:11.0pt;
2652         mso-bidi-font-size:14.0pt;
2653         font-family:"Comic Sans MS";
2654         mso-fareast-font-family:"Times New Roman";
2655         mso-bidi-font-family:"Courier New";
2656         mso-ansi-language:EN-GB;
2657         font-weight:bold;
2658         mso-bidi-font-weight:normal;}
2659 span.ListChar
2660         {mso-style-name:"List Char";
2661         mso-style-locked:yes;
2662         mso-style-parent:"Text body Char";
2663         mso-style-link:List;
2664         mso-ansi-font-size:12.0pt;
2665         font-family:Garamond;
2666         mso-ascii-font-family:Garamond;
2667         mso-hansi-font-family:Garamond;
2668         letter-spacing:-.25pt;
2669         mso-ansi-language:EN-US;
2670         mso-fareast-language:EN-US;}
2671 span.TextbodyChar
2672         {mso-style-name:"Text body Char";
2673         mso-style-locked:yes;
2674         mso-style-link:"Text body";
2675         mso-ansi-font-size:12.0pt;
2676         mso-ansi-language:EN-US;
2677         mso-fareast-language:EN-US;}
2678 p.Textbody, li.Textbody, div.Textbody
2679         {mso-style-name:"Text body";
2680         mso-style-link:"Text body Char";
2681         margin:0cm;
2682         margin-bottom:.0001pt;
2683         text-align:justify;
2684         mso-pagination:none;
2685         mso-hyphenate:none;
2686         mso-layout-grid-align:none;
2687         punctuation-wrap:simple;
2688         text-autospace:none;
2689         font-size:12.0pt;
2690         mso-bidi-font-size:10.0pt;
2691         font-family:"Times New Roman";
2692         mso-fareast-font-family:"Times New Roman";
2693         mso-bidi-font-family:"Times New Roman";}
2694 p.HeadingBase, li.HeadingBase, div.HeadingBase
2695         {mso-style-name:"Heading Base";
2696         mso-style-next:"Body Text";
2697         margin-top:12.0pt;
2698         margin-right:0cm;
2699         margin-bottom:6.0pt;
2700         margin-left:0cm;
2701         mso-pagination:widow-orphan;
2702         page-break-after:avoid;
2703         font-size:18.0pt;
2704         mso-bidi-font-size:10.0pt;
2705         font-family:Arial;
2706         mso-fareast-font-family:"Times New Roman";
2707         mso-bidi-font-family:"Times New Roman";
2708         mso-font-kerning:14.0pt;
2709         font-weight:bold;
2710         mso-bidi-font-weight:normal;}
2711 p.BlockQuotation, li.BlockQuotation, div.BlockQuotation
2712         {mso-style-name:"Block Quotation";
2713         mso-style-next:"Body Text";
2714         margin-top:0cm;
2715         margin-right:30.0pt;
2716         margin-bottom:12.0pt;
2717         margin-left:30.0pt;
2718         text-align:justify;
2719         mso-pagination:widow-orphan;
2720         background:#484848;
2721         mso-shading:windowtext;
2722         mso-pattern:gray-10 gray;
2723         border:none;
2724         mso-border-alt:solid white .75pt;
2725         padding:0cm;
2726         mso-padding-alt:12.0pt 12.0pt 12.0pt 12.0pt;
2727         font-size:12.0pt;
2728         mso-bidi-font-size:10.0pt;
2729         font-family:Garamond;
2730         mso-fareast-font-family:"Times New Roman";
2731         mso-bidi-font-family:"Times New Roman";
2732         letter-spacing:-.25pt;}
2733 p.BlockQuotationFirst, li.BlockQuotationFirst, div.BlockQuotationFirst
2734         {mso-style-name:"Block Quotation First";
2735         mso-style-next:"Block Quotation";
2736         margin-top:0cm;
2737         margin-right:24.0pt;
2738         margin-bottom:0cm;
2739         margin-left:24.0pt;
2740         margin-bottom:.0001pt;
2741         text-indent:3.0pt;
2742         mso-pagination:widow-orphan lines-together;
2743         background:#E5E5E5;
2744         mso-shading:windowtext;
2745         mso-pattern:gray-10 auto;
2746         border:none;
2747         mso-border-top-alt:solid white .75pt;
2748         mso-border-left-alt:solid white .75pt;
2749         mso-border-right-alt:solid white .75pt;
2750         padding:0cm;
2751         mso-padding-alt:6.0pt 6.0pt 0cm 6.0pt;
2752         font-size:10.5pt;
2753         mso-bidi-font-size:10.0pt;
2754         font-family:"Arial Black";
2755         mso-fareast-font-family:"Times New Roman";
2756         mso-bidi-font-family:"Times New Roman";
2757         letter-spacing:-.5pt;}
2758 p.BlockQuotationLast, li.BlockQuotationLast, div.BlockQuotationLast
2759         {mso-style-name:"Block Quotation Last";
2760         mso-style-parent:"Block Quotation";
2761         mso-style-next:"Body Text";
2762         margin-top:0cm;
2763         margin-right:36.0pt;
2764         margin-bottom:12.0pt;
2765         margin-left:36.0pt;
2766         mso-pagination:widow-orphan lines-together;
2767         font-size:10.0pt;
2768         font-family:"Times New Roman";
2769         mso-fareast-font-family:"Times New Roman";
2770         mso-bidi-font-family:"Times New Roman";
2771         font-style:italic;
2772         mso-bidi-font-style:normal;}
2773 p.BodyTextKeep, li.BodyTextKeep, div.BodyTextKeep
2774         {mso-style-name:"Body Text Keep";
2775         mso-style-parent:"Body Text";
2776         mso-style-next:"Body Text";
2777         margin-top:0cm;
2778         margin-right:0cm;
2779         margin-bottom:12.0pt;
2780         margin-left:0cm;
2781         text-align:justify;
2782         mso-pagination:widow-orphan;
2783         page-break-after:avoid;
2784         font-size:12.0pt;
2785         mso-bidi-font-size:10.0pt;
2786         font-family:Garamond;
2787         mso-fareast-font-family:"Times New Roman";
2788         mso-bidi-font-family:"Times New Roman";
2789         letter-spacing:-.25pt;}
2790 p.ChapterLabel, li.ChapterLabel, div.ChapterLabel
2791         {mso-style-name:"Chapter Label";
2792         mso-style-next:"Body Text";
2793         margin-top:0cm;
2794         margin-right:0cm;
2795         margin-bottom:12.0pt;
2796         margin-left:0cm;
2797         mso-pagination:widow-orphan;
2798         page-break-after:avoid;
2799         border:none;
2800         mso-border-bottom-alt:solid windowtext .75pt;
2801         padding:0cm;
2802         mso-padding-alt:0cm 0cm 3.0pt 0cm;
2803         font-size:7.5pt;
2804         mso-bidi-font-size:10.0pt;
2805         font-family:"Arial Black";
2806         mso-fareast-font-family:"Times New Roman";
2807         mso-bidi-font-family:"Times New Roman";
2808         text-transform:uppercase;
2809         letter-spacing:3.5pt;
2810         mso-font-kerning:14.0pt;}
2811 p.ChapterSubtitle, li.ChapterSubtitle, div.ChapterSubtitle
2812         {mso-style-name:"Chapter Subtitle";
2813         mso-style-next:"Body Text";
2814         margin-top:0cm;
2815         margin-right:90.0pt;
2816         margin-bottom:18.0pt;
2817         margin-left:0cm;
2818         mso-line-height-alt:12.0pt;
2819         mso-pagination:widow-orphan lines-together;
2820         page-break-after:avoid;
2821         font-size:14.0pt;
2822         mso-bidi-font-size:10.0pt;
2823         font-family:Garamond;
2824         mso-fareast-font-family:"Times New Roman";
2825         mso-bidi-font-family:"Times New Roman";
2826         letter-spacing:-1.0pt;
2827         mso-font-kerning:14.0pt;
2828         font-style:italic;
2829         mso-bidi-font-style:normal;}
2830 p.ChapterTitle, li.ChapterTitle, div.ChapterTitle
2831         {mso-style-name:"Chapter Title";
2832         mso-style-update:auto;
2833         mso-style-link:"Chapter Title Char";
2834         mso-style-next:"Chapter Subtitle";
2835         margin-top:30.0pt;
2836         margin-right:4.25pt;
2837         margin-bottom:102.0pt;
2838         margin-left:0cm;
2839         text-align:center;
2840         mso-line-height-alt:22.0pt;
2841         page-break-before:always;
2842         mso-pagination:widow-orphan lines-together;
2843         page-break-after:avoid;
2844         background:#CCCCCC;
2845         border:none;
2846         mso-border-alt:solid windowtext 3.0pt;
2847         padding:0cm;
2848         mso-padding-alt:1.0pt 4.0pt 1.0pt 4.0pt;
2849         font-size:36.0pt;
2850         mso-bidi-font-size:48.0pt;
2851         font-family:"Arial Black";
2852         mso-fareast-font-family:"Times New Roman";
2853         mso-bidi-font-family:"Times New Roman";
2854         color:white;
2855         letter-spacing:-1.75pt;
2856         mso-font-kerning:14.0pt;}
2857 span.ChapterTitleChar
2858         {mso-style-name:"Chapter Title Char";
2859         mso-style-locked:yes;
2860         mso-style-link:"Chapter Title";
2861         mso-ansi-font-size:36.0pt;
2862         mso-bidi-font-size:48.0pt;
2863         font-family:"Arial Black";
2864         mso-ascii-font-family:"Arial Black";
2865         mso-hansi-font-family:"Arial Black";
2866         color:white;
2867         letter-spacing:-1.75pt;
2868         mso-font-kerning:14.0pt;
2869         mso-ansi-language:EN-US;
2870         mso-fareast-language:EN-US;}
2871 p.CompanyName, li.CompanyName, div.CompanyName
2872         {mso-style-name:"Company Name";
2873         mso-style-next:Normal;
2874         margin-top:21.0pt;
2875         margin-right:0cm;
2876         margin-bottom:3.0pt;
2877         margin-left:0cm;
2878         line-height:16.0pt;
2879         mso-line-height-rule:exactly;
2880         mso-pagination:widow-orphan;
2881         font-size:19.0pt;
2882         mso-bidi-font-size:10.0pt;
2883         font-family:Garamond;
2884         mso-fareast-font-family:"Times New Roman";
2885         mso-bidi-font-family:"Times New Roman";
2886         text-transform:uppercase;
2887         mso-font-kerning:18.0pt;}
2888 p.DocumentLabel, li.DocumentLabel, div.DocumentLabel
2889         {mso-style-name:"Document Label";
2890         margin-top:12.0pt;
2891         margin-right:0cm;
2892         margin-bottom:18.0pt;
2893         margin-left:0cm;
2894         mso-pagination:widow-orphan;
2895         page-break-after:avoid;
2896         font-size:18.0pt;
2897         mso-bidi-font-size:10.0pt;
2898         font-family:Garamond;
2899         mso-fareast-font-family:"Times New Roman";
2900         mso-bidi-font-family:"Times New Roman";
2901         mso-font-kerning:14.0pt;
2902         font-weight:bold;
2903         mso-bidi-font-weight:normal;}
2904 p.FooterEven, li.FooterEven, div.FooterEven
2905         {mso-style-name:"Footer Even";
2906         mso-style-parent:Footer;
2907         margin:0cm;
2908         margin-bottom:.0001pt;
2909         text-align:center;
2910         mso-pagination:widow-orphan lines-together;
2911         tab-stops:center 216.0pt right 432.0pt;
2912         border:none;
2913         mso-border-top-alt:solid windowtext .75pt;
2914         padding:0cm;
2915         mso-padding-alt:3.0pt 0cm 0cm 0cm;
2916         font-size:8.0pt;
2917         mso-bidi-font-size:10.0pt;
2918         font-family:"Arial Black";
2919         mso-fareast-font-family:"Times New Roman";
2920         mso-bidi-font-family:"Times New Roman";}
2921 p.FooterFirst, li.FooterFirst, div.FooterFirst
2922         {mso-style-name:"Footer First";
2923         mso-style-parent:Footer;
2924         margin:0cm;
2925         margin-bottom:.0001pt;
2926         text-align:center;
2927         mso-pagination:widow-orphan lines-together;
2928         tab-stops:center 216.0pt;
2929         font-size:8.0pt;
2930         mso-bidi-font-size:10.0pt;
2931         font-family:"Arial Black";
2932         mso-fareast-font-family:"Times New Roman";
2933         mso-bidi-font-family:"Times New Roman";
2934         letter-spacing:-.5pt;}
2935 p.FooterOdd, li.FooterOdd, div.FooterOdd
2936         {mso-style-name:"Footer Odd";
2937         mso-style-parent:Footer;
2938         margin:0cm;
2939         margin-bottom:.0001pt;
2940         text-align:center;
2941         mso-pagination:widow-orphan lines-together;
2942         tab-stops:right 0cm center 216.0pt right 432.0pt;
2943         border:none;
2944         mso-border-top-alt:solid windowtext .75pt;
2945         padding:0cm;
2946         mso-padding-alt:3.0pt 0cm 0cm 0cm;
2947         font-size:8.0pt;
2948         mso-bidi-font-size:10.0pt;
2949         font-family:"Arial Black";
2950         mso-fareast-font-family:"Times New Roman";
2951         mso-bidi-font-family:"Times New Roman";}
2952 p.FootnoteBase, li.FootnoteBase, div.FootnoteBase
2953         {mso-style-name:"Footnote Base";
2954         margin-top:12.0pt;
2955         margin-right:0cm;
2956         margin-bottom:0cm;
2957         margin-left:0cm;
2958         margin-bottom:.0001pt;
2959         mso-pagination:widow-orphan;
2960         font-size:9.0pt;
2961         mso-bidi-font-size:10.0pt;
2962         font-family:Garamond;
2963         mso-fareast-font-family:"Times New Roman";
2964         mso-bidi-font-family:"Times New Roman";}
2965 p.HeaderBase, li.HeaderBase, div.HeaderBase
2966         {mso-style-name:"Header Base";
2967         margin:0cm;
2968         margin-bottom:.0001pt;
2969         mso-pagination:widow-orphan lines-together;
2970         tab-stops:center 216.0pt right 432.0pt;
2971         font-size:8.0pt;
2972         mso-bidi-font-size:10.0pt;
2973         font-family:Garamond;
2974         mso-fareast-font-family:"Times New Roman";
2975         mso-bidi-font-family:"Times New Roman";}
2976 p.HeaderEven, li.HeaderEven, div.HeaderEven
2977         {mso-style-name:"Header Even";
2978         mso-style-parent:Header;
2979         margin:0cm;
2980         margin-bottom:.0001pt;
2981         mso-pagination:widow-orphan lines-together;
2982         tab-stops:center 216.0pt right 432.0pt;
2983         font-size:7.0pt;
2984         mso-bidi-font-size:10.0pt;
2985         font-family:"Arial Black";
2986         mso-fareast-font-family:"Times New Roman";
2987         mso-bidi-font-family:"Times New Roman";
2988         text-transform:uppercase;
2989         letter-spacing:3.0pt;}
2990 p.HeaderFirst, li.HeaderFirst, div.HeaderFirst
2991         {mso-style-name:"Header First";
2992         mso-style-parent:Header;
2993         margin:0cm;
2994         margin-bottom:.0001pt;
2995         mso-pagination:widow-orphan lines-together;
2996         tab-stops:center 216.0pt;
2997         font-size:7.0pt;
2998         mso-bidi-font-size:10.0pt;
2999         font-family:Garamond;
3000         mso-fareast-font-family:"Times New Roman";
3001         mso-bidi-font-family:"Times New Roman";
3002         text-transform:uppercase;
3003         letter-spacing:3.0pt;
3004         font-weight:bold;
3005         mso-bidi-font-weight:normal;}
3006 p.HeaderOdd, li.HeaderOdd, div.HeaderOdd
3007         {mso-style-name:"Header Odd";
3008         mso-style-parent:Header;
3009         margin:0cm;
3010         margin-bottom:.0001pt;
3011         text-align:right;
3012         mso-pagination:widow-orphan lines-together;
3013         tab-stops:right 0cm center 216.0pt right 432.0pt;
3014         font-size:7.0pt;
3015         mso-bidi-font-size:10.0pt;
3016         font-family:"Arial Black";
3017         mso-fareast-font-family:"Times New Roman";
3018         mso-bidi-font-family:"Times New Roman";
3019         text-transform:uppercase;
3020         letter-spacing:3.0pt;}
3021 p.Icon1, li.Icon1, div.Icon1
3022         {mso-style-name:"Icon 1";
3023         margin-top:3.0pt;
3024         margin-right:0cm;
3025         margin-bottom:0cm;
3026         margin-left:0cm;
3027         margin-bottom:.0001pt;
3028         text-align:center;
3029         line-height:72.0pt;
3030         mso-line-height-rule:exactly;
3031         mso-pagination:widow-orphan;
3032         background:#E5E5E5;
3033         mso-shading:windowtext;
3034         mso-pattern:gray-10 auto;
3035         mso-element:frame;
3036         mso-element-frame-width:72.0pt;
3037         mso-element-frame-hspace:9.35pt;
3038         mso-element-wrap:around;
3039         mso-element-anchor-vertical:paragraph;
3040         mso-element-anchor-horizontal:margin;
3041         mso-element-top:.05pt;
3042         mso-height-rule:exactly;
3043         font-size:80.0pt;
3044         mso-bidi-font-size:10.0pt;
3045         font-family:Wingdings;
3046         mso-fareast-font-family:"Times New Roman";
3047         mso-bidi-font-family:"Times New Roman";
3048         color:white;
3049         letter-spacing:-.5pt;
3050         font-weight:bold;
3051         mso-bidi-font-weight:normal;}
3052 p.IndexBase, li.IndexBase, div.IndexBase
3053         {mso-style-name:"Index Base";
3054         margin:0cm;
3055         margin-bottom:.0001pt;
3056         line-height:12.0pt;
3057         mso-pagination:widow-orphan;
3058         tab-stops:right 198.0pt;
3059         font-size:9.0pt;
3060         mso-bidi-font-size:10.0pt;
3061         font-family:Garamond;
3062         mso-fareast-font-family:"Times New Roman";
3063         mso-bidi-font-family:"Times New Roman";}
3064 p.ListBulletFirst, li.ListBulletFirst, div.ListBulletFirst
3065         {mso-style-name:"List Bullet First";
3066         mso-style-parent:"List Bullet";
3067         mso-style-next:"List Bullet";
3068         margin-top:4.0pt;
3069         margin-right:0cm;
3070         margin-bottom:8.0pt;
3071         margin-left:18.0pt;
3072         text-indent:0cm;
3073         mso-pagination:widow-orphan;
3074         mso-list:l25 level1 lfo5;
3075         font-size:10.0pt;
3076         font-family:"Times New Roman";
3077         mso-fareast-font-family:"Times New Roman";
3078         mso-bidi-font-family:"Times New Roman";}
3079 p.ListBulletLast, li.ListBulletLast, div.ListBulletLast
3080         {mso-style-name:"List Bullet Last";
3081         mso-style-parent:"List Bullet";
3082         mso-style-next:"Body Text";
3083         margin-top:0cm;
3084         margin-right:0cm;
3085         margin-bottom:12.0pt;
3086         margin-left:18.0pt;
3087         text-indent:0cm;
3088         mso-pagination:widow-orphan;
3089         mso-list:l25 level1 lfo5;
3090         font-size:10.0pt;
3091         font-family:"Times New Roman";
3092         mso-fareast-font-family:"Times New Roman";
3093         mso-bidi-font-family:"Times New Roman";}
3094 p.ListFirst, li.ListFirst, div.ListFirst
3095         {mso-style-name:"List First";
3096         mso-style-parent:List;
3097         mso-style-next:List;
3098         margin-top:4.0pt;
3099         margin-right:0cm;
3100         margin-bottom:4.0pt;
3101         margin-left:36.0pt;
3102         text-indent:-18.0pt;
3103         mso-pagination:widow-orphan;
3104         tab-stops:36.0pt;
3105         font-size:10.0pt;
3106         font-family:"Times New Roman";
3107         mso-fareast-font-family:"Times New Roman";
3108         mso-bidi-font-family:"Times New Roman";}
3109 p.ListLast, li.ListLast, div.ListLast
3110         {mso-style-name:"List Last";
3111         mso-style-parent:List;
3112         mso-style-next:"Body Text";
3113         margin-top:0cm;
3114         margin-right:0cm;
3115         margin-bottom:12.0pt;
3116         margin-left:36.0pt;
3117         text-indent:-18.0pt;
3118         mso-pagination:widow-orphan;
3119         tab-stops:36.0pt;
3120         font-size:10.0pt;
3121         font-family:"Times New Roman";
3122         mso-fareast-font-family:"Times New Roman";
3123         mso-bidi-font-family:"Times New Roman";}
3124 p.ListNumberFirst, li.ListNumberFirst, div.ListNumberFirst
3125         {mso-style-name:"List Number First";
3126         mso-style-parent:"List Number";
3127         mso-style-next:"List Number";
3128         margin-top:4.0pt;
3129         margin-right:0cm;
3130         margin-bottom:8.0pt;
3131         margin-left:36.0pt;
3132         text-indent:-18.0pt;
3133         mso-pagination:widow-orphan;
3134         mso-list:l8 level1 lfo7;
3135         font-size:10.0pt;
3136         font-family:"Times New Roman";
3137         mso-fareast-font-family:"Times New Roman";
3138         mso-bidi-font-family:"Times New Roman";}
3139 p.ListNumberLast, li.ListNumberLast, div.ListNumberLast
3140         {mso-style-name:"List Number Last";
3141         mso-style-parent:"List Number";
3142         mso-style-next:"Body Text";
3143         margin-top:0cm;
3144         margin-right:0cm;
3145         margin-bottom:12.0pt;
3146         margin-left:36.0pt;
3147         text-indent:-18.0pt;
3148         mso-pagination:widow-orphan;
3149         mso-list:l8 level1 lfo7;
3150         font-size:10.0pt;
3151         font-family:"Times New Roman";
3152         mso-fareast-font-family:"Times New Roman";
3153         mso-bidi-font-family:"Times New Roman";}
3154 p.PartLabel, li.PartLabel, div.PartLabel
3155         {mso-style-name:"Part Label";
3156         mso-style-link:"Part Label Char";
3157         mso-style-next:Normal;
3158         margin-top:16.0pt;
3159         margin-right:0cm;
3160         margin-bottom:0cm;
3161         margin-left:0cm;
3162         margin-bottom:.0001pt;
3163         text-align:center;
3164         line-height:78.0pt;
3165         mso-line-height-rule:exactly;
3166         mso-pagination:widow-orphan;
3167         background:#CCCCCC;
3168         mso-shading:windowtext;
3169         mso-pattern:gray-20 auto;
3170         mso-element:frame;
3171         mso-element-frame-width:102.25pt;
3172         mso-element-frame-hspace:9.35pt;
3173         mso-element-frame-vspace:9.35pt;
3174         mso-element-wrap:no-wrap-beside;
3175         mso-element-anchor-vertical:page;
3176         mso-element-anchor-horizontal:margin;
3177         mso-element-left:right;
3178         mso-element-top:48.3pt;
3179         mso-height-rule:exactly;
3180         font-size:98.0pt;
3181         mso-bidi-font-size:10.0pt;
3182         font-family:"Arial Black";
3183         mso-fareast-font-family:"Times New Roman";
3184         mso-bidi-font-family:"Times New Roman";
3185         color:white;}
3186 span.PartLabelChar
3187         {mso-style-name:"Part Label Char";
3188         mso-style-locked:yes;
3189         mso-style-link:"Part Label";
3190         mso-ansi-font-size:98.0pt;
3191         font-family:"Arial Black";
3192         mso-ascii-font-family:"Arial Black";
3193         mso-hansi-font-family:"Arial Black";
3194         color:white;
3195         mso-ansi-language:EN-US;
3196         mso-fareast-language:EN-US;}
3197 p.PartSubtitle, li.PartSubtitle, div.PartSubtitle
3198         {mso-style-name:"Part Subtitle";
3199         mso-style-next:"Body Text";
3200         margin-top:18.0pt;
3201         margin-right:0cm;
3202         margin-bottom:6.0pt;
3203         margin-left:0cm;
3204         text-align:center;
3205         mso-pagination:widow-orphan;
3206         page-break-after:avoid;
3207         font-size:16.0pt;
3208         mso-bidi-font-size:10.0pt;
3209         font-family:Arial;
3210         mso-fareast-font-family:"Times New Roman";
3211         mso-bidi-font-family:"Times New Roman";
3212         mso-font-kerning:14.0pt;
3213         font-style:italic;
3214         mso-bidi-font-style:normal;}
3215 p.PartTitle, li.PartTitle, div.PartTitle
3216         {mso-style-name:"Part Title";
3217         mso-style-next:"Part Label";
3218         margin:0cm;
3219         margin-bottom:.0001pt;
3220         text-align:center;
3221         line-height:24.0pt;
3222         mso-line-height-rule:exactly;
3223         page-break-before:always;
3224         mso-pagination:widow-orphan;
3225         page-break-after:avoid;
3226         background:#CCCCCC;
3227         mso-shading:windowtext;
3228         mso-pattern:gray-20 auto;
3229         mso-element:frame;
3230         mso-element-frame-width:102.25pt;
3231         mso-element-frame-hspace:9.35pt;
3232         mso-element-frame-vspace:9.35pt;
3233         mso-element-wrap:no-wrap-beside;
3234         mso-element-anchor-vertical:page;
3235         mso-element-anchor-horizontal:margin;
3236         mso-element-left:right;
3237         mso-element-top:48.3pt;
3238         mso-height-rule:exactly;
3239         font-size:18.0pt;
3240         mso-bidi-font-size:10.0pt;
3241         font-family:"Arial Black";
3242         mso-fareast-font-family:"Times New Roman";
3243         mso-bidi-font-family:"Times New Roman";
3244         letter-spacing:-2.5pt;}
3245 p.Picture, li.Picture, div.Picture
3246         {mso-style-name:Picture;
3247         mso-style-parent:"Body Text";
3248         mso-style-next:Caption;
3249         margin-top:0cm;
3250         margin-right:0cm;
3251         margin-bottom:12.0pt;
3252         margin-left:0cm;
3253         text-align:justify;
3254         mso-pagination:widow-orphan;
3255         page-break-after:avoid;
3256         font-size:12.0pt;
3257         mso-bidi-font-size:10.0pt;
3258         font-family:Garamond;
3259         mso-fareast-font-family:"Times New Roman";
3260         mso-bidi-font-family:"Times New Roman";
3261         letter-spacing:-.25pt;}
3262 p.ReturnAddress, li.ReturnAddress, div.ReturnAddress
3263         {mso-style-name:"Return Address";
3264         margin:0cm;
3265         margin-bottom:.0001pt;
3266         text-align:center;
3267         mso-pagination:widow-orphan;
3268         font-size:10.0pt;
3269         font-family:Garamond;
3270         mso-fareast-font-family:"Times New Roman";
3271         mso-bidi-font-family:"Times New Roman";
3272         letter-spacing:-.15pt;}
3273 p.SectionHeading, li.SectionHeading, div.SectionHeading
3274         {mso-style-name:"Section Heading";
3275         mso-style-next:"Body Text";
3276         margin:0cm;
3277         margin-bottom:.0001pt;
3278         line-height:32.0pt;
3279         mso-pagination:widow-orphan;
3280         font-size:7.5pt;
3281         mso-bidi-font-size:10.0pt;
3282         font-family:"Arial Black";
3283         mso-fareast-font-family:"Times New Roman";
3284         mso-bidi-font-family:"Times New Roman";
3285         text-transform:uppercase;
3286         letter-spacing:3.0pt;}
3287 p.SectionLabel, li.SectionLabel, div.SectionLabel
3288         {mso-style-name:"Section Label";
3289         mso-style-next:Normal;
3290         margin-top:102.0pt;
3291         margin-right:0cm;
3292         margin-bottom:18.0pt;
3293         margin-left:0cm;
3294         line-height:24.0pt;
3295         mso-pagination:widow-orphan;
3296         font-size:24.0pt;
3297         mso-bidi-font-size:10.0pt;
3298         font-family:"Arial Black";
3299         mso-fareast-font-family:"Times New Roman";
3300         mso-bidi-font-family:"Times New Roman";
3301         color:gray;
3302         letter-spacing:-1.75pt;}
3303 p.SubtitleCover, li.SubtitleCover, div.SubtitleCover
3304         {mso-style-name:"Subtitle Cover";
3305         mso-style-next:Normal;
3306         margin-top:0cm;
3307         margin-right:0cm;
3308         margin-bottom:264.0pt;
3309         margin-left:0cm;
3310         line-height:24.0pt;
3311         mso-line-height-rule:exactly;
3312         mso-pagination:widow-orphan;
3313         page-break-after:avoid;
3314         border:none;
3315         mso-border-top-alt:solid windowtext .75pt;
3316         padding:0cm;
3317         mso-padding-alt:1.0pt 0cm 0cm 0cm;
3318         font-size:22.0pt;
3319         mso-bidi-font-size:10.0pt;
3320         font-family:Garamond;
3321         mso-fareast-font-family:"Times New Roman";
3322         mso-bidi-font-family:"Times New Roman";
3323         letter-spacing:-.75pt;
3324         mso-font-kerning:14.0pt;}
3325 p.TitleCover, li.TitleCover, div.TitleCover
3326         {mso-style-name:"Title Cover";
3327         mso-style-parent:"Heading Base";
3328         mso-style-next:"Subtitle Cover";
3329         margin-top:0cm;
3330         margin-right:30.0pt;
3331         margin-bottom:0cm;
3332         margin-left:30.0pt;
3333         margin-bottom:.0001pt;
3334         text-align:right;
3335         line-height:72.0pt;
3336         mso-line-height-rule:exactly;
3337         mso-pagination:widow-orphan;
3338         background:#E5E5E5;
3339         mso-shading:windowtext;
3340         mso-pattern:gray-10 auto;
3341         border:none;
3342         mso-border-alt:solid white .75pt;
3343         padding:0cm;
3344         mso-padding-alt:31.0pt 31.0pt 31.0pt 31.0pt;
3345         font-size:72.0pt;
3346         mso-bidi-font-size:10.0pt;
3347         font-family:Garamond;
3348         mso-fareast-font-family:"Times New Roman";
3349         mso-bidi-font-family:"Times New Roman";
3350         letter-spacing:-3.5pt;
3351         mso-font-kerning:14.0pt;}
3352 p.TOCBase, li.TOCBase, div.TOCBase
3353         {mso-style-name:"TOC Base";
3354         mso-style-parent:"TOC 2";
3355         margin-top:0cm;
3356         margin-right:0cm;
3357         margin-bottom:0cm;
3358         margin-left:8.0pt;
3359         margin-bottom:.0001pt;
3360         mso-pagination:widow-orphan;
3361         font-size:11.0pt;
3362         font-family:Cambria;
3363         mso-ascii-font-family:Cambria;
3364         mso-ascii-theme-font:minor-latin;
3365         mso-fareast-font-family:"Times New Roman";
3366         mso-hansi-font-family:Cambria;
3367         mso-hansi-theme-font:minor-latin;
3368         mso-bidi-font-family:"Times New Roman";
3369         font-weight:bold;
3370         mso-bidi-font-weight:normal;}
3371 span.Lead-inEmphasis
3372         {mso-style-name:"Lead-in Emphasis";
3373         mso-style-parent:"";
3374         mso-ansi-font-size:11.0pt;
3375         text-transform:uppercase;}
3376 span.Superscript
3377         {mso-style-name:Superscript;
3378         mso-style-parent:"";
3379         position:relative;
3380         top:0pt;
3381         mso-text-raise:0pt;
3382         vertical-align:super;}
3383 p.Heading, li.Heading, div.Heading
3384         {mso-style-name:Heading;
3385         mso-style-next:Normal;
3386         margin-top:12.0pt;
3387         margin-right:0cm;
3388         margin-bottom:6.0pt;
3389         margin-left:0cm;
3390         mso-pagination:none;
3391         page-break-after:avoid;
3392         mso-hyphenate:none;
3393         mso-layout-grid-align:none;
3394         punctuation-wrap:simple;
3395         text-autospace:none;
3396         font-size:14.0pt;
3397         mso-bidi-font-size:10.0pt;
3398         font-family:Helvetica;
3399         mso-fareast-font-family:"Times New Roman";
3400         mso-bidi-font-family:"Times New Roman";}
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3403         mso-style-parent:"";
3404         mso-ansi-font-size:12.0pt;}
3405 span.FootnoteSymbol
3406         {mso-style-name:"Footnote Symbol";
3407         mso-style-parent:WW-Absatz-Standardschriftart;
3408         mso-ansi-font-size:12.0pt;
3409         vertical-align:super;}
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3413         mso-ansi-font-size:12.0pt;}
3414 span.WW-FootnoteSymbol
3415         {mso-style-name:"WW-Footnote Symbol";
3416         mso-style-parent:WW-Absatz-Standardschriftart1;
3417         mso-ansi-font-size:12.0pt;
3418         vertical-align:super;}
3419 span.WW-Absatz-Standardschriftart11
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3423 span.WW-FootnoteSymbol1
3424         {mso-style-name:"WW-Footnote Symbol1";
3425         mso-style-parent:WW-Absatz-Standardschriftart11;
3426         mso-ansi-font-size:12.0pt;
3427         vertical-align:super;}
3428 span.WW-Absatz-Standardschriftart111
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3431         mso-ansi-font-size:12.0pt;}
3432 span.WW-FootnoteSymbol11
3433         {mso-style-name:"WW-Footnote Symbol11";
3434         mso-style-parent:WW-Absatz-Standardschriftart111;
3435         mso-ansi-font-size:12.0pt;
3436         vertical-align:super;}
3437 span.WW-Absatz-Standardschriftart1111
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3441 span.WW-FootnoteSymbol111
3442         {mso-style-name:"WW-Footnote Symbol111";
3443         mso-style-parent:WW-Absatz-Standardschriftart1111;
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3445         vertical-align:super;}
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3450 span.WW-FootnoteSymbol1111
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3460         {mso-style-name:"WW-Footnote Symbol11111";
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3472         vertical-align:super;}
3473 span.WW-Absatz-Standardschriftart11111111
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3481         vertical-align:super;}
3482 span.WW-Absatz-Standardschriftart111111111
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3490         vertical-align:super;}
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3497         mso-style-parent:"";
3498         mso-ansi-font-size:12.0pt;}
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3506         mso-ansi-font-size:12.0pt;}
3507 span.WW-EndnoteSymbol111
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3510         mso-ansi-font-size:12.0pt;}
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3514         mso-ansi-font-size:12.0pt;}
3515 span.WW-EndnoteSymbol11111
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3518         mso-ansi-font-size:12.0pt;}
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3523 span.WW-EndnoteSymbol1111111
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3525         mso-style-parent:"";
3526         mso-ansi-font-size:12.0pt;}
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3531         color:navy;
3532         text-decoration:underline;
3533         text-underline:single;}
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3536         mso-style-parent:"";
3537         mso-ansi-font-size:12.0pt;
3538         color:navy;
3539         text-decoration:underline;
3540         text-underline:single;}
3541 span.WW-Internetlink1
3542         {mso-style-name:"WW-Internet link1";
3543         mso-style-parent:"";
3544         mso-ansi-font-size:12.0pt;
3545         color:navy;
3546         text-decoration:underline;
3547         text-underline:single;}
3548 span.WW-Internetlink11
3549         {mso-style-name:"WW-Internet link11";
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3552         color:navy;
3553         text-decoration:underline;
3554         text-underline:single;}
3555 span.WW-Internetlink111
3556         {mso-style-name:"WW-Internet link111";
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3559         color:navy;
3560         text-decoration:underline;
3561         text-underline:single;}
3562 span.WW-Internetlink1111
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3565         mso-ansi-font-size:12.0pt;
3566         color:navy;
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3569 span.WW-Internetlink11111
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3575         text-underline:single;}
3576 span.WW-Internetlink111111
3577         {mso-style-name:"WW-Internet link111111";
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3583 span.WW-Internetlink1111111
3584         {mso-style-name:"WW-Internet link1111111";
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3586         mso-ansi-font-size:12.0pt;
3587         color:navy;
3588         text-decoration:underline;
3589         text-underline:single;}
3590 span.VisitedInternetLink
3591         {mso-style-name:"Visited Internet Link";
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3593         mso-ansi-font-size:12.0pt;
3594         color:maroon;
3595         text-decoration:underline;
3596         text-underline:single;}
3597 span.WW-VisitedInternetLink
3598         {mso-style-name:"WW-Visited Internet Link";
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3600         mso-ansi-font-size:12.0pt;
3601         color:maroon;
3602         text-decoration:underline;
3603         text-underline:single;}
3604 span.WW-VisitedInternetLink1
3605         {mso-style-name:"WW-Visited Internet Link1";
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3607         mso-ansi-font-size:12.0pt;
3608         color:maroon;
3609         text-decoration:underline;
3610         text-underline:single;}
3611 span.WW-VisitedInternetLink11
3612         {mso-style-name:"WW-Visited Internet Link11";
3613         mso-style-parent:"";
3614         mso-ansi-font-size:12.0pt;
3615         color:maroon;
3616         text-decoration:underline;
3617         text-underline:single;}
3618 span.WW-VisitedInternetLink111
3619         {mso-style-name:"WW-Visited Internet Link111";
3620         mso-style-parent:"";
3621         mso-ansi-font-size:12.0pt;
3622         color:maroon;
3623         text-decoration:underline;
3624         text-underline:single;}
3625 span.WW-VisitedInternetLink1111
3626         {mso-style-name:"WW-Visited Internet Link1111";
3627         mso-style-parent:"";
3628         mso-ansi-font-size:12.0pt;
3629         color:maroon;
3630         text-decoration:underline;
3631         text-underline:single;}
3632 span.WW-VisitedInternetLink11111
3633         {mso-style-name:"WW-Visited Internet Link11111";
3634         mso-style-parent:"";
3635         mso-ansi-font-size:12.0pt;
3636         color:maroon;
3637         text-decoration:underline;
3638         text-underline:single;}
3639 span.WW-VisitedInternetLink111111
3640         {mso-style-name:"WW-Visited Internet Link111111";
3641         mso-style-parent:"";
3642         mso-ansi-font-size:12.0pt;
3643         color:maroon;
3644         text-decoration:underline;
3645         text-underline:single;}
3646 span.WW-VisitedInternetLink1111111
3647         {mso-style-name:"WW-Visited Internet Link1111111";
3648         mso-style-parent:"";
3649         mso-ansi-font-size:12.0pt;
3650         color:maroon;
3651         text-decoration:underline;
3652         text-underline:single;}
3653 span.NumberingSymbols
3654         {mso-style-name:"Numbering Symbols";
3655         mso-style-parent:"";
3656         mso-ansi-font-size:12.0pt;}
3657 span.WW-NumberingSymbols
3658         {mso-style-name:"WW-Numbering Symbols";
3659         mso-style-parent:"";
3660         mso-ansi-font-size:12.0pt;}
3661 span.WW-NumberingSymbols1
3662         {mso-style-name:"WW-Numbering Symbols1";
3663         mso-style-parent:"";
3664         mso-ansi-font-size:12.0pt;}
3665 span.WW-NumberingSymbols11
3666         {mso-style-name:"WW-Numbering Symbols11";
3667         mso-style-parent:"";
3668         mso-ansi-font-size:12.0pt;}
3669 span.WW-NumberingSymbols111
3670         {mso-style-name:"WW-Numbering Symbols111";
3671         mso-style-parent:"";
3672         mso-ansi-font-size:12.0pt;}
3673 span.WW-NumberingSymbols1111
3674         {mso-style-name:"WW-Numbering Symbols1111";
3675         mso-style-parent:"";
3676         mso-ansi-font-size:12.0pt;}
3677 span.WW-NumberingSymbols11111
3678         {mso-style-name:"WW-Numbering Symbols11111";
3679         mso-style-parent:"";
3680         mso-ansi-font-size:12.0pt;}
3681 span.BulletSymbols
3682         {mso-style-name:"Bullet Symbols";
3683         mso-style-parent:"";
3684         mso-ansi-font-size:9.0pt;
3685         font-family:starbats;
3686         mso-ascii-font-family:starbats;
3687         mso-hansi-font-family:starbats;}
3688 span.WW-BulletSymbols
3689         {mso-style-name:"WW-Bullet Symbols";
3690         mso-style-parent:"";
3691         mso-ansi-font-size:9.0pt;
3692         font-family:starbats;
3693         mso-ascii-font-family:starbats;
3694         mso-hansi-font-family:starbats;}
3695 span.WW-BulletSymbols1
3696         {mso-style-name:"WW-Bullet Symbols1";
3697         mso-style-parent:"";
3698         mso-ansi-font-size:9.0pt;
3699         font-family:starbats;
3700         mso-ascii-font-family:starbats;
3701         mso-hansi-font-family:starbats;}
3702 span.WW-BulletSymbols11
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3704         mso-style-parent:"";
3705         mso-ansi-font-size:9.0pt;
3706         font-family:starbats;
3707         mso-ascii-font-family:starbats;
3708         mso-hansi-font-family:starbats;}
3709 p.Index, li.Index, div.Index
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3840         margin-top:0cm;
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3845         text-align:justify;
3846         mso-pagination:none;
3847         mso-hyphenate:none;
3848         mso-layout-grid-align:none;
3849         punctuation-wrap:simple;
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3853         font-family:"Times New Roman";
3854         mso-fareast-font-family:"Times New Roman";
3855         mso-bidi-font-family:"Times New Roman";}
3856 p.ListContents, li.ListContents, div.ListContents
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3858         margin-top:0cm;
3859         margin-right:0cm;
3860         margin-bottom:0cm;
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3863         mso-pagination:none;
3864         mso-hyphenate:none;
3865         mso-layout-grid-align:none;
3866         punctuation-wrap:simple;
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3869         mso-bidi-font-size:10.0pt;
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3871         mso-fareast-font-family:"Times New Roman";
3872         mso-bidi-font-family:"Times New Roman";}
3873 p.FAQexample, li.FAQexample, div.FAQexample
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3875         mso-style-parent:example;
3876         margin-top:12.0pt;
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3881         line-height:200%;
3882         mso-pagination:widow-orphan lines-together;
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3889         mso-fareast-font-family:"Times New Roman";
3890         mso-bidi-font-family:"Courier New";
3891         font-weight:bold;
3892         mso-bidi-font-weight:normal;}
3893 p.FAQexampleCxSpFirst, li.FAQexampleCxSpFirst, div.FAQexampleCxSpFirst
3894         {mso-style-name:FAQ_exampleCxSpFirst;
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3898         margin-right:0cm;
3899         margin-bottom:0cm;
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3903         line-height:200%;
3904         mso-pagination:widow-orphan lines-together;
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3907         punctuation-wrap:simple;
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3911         mso-fareast-font-family:"Times New Roman";
3912         mso-bidi-font-family:"Courier New";
3913         font-weight:bold;
3914         mso-bidi-font-weight:normal;}
3915 p.FAQexampleCxSpMiddle, li.FAQexampleCxSpMiddle, div.FAQexampleCxSpMiddle
3916         {mso-style-name:FAQ_exampleCxSpMiddle;
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3919         margin-top:0cm;
3920         margin-right:0cm;
3921         margin-bottom:0cm;
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3924         mso-add-space:auto;
3925         line-height:200%;
3926         mso-pagination:widow-orphan lines-together;
3927         page-break-after:avoid;
3928         mso-layout-grid-align:none;
3929         punctuation-wrap:simple;
3930         text-autospace:none;
3931         font-size:10.0pt;
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3933         mso-fareast-font-family:"Times New Roman";
3934         mso-bidi-font-family:"Courier New";
3935         font-weight:bold;
3936         mso-bidi-font-weight:normal;}
3937 p.FAQexampleCxSpLast, li.FAQexampleCxSpLast, div.FAQexampleCxSpLast
3938         {mso-style-name:FAQ_exampleCxSpLast;
3939         mso-style-parent:example;
3940         mso-style-type:export-only;
3941         margin-top:0cm;
3942         margin-right:0cm;
3943         margin-bottom:12.0pt;
3944         margin-left:1.0cm;
3945         mso-add-space:auto;
3946         line-height:200%;
3947         mso-pagination:widow-orphan lines-together;
3948         page-break-after:avoid;
3949         mso-layout-grid-align:none;
3950         punctuation-wrap:simple;
3951         text-autospace:none;
3952         font-size:10.0pt;
3953         font-family:"Courier New";
3954         mso-fareast-font-family:"Times New Roman";
3955         mso-bidi-font-family:"Courier New";
3956         font-weight:bold;
3957         mso-bidi-font-weight:normal;}
3958 p.Firstlineindent, li.Firstlineindent, div.Firstlineindent
3959         {mso-style-name:"First line indent";
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3961         margin:0cm;
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3963         text-align:justify;
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3965         mso-pagination:none;
3966         mso-hyphenate:none;
3967         mso-layout-grid-align:none;
3968         punctuation-wrap:simple;
3969         text-autospace:none;
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3971         mso-bidi-font-size:10.0pt;
3972         font-family:"Times New Roman";
3973         mso-fareast-font-family:"Times New Roman";
3974         mso-bidi-font-family:"Times New Roman";}
3975 p.Hangingindent, li.Hangingindent, div.Hangingindent
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3977         mso-style-parent:"Text body";
3978         margin-top:0cm;
3979         margin-right:0cm;
3980         margin-bottom:0cm;
3981         margin-left:1.0cm;
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3983         text-align:justify;
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3985         mso-pagination:none;
3986         mso-hyphenate:none;
3987         tab-stops:1.0cm;
3988         mso-layout-grid-align:none;
3989         punctuation-wrap:simple;
3990         text-autospace:none;
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3994         mso-fareast-font-family:"Times New Roman";
3995         mso-bidi-font-family:"Times New Roman";}
3996 p.Numbering3, li.Numbering3, div.Numbering3
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4000         margin-right:0cm;
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4005         mso-pagination:none;
4006         mso-hyphenate:none;
4007         mso-layout-grid-align:none;
4008         punctuation-wrap:simple;
4009         text-autospace:none;
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4015 p.TableContents, li.TableContents, div.TableContents
4016         {mso-style-name:"Table Contents";
4017         mso-style-parent:"Text body";
4018         margin:0cm;
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4020         text-align:justify;
4021         mso-pagination:none;
4022         mso-hyphenate:none;
4023         mso-layout-grid-align:none;
4024         punctuation-wrap:simple;
4025         text-autospace:none;
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4027         mso-bidi-font-size:10.0pt;
4028         font-family:"Times New Roman";
4029         mso-fareast-font-family:"Times New Roman";
4030         mso-bidi-font-family:"Times New Roman";}
4031 p.TableHeading, li.TableHeading, div.TableHeading
4032         {mso-style-name:"Table Heading";
4033         mso-style-parent:"Table Contents";
4034         margin:0cm;
4035         margin-bottom:.0001pt;
4036         text-align:center;
4037         mso-pagination:none;
4038         mso-hyphenate:none;
4039         mso-layout-grid-align:none;
4040         punctuation-wrap:simple;
4041         text-autospace:none;
4042         font-size:12.0pt;
4043         mso-bidi-font-size:10.0pt;
4044         font-family:"Times New Roman";
4045         mso-fareast-font-family:"Times New Roman";
4046         mso-bidi-font-family:"Times New Roman";
4047         font-weight:bold;
4048         mso-bidi-font-weight:normal;
4049         font-style:italic;
4050         mso-bidi-font-style:normal;}
4051 p.author, li.author, div.author
4052         {mso-style-name:author;
4053         margin:0cm;
4054         margin-bottom:.0001pt;
4055         text-align:justify;
4056         mso-pagination:none;
4057         mso-hyphenate:none;
4058         mso-layout-grid-align:none;
4059         punctuation-wrap:simple;
4060         text-autospace:none;
4061         font-size:12.0pt;
4062         mso-bidi-font-size:10.0pt;
4063         font-family:"Times New Roman";
4064         mso-fareast-font-family:"Times New Roman";
4065         mso-bidi-font-family:"Times New Roman";
4066         font-weight:bold;
4067         mso-bidi-font-weight:normal;}
4068 p.numberedlist, li.numberedlist, div.numberedlist
4069         {mso-style-name:"numbered list";
4070         mso-style-update:auto;
4071         mso-style-parent:"Heading 4";
4072         margin-top:3.0pt;
4073         margin-right:0cm;
4074         margin-bottom:3.0pt;
4075         margin-left:0cm;
4076         mso-pagination:none;
4077         page-break-after:avoid;
4078         mso-outline-level:4;
4079         mso-hyphenate:none;
4080         mso-layout-grid-align:none;
4081         punctuation-wrap:simple;
4082         text-autospace:none;
4083         font-size:10.0pt;
4084         mso-bidi-font-size:12.0pt;
4085         font-family:"Arial Black";
4086         mso-fareast-font-family:"Times New Roman";
4087         mso-bidi-font-family:"Courier New";
4088         letter-spacing:1.0pt;
4089         mso-ansi-language:AF;
4090         font-weight:bold;
4091         mso-bidi-font-weight:normal;
4092         font-style:italic;
4093         mso-bidi-font-style:normal;}
4094 p.Noteboxtitle, li.Noteboxtitle, div.Noteboxtitle
4095         {mso-style-name:"Notebox\.title";
4096         margin:0cm;
4097         margin-bottom:.0001pt;
4098         text-align:center;
4099         mso-pagination:none;
4100         mso-hyphenate:none;
4101         mso-layout-grid-align:none;
4102         punctuation-wrap:simple;
4103         text-autospace:none;
4104         font-size:18.0pt;
4105         mso-bidi-font-size:10.0pt;
4106         font-family:Arial;
4107         mso-fareast-font-family:"Times New Roman";
4108         mso-bidi-font-family:Arial;
4109         font-weight:bold;}
4110 p.noteboxexample, li.noteboxexample, div.noteboxexample
4111         {mso-style-name:"notebox\.example";
4112         margin:0cm;
4113         margin-bottom:.0001pt;
4114         text-indent:36.0pt;
4115         mso-pagination:none;
4116         mso-hyphenate:none;
4117         mso-layout-grid-align:none;
4118         punctuation-wrap:simple;
4119         text-autospace:none;
4120         font-size:12.0pt;
4121         mso-bidi-font-size:10.0pt;
4122         font-family:"Times New Roman";
4123         mso-fareast-font-family:"Times New Roman";
4124         mso-bidi-font-family:"Times New Roman";
4125         font-weight:bold;}
4126 p.noteboxbody, li.noteboxbody, div.noteboxbody
4127         {mso-style-name:"notebox\.body";
4128         margin:0cm;
4129         margin-bottom:.0001pt;
4130         mso-pagination:none;
4131         mso-hyphenate:none;
4132         mso-layout-grid-align:none;
4133         punctuation-wrap:simple;
4134         text-autospace:none;
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4136         mso-bidi-font-size:10.0pt;
4137         font-family:"Times New Roman";
4138         mso-fareast-font-family:"Times New Roman";
4139         mso-bidi-font-family:"Times New Roman";
4140         font-style:italic;}
4141 p.Note, li.Note, div.Note
4142         {mso-style-name:Note;
4143         mso-style-update:auto;
4144         mso-style-link:"Note Char";
4145         margin-top:6.0pt;
4146         margin-right:0cm;
4147         margin-bottom:12.0pt;
4148         margin-left:42.55pt;
4149         text-align:justify;
4150         mso-pagination:none;
4151         mso-hyphenate:none;
4152         tab-stops:1.0cm;
4153         mso-layout-grid-align:none;
4154         punctuation-wrap:simple;
4155         text-autospace:none;
4156         font-size:10.0pt;
4157         mso-bidi-font-size:8.0pt;
4158         font-family:"Times New Roman";
4159         mso-fareast-font-family:"Times New Roman";
4160         mso-bidi-font-family:"Times New Roman";
4161         mso-ansi-language:EN-GB;
4162         font-weight:bold;
4163         mso-bidi-font-weight:normal;}
4164 span.NoteChar
4165         {mso-style-name:"Note Char";
4166         mso-style-locked:yes;
4167         mso-style-link:Note;
4168         mso-bidi-font-size:8.0pt;
4169         mso-ansi-language:EN-GB;
4170         mso-fareast-language:EN-US;
4171         font-weight:bold;
4172         mso-bidi-font-weight:normal;}
4173 p.Table, li.Table, div.Table
4174         {mso-style-name:Table;
4175         mso-style-parent:Index;
4176         margin:0cm;
4177         margin-bottom:.0001pt;
4178         mso-pagination:none;
4179         mso-hyphenate:none;
4180         mso-layout-grid-align:none;
4181         punctuation-wrap:simple;
4182         text-autospace:none;
4183         font-size:12.0pt;
4184         mso-bidi-font-size:10.0pt;
4185         font-family:"Courier New";
4186         mso-fareast-font-family:"Times New Roman";
4187         mso-bidi-font-family:"Courier New";}
4188 p.flag, li.flag, div.flag
4189         {mso-style-name:flag;
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4191         margin-top:12.0pt;
4192         margin-right:0cm;
4193         margin-bottom:3.0pt;
4194         margin-left:1.0cm;
4195         mso-pagination:none;
4196         page-break-after:avoid;
4197         mso-outline-level:4;
4198         mso-hyphenate:none;
4199         mso-layout-grid-align:none;
4200         punctuation-wrap:simple;
4201         text-autospace:none;
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4203         font-family:"Times New Roman";
4204         mso-fareast-font-family:"Times New Roman";
4205         mso-bidi-font-family:"Courier New";
4206         letter-spacing:1.0pt;
4207         mso-ansi-language:AF;
4208         font-weight:bold;
4209         mso-bidi-font-weight:normal;
4210         font-style:italic;
4211         mso-bidi-font-style:normal;}
4212 p.flagusage, li.flagusage, div.flagusage
4213         {mso-style-name:"flag usage";
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4215         mso-style-parent:example;
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4217         margin-right:0cm;
4218         margin-bottom:3.0pt;
4219         margin-left:0cm;
4220         text-indent:36.0pt;
4221         mso-pagination:none;
4222         mso-hyphenate:none;
4223         mso-layout-grid-align:none;
4224         punctuation-wrap:simple;
4225         text-autospace:none;
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4227         font-family:"Times New Roman";
4228         mso-fareast-font-family:"Times New Roman";
4229         mso-bidi-font-family:"Courier New";
4230         mso-ansi-language:FR;
4231         font-weight:bold;
4232         mso-bidi-font-weight:normal;}
4233 p.flagdefault, li.flagdefault, div.flagdefault
4234         {mso-style-name:"flag default";
4235         mso-style-parent:"Heading 5";
4236         margin-top:3.0pt;
4237         margin-right:0cm;
4238         margin-bottom:3.0pt;
4239         margin-left:18.0pt;
4240         mso-pagination:none;
4241         mso-outline-level:5;
4242         mso-hyphenate:none;
4243         mso-layout-grid-align:none;
4244         punctuation-wrap:simple;
4245         text-autospace:none;
4246         font-size:13.0pt;
4247         font-family:"Times New Roman";
4248         mso-fareast-font-family:"Times New Roman";
4249         mso-bidi-font-family:"Times New Roman";
4250         font-weight:bold;}
4251 p.flagdescription, li.flagdescription, div.flagdescription
4252         {mso-style-name:"flag description";
4253         mso-style-update:auto;
4254         mso-style-link:"flag description Char";
4255         margin-top:6.0pt;
4256         margin-right:0cm;
4257         margin-bottom:0cm;
4258         margin-left:42.55pt;
4259         margin-bottom:.0001pt;
4260         text-align:justify;
4261         mso-pagination:none;
4262         mso-hyphenate:none;
4263         mso-layout-grid-align:none;
4264         punctuation-wrap:simple;
4265         text-autospace:none;
4266         font-size:10.0pt;
4267         font-family:"Times New Roman";
4268         mso-fareast-font-family:"Times New Roman";
4269         mso-bidi-font-family:"Times New Roman";}
4270 span.flagdescriptionChar
4271         {mso-style-name:"flag description Char";
4272         mso-style-locked:yes;
4273         mso-style-link:"flag description";
4274         mso-ansi-language:EN-US;
4275         mso-fareast-language:EN-US;}
4276 p.flagNote, li.flagNote, div.flagNote
4277         {mso-style-name:"flag Note";
4278         margin:0cm;
4279         margin-bottom:.0001pt;
4280         text-align:justify;
4281         text-indent:.05pt;
4282         mso-pagination:none;
4283         mso-hyphenate:none;
4284         mso-layout-grid-align:none;
4285         punctuation-wrap:simple;
4286         text-autospace:none;
4287         font-size:12.0pt;
4288         mso-bidi-font-size:10.0pt;
4289         font-family:"Times New Roman";
4290         mso-fareast-font-family:"Times New Roman";
4291         mso-bidi-font-family:"Times New Roman";
4292         font-weight:bold;}
4293 p.flagdescriptionid1, li.flagdescriptionid1, div.flagdescriptionid1
4294         {mso-style-name:"flag description id1";
4295         mso-style-parent:"flag description";
4296         margin-top:6.0pt;
4297         margin-right:0cm;
4298         margin-bottom:0cm;
4299         margin-left:70.9pt;
4300         margin-bottom:.0001pt;
4301         text-align:justify;
4302         mso-pagination:none;
4303         mso-hyphenate:none;
4304         mso-layout-grid-align:none;
4305         punctuation-wrap:simple;
4306         text-autospace:none;
4307         font-size:10.0pt;
4308         font-family:"Times New Roman";
4309         mso-fareast-font-family:"Times New Roman";
4310         mso-bidi-font-family:"Times New Roman";}
4311 p.output, li.output, div.output
4312         {mso-style-name:output;
4313         margin-top:0cm;
4314         margin-right:0cm;
4315         margin-bottom:0cm;
4316         margin-left:18.0pt;
4317         margin-bottom:.0001pt;
4318         text-align:justify;
4319         text-indent:.05pt;
4320         mso-pagination:none;
4321         mso-hyphenate:none;
4322         mso-layout-grid-align:none;
4323         punctuation-wrap:simple;
4324         text-autospace:none;
4325         font-size:8.0pt;
4326         mso-bidi-font-size:10.0pt;
4327         font-family:Courier;
4328         mso-fareast-font-family:"Times New Roman";
4329         mso-bidi-font-family:"Times New Roman";}
4330 p.instruction, li.instruction, div.instruction
4331         {mso-style-name:instruction;
4332         mso-style-update:auto;
4333         mso-style-parent:example;
4334         margin-top:0cm;
4335         margin-right:0cm;
4336         margin-bottom:0cm;
4337         margin-left:42.55pt;
4338         margin-bottom:.0001pt;
4339         line-height:200%;
4340         mso-pagination:widow-orphan lines-together;
4341         page-break-after:avoid;
4342         mso-layout-grid-align:none;
4343         punctuation-wrap:simple;
4344         text-autospace:none;
4345         font-size:10.0pt;
4346         font-family:"Courier New";
4347         mso-fareast-font-family:"Times New Roman";
4348         mso-bidi-font-family:"Courier New";
4349         font-weight:bold;
4350         mso-bidi-font-weight:normal;}
4351 p.Format, li.Format, div.Format
4352         {mso-style-name:Format;
4353         mso-style-parent:example;
4354         margin-top:12.0pt;
4355         margin-right:0cm;
4356         margin-bottom:12.0pt;
4357         margin-left:1.0cm;
4358         mso-add-space:auto;
4359         line-height:200%;
4360         mso-pagination:widow-orphan lines-together;
4361         page-break-after:avoid;
4362         mso-layout-grid-align:none;
4363         punctuation-wrap:simple;
4364         text-autospace:none;
4365         font-size:10.0pt;
4366         font-family:"Courier New";
4367         mso-fareast-font-family:"Times New Roman";
4368         mso-bidi-font-family:"Courier New";
4369         mso-ansi-language:EN-GB;
4370         font-weight:bold;
4371         mso-bidi-font-weight:normal;}
4372 p.FormatCxSpFirst, li.FormatCxSpFirst, div.FormatCxSpFirst
4373         {mso-style-name:FormatCxSpFirst;
4374         mso-style-parent:example;
4375         mso-style-type:export-only;
4376         margin-top:12.0pt;
4377         margin-right:0cm;
4378         margin-bottom:0cm;
4379         margin-left:1.0cm;
4380         margin-bottom:.0001pt;
4381         mso-add-space:auto;
4382         line-height:200%;
4383         mso-pagination:widow-orphan lines-together;
4384         page-break-after:avoid;
4385         mso-layout-grid-align:none;
4386         punctuation-wrap:simple;
4387         text-autospace:none;
4388         font-size:10.0pt;
4389         font-family:"Courier New";
4390         mso-fareast-font-family:"Times New Roman";
4391         mso-bidi-font-family:"Courier New";
4392         mso-ansi-language:EN-GB;
4393         font-weight:bold;
4394         mso-bidi-font-weight:normal;}
4395 p.FormatCxSpMiddle, li.FormatCxSpMiddle, div.FormatCxSpMiddle
4396         {mso-style-name:FormatCxSpMiddle;
4397         mso-style-parent:example;
4398         mso-style-type:export-only;
4399         margin-top:0cm;
4400         margin-right:0cm;
4401         margin-bottom:0cm;
4402         margin-left:1.0cm;
4403         margin-bottom:.0001pt;
4404         mso-add-space:auto;
4405         line-height:200%;
4406         mso-pagination:widow-orphan lines-together;
4407         page-break-after:avoid;
4408         mso-layout-grid-align:none;
4409         punctuation-wrap:simple;
4410         text-autospace:none;
4411         font-size:10.0pt;
4412         font-family:"Courier New";
4413         mso-fareast-font-family:"Times New Roman";
4414         mso-bidi-font-family:"Courier New";
4415         mso-ansi-language:EN-GB;
4416         font-weight:bold;
4417         mso-bidi-font-weight:normal;}
4418 p.FormatCxSpLast, li.FormatCxSpLast, div.FormatCxSpLast
4419         {mso-style-name:FormatCxSpLast;
4420         mso-style-parent:example;
4421         mso-style-type:export-only;
4422         margin-top:0cm;
4423         margin-right:0cm;
4424         margin-bottom:12.0pt;
4425         margin-left:1.0cm;
4426         mso-add-space:auto;
4427         line-height:200%;
4428         mso-pagination:widow-orphan lines-together;
4429         page-break-after:avoid;
4430         mso-layout-grid-align:none;
4431         punctuation-wrap:simple;
4432         text-autospace:none;
4433         font-size:10.0pt;
4434         font-family:"Courier New";
4435         mso-fareast-font-family:"Times New Roman";
4436         mso-bidi-font-family:"Courier New";
4437         mso-ansi-language:EN-GB;
4438         font-weight:bold;
4439         mso-bidi-font-weight:normal;}
4440 p.ListinFlag, li.ListinFlag, div.ListinFlag
4441         {mso-style-name:"List in Flag";
4442         mso-style-parent:List;
4443         margin:0cm;
4444         margin-bottom:.0001pt;
4445         text-align:justify;
4446         mso-pagination:none;
4447         mso-hyphenate:none;
4448         mso-layout-grid-align:none;
4449         punctuation-wrap:simple;
4450         text-autospace:none;
4451         font-size:12.0pt;
4452         mso-bidi-font-size:10.0pt;
4453         font-family:"Times New Roman";
4454         mso-fareast-font-family:"Times New Roman";
4455         mso-bidi-font-family:"Times New Roman";}
4456 p.example2, li.example2, div.example2
4457         {mso-style-name:example2;
4458         mso-style-parent:example;
4459         margin-top:12.0pt;
4460         margin-right:0cm;
4461         margin-bottom:12.0pt;
4462         margin-left:2.0cm;
4463         mso-add-space:auto;
4464         line-height:200%;
4465         mso-pagination:widow-orphan lines-together;
4466         page-break-after:avoid;
4467         mso-layout-grid-align:none;
4468         punctuation-wrap:simple;
4469         text-autospace:none;
4470         font-size:10.0pt;
4471         font-family:"Courier New";
4472         mso-fareast-font-family:"Times New Roman";
4473         mso-bidi-font-family:"Courier New";
4474         font-weight:bold;
4475         mso-bidi-font-weight:normal;}
4476 p.example2CxSpFirst, li.example2CxSpFirst, div.example2CxSpFirst
4477         {mso-style-name:example2CxSpFirst;
4478         mso-style-parent:example;
4479         mso-style-type:export-only;
4480         margin-top:12.0pt;
4481         margin-right:0cm;
4482         margin-bottom:0cm;
4483         margin-left:2.0cm;
4484         margin-bottom:.0001pt;
4485         mso-add-space:auto;
4486         line-height:200%;
4487         mso-pagination:widow-orphan lines-together;
4488         page-break-after:avoid;
4489         mso-layout-grid-align:none;
4490         punctuation-wrap:simple;
4491         text-autospace:none;
4492         font-size:10.0pt;
4493         font-family:"Courier New";
4494         mso-fareast-font-family:"Times New Roman";
4495         mso-bidi-font-family:"Courier New";
4496         font-weight:bold;
4497         mso-bidi-font-weight:normal;}
4498 p.example2CxSpMiddle, li.example2CxSpMiddle, div.example2CxSpMiddle
4499         {mso-style-name:example2CxSpMiddle;
4500         mso-style-parent:example;
4501         mso-style-type:export-only;
4502         margin-top:0cm;
4503         margin-right:0cm;
4504         margin-bottom:0cm;
4505         margin-left:2.0cm;
4506         margin-bottom:.0001pt;
4507         mso-add-space:auto;
4508         line-height:200%;
4509         mso-pagination:widow-orphan lines-together;
4510         page-break-after:avoid;
4511         mso-layout-grid-align:none;
4512         punctuation-wrap:simple;
4513         text-autospace:none;
4514         font-size:10.0pt;
4515         font-family:"Courier New";
4516         mso-fareast-font-family:"Times New Roman";
4517         mso-bidi-font-family:"Courier New";
4518         font-weight:bold;
4519         mso-bidi-font-weight:normal;}
4520 p.example2CxSpLast, li.example2CxSpLast, div.example2CxSpLast
4521         {mso-style-name:example2CxSpLast;
4522         mso-style-parent:example;
4523         mso-style-type:export-only;
4524         margin-top:0cm;
4525         margin-right:0cm;
4526         margin-bottom:12.0pt;
4527         margin-left:2.0cm;
4528         mso-add-space:auto;
4529         line-height:200%;
4530         mso-pagination:widow-orphan lines-together;
4531         page-break-after:avoid;
4532         mso-layout-grid-align:none;
4533         punctuation-wrap:simple;
4534         text-autospace:none;
4535         font-size:10.0pt;
4536         font-family:"Courier New";
4537         mso-fareast-font-family:"Times New Roman";
4538         mso-bidi-font-family:"Courier New";
4539         font-weight:bold;
4540         mso-bidi-font-weight:normal;}
4541 p.StyleNote, li.StyleNote, div.StyleNote
4542         {mso-style-name:"Style Note";
4543         mso-style-parent:Note;
4544         margin-top:6.0pt;
4545         margin-right:0cm;
4546         margin-bottom:12.0pt;
4547         margin-left:-35.45pt;
4548         text-align:justify;
4549         mso-pagination:none;
4550         mso-hyphenate:none;
4551         tab-stops:1.0cm;
4552         mso-layout-grid-align:none;
4553         punctuation-wrap:simple;
4554         text-autospace:none;
4555         font-size:10.0pt;
4556         mso-bidi-font-size:8.0pt;
4557         font-family:"Times New Roman";
4558         mso-fareast-font-family:"Times New Roman";
4559         mso-bidi-font-family:"Times New Roman";
4560         mso-ansi-language:EN-GB;
4561         font-weight:bold;}
4562 p.examplefile, li.examplefile, div.examplefile
4563         {mso-style-name:example_file;
4564         mso-style-update:auto;
4565         margin-top:6.0pt;
4566         margin-right:0cm;
4567         margin-bottom:6.0pt;
4568         margin-left:0cm;
4569         mso-add-space:auto;
4570         text-align:justify;
4571         mso-pagination:none;
4572         mso-hyphenate:none;
4573         background:#E6E6E6;
4574         mso-layout-grid-align:none;
4575         punctuation-wrap:simple;
4576         text-autospace:none;
4577         border:none;
4578         mso-border-alt:solid windowtext .5pt;
4579         padding:0cm;
4580         mso-padding-alt:1.0pt 4.0pt 1.0pt 4.0pt;
4581         font-size:10.0pt;
4582         font-family:"Courier New";
4583         mso-fareast-font-family:"Times New Roman";
4584         mso-bidi-font-family:"Courier New";}
4585 p.examplefileCxSpFirst, li.examplefileCxSpFirst, div.examplefileCxSpFirst
4586         {mso-style-name:example_fileCxSpFirst;
4587         mso-style-update:auto;
4588         mso-style-type:export-only;
4589         margin-top:6.0pt;
4590         margin-right:0cm;
4591         margin-bottom:0cm;
4592         margin-left:0cm;
4593         margin-bottom:.0001pt;
4594         mso-add-space:auto;
4595         text-align:justify;
4596         mso-pagination:none;
4597         mso-hyphenate:none;
4598         background:#E6E6E6;
4599         mso-layout-grid-align:none;
4600         punctuation-wrap:simple;
4601         text-autospace:none;
4602         border:none;
4603         mso-border-alt:solid windowtext .5pt;
4604         padding:0cm;
4605         mso-padding-alt:1.0pt 4.0pt 1.0pt 4.0pt;
4606         font-size:10.0pt;
4607         font-family:"Courier New";
4608         mso-fareast-font-family:"Times New Roman";
4609         mso-bidi-font-family:"Courier New";}
4610 p.examplefileCxSpMiddle, li.examplefileCxSpMiddle, div.examplefileCxSpMiddle
4611         {mso-style-name:example_fileCxSpMiddle;
4612         mso-style-update:auto;
4613         mso-style-type:export-only;
4614         margin:0cm;
4615         margin-bottom:.0001pt;
4616         mso-add-space:auto;
4617         text-align:justify;
4618         mso-pagination:none;
4619         mso-hyphenate:none;
4620         background:#E6E6E6;
4621         mso-layout-grid-align:none;
4622         punctuation-wrap:simple;
4623         text-autospace:none;
4624         border:none;
4625         mso-border-alt:solid windowtext .5pt;
4626         padding:0cm;
4627         mso-padding-alt:1.0pt 4.0pt 1.0pt 4.0pt;
4628         font-size:10.0pt;
4629         font-family:"Courier New";
4630         mso-fareast-font-family:"Times New Roman";
4631         mso-bidi-font-family:"Courier New";}
4632 p.examplefileCxSpLast, li.examplefileCxSpLast, div.examplefileCxSpLast
4633         {mso-style-name:example_fileCxSpLast;
4634         mso-style-update:auto;
4635         mso-style-type:export-only;
4636         margin-top:0cm;
4637         margin-right:0cm;
4638         margin-bottom:6.0pt;
4639         margin-left:0cm;
4640         mso-add-space:auto;
4641         text-align:justify;
4642         mso-pagination:none;
4643         mso-hyphenate:none;
4644         background:#E6E6E6;
4645         mso-layout-grid-align:none;
4646         punctuation-wrap:simple;
4647         text-autospace:none;
4648         border:none;
4649         mso-border-alt:solid windowtext .5pt;
4650         padding:0cm;
4651         mso-padding-alt:1.0pt 4.0pt 1.0pt 4.0pt;
4652         font-size:10.0pt;
4653         font-family:"Courier New";
4654         mso-fareast-font-family:"Times New Roman";
4655         mso-bidi-font-family:"Courier New";}
4656 p.Warning, li.Warning, div.Warning
4657         {mso-style-name:Warning;
4658         mso-style-update:auto;
4659         mso-style-link:"Warning Char";
4660         mso-margin-top-alt:auto;
4661         margin-right:0cm;
4662         mso-margin-bottom-alt:auto;
4663         margin-left:0cm;
4664         mso-pagination:widow-orphan;
4665         background:#F7CBB7;
4666         border:none;
4667         mso-border-alt:solid windowtext 1.5pt;
4668         padding:0cm;
4669         mso-padding-alt:0cm 0cm 0cm 0cm;
4670         font-size:10.0pt;
4671         font-family:Garamond;
4672         mso-fareast-font-family:"Times New Roman";
4673         mso-bidi-font-family:"Times New Roman";
4674         font-weight:bold;
4675         mso-bidi-font-weight:normal;}
4676 span.WarningChar
4677         {mso-style-name:"Warning Char";
4678         mso-style-locked:yes;
4679         mso-style-parent:"Note Char";
4680         mso-style-link:Warning;
4681         mso-bidi-font-size:8.0pt;
4682         font-family:Garamond;
4683         mso-ascii-font-family:Garamond;
4684         mso-hansi-font-family:Garamond;
4685         mso-ansi-language:EN-US;
4686         mso-fareast-language:EN-US;
4687         font-weight:bold;
4688         mso-bidi-font-weight:normal;}
4689 p.Heaing3, li.Heaing3, div.Heaing3
4690         {mso-style-name:"Heaing 3";
4691         mso-style-parent:Note;
4692         margin-top:6.0pt;
4693         margin-right:0cm;
4694         margin-bottom:12.0pt;
4695         margin-left:42.55pt;
4696         text-align:justify;
4697         mso-pagination:none;
4698         mso-hyphenate:none;
4699         tab-stops:1.0cm;
4700         mso-layout-grid-align:none;
4701         punctuation-wrap:simple;
4702         text-autospace:none;
4703         font-size:10.0pt;
4704         mso-bidi-font-size:8.0pt;
4705         font-family:"Times New Roman";
4706         mso-fareast-font-family:"Times New Roman";
4707         mso-bidi-font-family:"Times New Roman";
4708         mso-ansi-language:EN-GB;
4709         font-weight:bold;
4710         mso-bidi-font-weight:normal;}
4711 p.NormalJustified, li.NormalJustified, div.NormalJustified
4712         {mso-style-name:"Normal + Justified";
4713         mso-style-link:"Normal + Justified Char";
4714         margin:0cm;
4715         margin-bottom:.0001pt;
4716         text-align:justify;
4717         mso-pagination:none;
4718         mso-hyphenate:none;
4719         mso-layout-grid-align:none;
4720         punctuation-wrap:simple;
4721         text-autospace:none;
4722         font-size:12.0pt;
4723         mso-bidi-font-size:10.0pt;
4724         font-family:"Times New Roman";
4725         mso-fareast-font-family:"Times New Roman";
4726         mso-bidi-font-family:"Times New Roman";
4727         mso-ansi-language:EN-GB;}
4728 span.NormalJustifiedChar
4729         {mso-style-name:"Normal + Justified Char";
4730         mso-style-locked:yes;
4731         mso-style-link:"Normal + Justified";
4732         mso-ansi-font-size:12.0pt;
4733         mso-ansi-language:EN-GB;
4734         mso-fareast-language:EN-US;}
4735 p.MyNormalID, li.MyNormalID, div.MyNormalID
4736         {mso-style-name:MyNormalID;
4737         mso-style-update:auto;
4738         mso-style-parent:"List Bullet";
4739         margin-top:0cm;
4740         margin-right:0cm;
4741         margin-bottom:0cm;
4742         margin-left:31.2pt;
4743         margin-bottom:.0001pt;
4744         text-indent:0cm;
4745         mso-pagination:none;
4746         mso-list:l8 level1 lfo7;
4747         mso-hyphenate:none;
4748         tab-stops:list 18.0pt;
4749         mso-layout-grid-align:none;
4750         punctuation-wrap:simple;
4751         text-autospace:none;
4752         font-size:12.0pt;
4753         mso-bidi-font-size:10.0pt;
4754         font-family:"Times New Roman";
4755         mso-fareast-font-family:"Times New Roman";
4756         mso-bidi-font-family:"Times New Roman";}
4757 p.MyExample, li.MyExample, div.MyExample
4758         {mso-style-name:MyExample;
4759         mso-style-update:auto;
4760         mso-margin-top-alt:auto;
4761         margin-right:0cm;
4762         mso-margin-bottom-alt:auto;
4763         margin-left:2.0cm;
4764         mso-pagination:none;
4765         mso-hyphenate:none;
4766         background:#FFFFCC;
4767         mso-layout-grid-align:none;
4768         punctuation-wrap:simple;
4769         text-autospace:none;
4770         border:none;
4771         mso-border-top-alt:solid black .25pt;
4772         mso-border-bottom-alt:solid black .25pt;
4773         padding:0cm;
4774         mso-padding-alt:10.0pt 0cm 10.0pt 0cm;
4775         font-size:9.0pt;
4776         font-family:"Courier New";
4777         mso-fareast-font-family:"Times New Roman";
4778         mso-bidi-font-family:"Times New Roman";
4779         font-weight:bold;
4780         mso-bidi-font-weight:normal;}
4781 p.Style1, li.Style1, div.Style1
4782         {mso-style-name:Style1;
4783         mso-style-update:auto;
4784         margin:0cm;
4785         margin-bottom:.0001pt;
4786         mso-pagination:widow-orphan;
4787         font-size:8.0pt;
4788         mso-bidi-font-size:10.0pt;
4789         font-family:Garamond;
4790         mso-fareast-font-family:"Times New Roman";
4791         mso-bidi-font-family:"Times New Roman";
4792         mso-ansi-language:EN-GB;
4793         font-weight:bold;
4794         mso-bidi-font-weight:normal;}
4795 p.StyleHeading6Bold, li.StyleHeading6Bold, div.StyleHeading6Bold
4796         {mso-style-name:"Style Heading 6 + Bold";
4797         mso-style-update:auto;
4798         mso-style-link:"Style Heading 6 + Bold Char";
4799         margin:0cm;
4800         margin-bottom:.0001pt;
4801         mso-pagination:widow-orphan;
4802         font-size:8.0pt;
4803         mso-bidi-font-size:10.0pt;
4804         font-family:Garamond;
4805         mso-fareast-font-family:"Times New Roman";
4806         mso-bidi-font-family:"Times New Roman";
4807         font-weight:bold;}
4808 span.StyleHeading6BoldChar
4809         {mso-style-name:"Style Heading 6 + Bold Char";
4810         mso-style-locked:yes;
4811         mso-style-link:"Style Heading 6 + Bold";
4812         mso-ansi-font-size:8.0pt;
4813         font-family:Garamond;
4814         mso-ascii-font-family:Garamond;
4815         mso-hansi-font-family:Garamond;
4816         mso-ansi-language:EN-US;
4817         mso-fareast-language:EN-US;
4818         font-weight:bold;}
4819 p.MyNormaBoldl, li.MyNormaBoldl, div.MyNormaBoldl
4820         {mso-style-name:MyNormaBoldl;
4821         mso-style-parent:MyNormal;
4822         mso-style-link:"MyNormaBoldl Char";
4823         margin-top:2.0pt;
4824         margin-right:0cm;
4825         margin-bottom:6.0pt;
4826         margin-left:42.55pt;
4827         text-align:justify;
4828         mso-pagination:none;
4829         mso-hyphenate:none;
4830         mso-layout-grid-align:none;
4831         punctuation-wrap:simple;
4832         text-autospace:none;
4833         font-size:11.0pt;
4834         font-family:"Times New Roman";
4835         mso-fareast-font-family:"Times New Roman";
4836         mso-bidi-font-family:"Courier New";
4837         mso-ansi-language:AF;}
4838 p.Mylist, li.Mylist, div.Mylist
4839         {mso-style-name:Mylist;
4840         mso-style-parent:MyNormal;
4841         margin-top:2.0pt;
4842         margin-right:0cm;
4843         margin-bottom:6.0pt;
4844         margin-left:128.7pt;
4845         text-align:justify;
4846         text-indent:-72.0pt;
4847         mso-pagination:none;
4848         mso-hyphenate:none;
4849         mso-layout-grid-align:none;
4850         punctuation-wrap:simple;
4851         text-autospace:none;
4852         font-size:11.0pt;
4853         font-family:"Times New Roman";
4854         mso-fareast-font-family:"Times New Roman";
4855         mso-bidi-font-family:"Courier New";
4856         mso-ansi-language:AF;
4857         font-style:italic;
4858         mso-bidi-font-style:normal;}
4859 p.MyNormalBold, li.MyNormalBold, div.MyNormalBold
4860         {mso-style-name:MyNormalBold;
4861         mso-style-parent:MyNormalID;
4862         margin-top:6.0pt;
4863         margin-right:0cm;
4864         margin-bottom:12.0pt;
4865         margin-left:31.2pt;
4866         text-indent:0cm;
4867         mso-pagination:lines-together;
4868         mso-list:l8 level1 lfo7;
4869         tab-stops:list 18.0pt;
4870         mso-layout-grid-align:none;
4871         punctuation-wrap:simple;
4872         text-autospace:none;
4873         font-size:12.0pt;
4874         mso-bidi-font-size:10.0pt;
4875         font-family:"Times New Roman";
4876         mso-fareast-font-family:"Times New Roman";
4877         mso-bidi-font-family:"Times New Roman";}
4878 p.StyleflagdescriptionBoldItalic, li.StyleflagdescriptionBoldItalic, div.StyleflagdescriptionBoldItalic
4879         {mso-style-name:"Style flag description + Bold Italic";
4880         mso-style-update:auto;
4881         mso-style-parent:"flag description";
4882         mso-style-link:"Style flag description + Bold Italic Char";
4883         margin-top:3.0pt;
4884         margin-right:0cm;
4885         margin-bottom:3.0pt;
4886         margin-left:42.55pt;
4887         text-align:justify;
4888         mso-pagination:none;
4889         mso-hyphenate:none;
4890         mso-layout-grid-align:none;
4891         punctuation-wrap:simple;
4892         text-autospace:none;
4893         font-size:10.0pt;
4894         font-family:"Times New Roman";
4895         mso-fareast-font-family:"Times New Roman";
4896         mso-bidi-font-family:"Times New Roman";
4897         font-weight:bold;
4898         font-style:italic;}
4899 span.StyleflagdescriptionBoldItalicChar
4900         {mso-style-name:"Style flag description + Bold Italic Char";
4901         mso-style-locked:yes;
4902         mso-style-parent:"flag description Char";
4903         mso-style-link:"Style flag description + Bold Italic";
4904         mso-ansi-language:EN-US;
4905         mso-fareast-language:EN-US;
4906         font-weight:bold;
4907         font-style:italic;}
4908 p.Formula, li.Formula, div.Formula
4909         {mso-style-name:Formula;
4910         mso-style-parent:"flag description";
4911         margin-top:6.0pt;
4912         margin-right:0cm;
4913         margin-bottom:0cm;
4914         margin-left:42.55pt;
4915         margin-bottom:.0001pt;
4916         text-align:justify;
4917         mso-pagination:none;
4918         mso-hyphenate:none;
4919         mso-layout-grid-align:none;
4920         punctuation-wrap:simple;
4921         text-autospace:none;
4922         font-size:10.0pt;
4923         font-family:"Times New Roman";
4924         mso-fareast-font-family:"Times New Roman";
4925         mso-bidi-font-family:"Times New Roman";}
4926 p.examplefilesmall, li.examplefilesmall, div.examplefilesmall
4927         {mso-style-name:example_file_small;
4928         mso-style-parent:example_file;
4929         margin-top:6.0pt;
4930         margin-right:1.0cm;
4931         margin-bottom:6.0pt;
4932         margin-left:0cm;
4933         mso-add-space:auto;
4934         text-align:justify;
4935         mso-pagination:none;
4936         mso-hyphenate:none;
4937         background:#E6E6E6;
4938         mso-layout-grid-align:none;
4939         punctuation-wrap:simple;
4940         text-autospace:none;
4941         border:none;
4942         mso-border-alt:solid windowtext .5pt;
4943         padding:0cm;
4944         mso-padding-alt:1.0pt 4.0pt 1.0pt 4.0pt;
4945         font-size:8.0pt;
4946         mso-bidi-font-size:10.0pt;
4947         font-family:"Courier New";
4948         mso-fareast-font-family:"Times New Roman";
4949         mso-bidi-font-family:"Courier New";}
4950 p.examplefilesmallCxSpFirst, li.examplefilesmallCxSpFirst, div.examplefilesmallCxSpFirst
4951         {mso-style-name:example_file_smallCxSpFirst;
4952         mso-style-parent:example_file;
4953         mso-style-type:export-only;
4954         margin-top:6.0pt;
4955         margin-right:1.0cm;
4956         margin-bottom:0cm;
4957         margin-left:0cm;
4958         margin-bottom:.0001pt;
4959         mso-add-space:auto;
4960         text-align:justify;
4961         mso-pagination:none;
4962         mso-hyphenate:none;
4963         background:#E6E6E6;
4964         mso-layout-grid-align:none;
4965         punctuation-wrap:simple;
4966         text-autospace:none;
4967         border:none;
4968         mso-border-alt:solid windowtext .5pt;
4969         padding:0cm;
4970         mso-padding-alt:1.0pt 4.0pt 1.0pt 4.0pt;
4971         font-size:8.0pt;
4972         mso-bidi-font-size:10.0pt;
4973         font-family:"Courier New";
4974         mso-fareast-font-family:"Times New Roman";
4975         mso-bidi-font-family:"Courier New";}
4976 p.examplefilesmallCxSpMiddle, li.examplefilesmallCxSpMiddle, div.examplefilesmallCxSpMiddle
4977         {mso-style-name:example_file_smallCxSpMiddle;
4978         mso-style-parent:example_file;
4979         mso-style-type:export-only;
4980         margin-top:0cm;
4981         margin-right:1.0cm;
4982         margin-bottom:0cm;
4983         margin-left:0cm;
4984         margin-bottom:.0001pt;
4985         mso-add-space:auto;
4986         text-align:justify;
4987         mso-pagination:none;
4988         mso-hyphenate:none;
4989         background:#E6E6E6;
4990         mso-layout-grid-align:none;
4991         punctuation-wrap:simple;
4992         text-autospace:none;
4993         border:none;
4994         mso-border-alt:solid windowtext .5pt;
4995         padding:0cm;
4996         mso-padding-alt:1.0pt 4.0pt 1.0pt 4.0pt;
4997         font-size:8.0pt;
4998         mso-bidi-font-size:10.0pt;
4999         font-family:"Courier New";
5000         mso-fareast-font-family:"Times New Roman";
5001         mso-bidi-font-family:"Courier New";}
5002 p.examplefilesmallCxSpLast, li.examplefilesmallCxSpLast, div.examplefilesmallCxSpLast
5003         {mso-style-name:example_file_smallCxSpLast;
5004         mso-style-parent:example_file;
5005         mso-style-type:export-only;
5006         margin-top:0cm;
5007         margin-right:1.0cm;
5008         margin-bottom:6.0pt;
5009         margin-left:0cm;
5010         mso-add-space:auto;
5011         text-align:justify;
5012         mso-pagination:none;
5013         mso-hyphenate:none;
5014         background:#E6E6E6;
5015         mso-layout-grid-align:none;
5016         punctuation-wrap:simple;
5017         text-autospace:none;
5018         border:none;
5019         mso-border-alt:solid windowtext .5pt;
5020         padding:0cm;
5021         mso-padding-alt:1.0pt 4.0pt 1.0pt 4.0pt;
5022         font-size:8.0pt;
5023         mso-bidi-font-size:10.0pt;
5024         font-family:"Courier New";
5025         mso-fareast-font-family:"Times New Roman";
5026         mso-bidi-font-family:"Courier New";}
5027 p.StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut, li.StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut, div.StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut
5028         {mso-style-name:"Style notebox\.body + Bold Not Italic Box\: \(Single solid line Aut\.\.\.";
5029         mso-style-parent:"notebox\.body";
5030         margin:0cm;
5031         margin-bottom:.0001pt;
5032         mso-pagination:none;
5033         mso-hyphenate:none;
5034         background:#FFFF89;
5035         mso-layout-grid-align:none;
5036         punctuation-wrap:simple;
5037         text-autospace:none;
5038         border:none;
5039         mso-border-alt:solid windowtext 1.5pt;
5040         padding:0cm;
5041         mso-padding-alt:1.0pt 4.0pt 1.0pt 4.0pt;
5042         font-size:12.0pt;
5043         mso-bidi-font-size:10.0pt;
5044         font-family:"Times New Roman";
5045         mso-fareast-font-family:"Times New Roman";
5046         mso-bidi-font-family:"Times New Roman";
5047         font-weight:bold;}
5048 p.MyNormalJustified, li.MyNormalJustified, div.MyNormalJustified
5049         {mso-style-name:MyNormalJustified;
5050         mso-style-parent:MyNormal;
5051         margin-top:2.0pt;
5052         margin-right:0cm;
5053         margin-bottom:6.0pt;
5054         margin-left:42.55pt;
5055         mso-pagination:none;
5056         mso-hyphenate:none;
5057         mso-layout-grid-align:none;
5058         punctuation-wrap:simple;
5059         text-autospace:none;
5060         font-size:11.0pt;
5061         font-family:"Times New Roman";
5062         mso-fareast-font-family:"Times New Roman";
5063         mso-bidi-font-family:"Courier New";}
5064 p.flagheading2, li.flagheading2, div.flagheading2
5065         {mso-style-name:"flag heading 2";
5066         mso-style-update:auto;
5067         mso-style-parent:"flag description";
5068         margin-top:6.0pt;
5069         margin-right:0cm;
5070         margin-bottom:0cm;
5071         margin-left:45.0pt;
5072         margin-bottom:.0001pt;
5073         text-align:justify;
5074         mso-pagination:none;
5075         mso-hyphenate:none;
5076         mso-layout-grid-align:none;
5077         punctuation-wrap:simple;
5078         text-autospace:none;
5079         font-size:10.0pt;
5080         font-family:"Times New Roman";
5081         mso-fareast-font-family:"Times New Roman";
5082         mso-bidi-font-family:"Times New Roman";
5083         font-weight:bold;
5084         mso-bidi-font-weight:normal;
5085         font-style:italic;
5086         mso-bidi-font-style:normal;
5087         text-decoration:underline;
5088         text-underline:single;}
5089 p.example1, li.example1, div.example1
5090         {mso-style-name:example1;
5091         mso-style-parent:example2;
5092         margin-top:12.0pt;
5093         margin-right:0cm;
5094         margin-bottom:12.0pt;
5095         margin-left:2.0cm;
5096         mso-add-space:auto;
5097         line-height:200%;
5098         mso-pagination:widow-orphan lines-together;
5099         page-break-after:avoid;
5100         mso-layout-grid-align:none;
5101         punctuation-wrap:simple;
5102         text-autospace:none;
5103         font-size:10.0pt;
5104         font-family:"Courier New";
5105         mso-fareast-font-family:"Times New Roman";
5106         mso-bidi-font-family:"Courier New";
5107         font-weight:bold;
5108         mso-bidi-font-weight:normal;}
5109 p.example1CxSpFirst, li.example1CxSpFirst, div.example1CxSpFirst
5110         {mso-style-name:example1CxSpFirst;
5111         mso-style-parent:example2;
5112         mso-style-type:export-only;
5113         margin-top:12.0pt;
5114         margin-right:0cm;
5115         margin-bottom:0cm;
5116         margin-left:2.0cm;
5117         margin-bottom:.0001pt;
5118         mso-add-space:auto;
5119         line-height:200%;
5120         mso-pagination:widow-orphan lines-together;
5121         page-break-after:avoid;
5122         mso-layout-grid-align:none;
5123         punctuation-wrap:simple;
5124         text-autospace:none;
5125         font-size:10.0pt;
5126         font-family:"Courier New";
5127         mso-fareast-font-family:"Times New Roman";
5128         mso-bidi-font-family:"Courier New";
5129         font-weight:bold;
5130         mso-bidi-font-weight:normal;}
5131 p.example1CxSpMiddle, li.example1CxSpMiddle, div.example1CxSpMiddle
5132         {mso-style-name:example1CxSpMiddle;
5133         mso-style-parent:example2;
5134         mso-style-type:export-only;
5135         margin-top:0cm;
5136         margin-right:0cm;
5137         margin-bottom:0cm;
5138         margin-left:2.0cm;
5139         margin-bottom:.0001pt;
5140         mso-add-space:auto;
5141         line-height:200%;
5142         mso-pagination:widow-orphan lines-together;
5143         page-break-after:avoid;
5144         mso-layout-grid-align:none;
5145         punctuation-wrap:simple;
5146         text-autospace:none;
5147         font-size:10.0pt;
5148         font-family:"Courier New";
5149         mso-fareast-font-family:"Times New Roman";
5150         mso-bidi-font-family:"Courier New";
5151         font-weight:bold;
5152         mso-bidi-font-weight:normal;}
5153 p.example1CxSpLast, li.example1CxSpLast, div.example1CxSpLast
5154         {mso-style-name:example1CxSpLast;
5155         mso-style-parent:example2;
5156         mso-style-type:export-only;
5157         margin-top:0cm;
5158         margin-right:0cm;
5159         margin-bottom:12.0pt;
5160         margin-left:2.0cm;
5161         mso-add-space:auto;
5162         line-height:200%;
5163         mso-pagination:widow-orphan lines-together;
5164         page-break-after:avoid;
5165         mso-layout-grid-align:none;
5166         punctuation-wrap:simple;
5167         text-autospace:none;
5168         font-size:10.0pt;
5169         font-family:"Courier New";
5170         mso-fareast-font-family:"Times New Roman";
5171         mso-bidi-font-family:"Courier New";
5172         font-weight:bold;
5173         mso-bidi-font-weight:normal;}
5174 span.MyNormaBoldlChar
5175         {mso-style-name:"MyNormaBoldl Char";
5176         mso-style-locked:yes;
5177         mso-style-parent:"MyNormal Char";
5178         mso-style-link:MyNormaBoldl;
5179         mso-ansi-font-size:11.0pt;
5180         mso-bidi-font-size:11.0pt;
5181         font-family:"Courier New";
5182         mso-ascii-font-family:"Courier New";
5183         mso-hansi-font-family:"Courier New";
5184         mso-bidi-font-family:"Courier New";
5185         mso-ansi-language:AF;
5186         mso-fareast-language:EN-US;}
5187 p.MyNormal2, li.MyNormal2, div.MyNormal2
5188         {mso-style-name:MyNormal2;
5189         mso-style-parent:MyNormal;
5190         margin-top:2.0pt;
5191         margin-right:0cm;
5192         margin-bottom:6.0pt;
5193         margin-left:42.55pt;
5194         text-align:justify;
5195         mso-pagination:none;
5196         mso-hyphenate:none;
5197         mso-layout-grid-align:none;
5198         punctuation-wrap:simple;
5199         text-autospace:none;
5200         font-size:11.0pt;
5201         font-family:"Times New Roman";
5202         mso-fareast-font-family:"Times New Roman";
5203         mso-bidi-font-family:"Courier New";
5204         mso-ansi-language:AF;}
5205 span.msoIns
5206         {mso-style-type:export-only;
5207         mso-style-name:"";
5208         text-decoration:underline;
5209         text-underline:single;
5210         color:teal;}
5211 span.msoDel
5212         {mso-style-type:export-only;
5213         mso-style-name:"";
5214         text-decoration:line-through;
5215         color:red;}
5216 span.msoChangeProp
5217         {mso-style-type:export-only;
5218         mso-style-name:"";
5219         color:black;}
5220  /* Page Definitions */
5221 @page
5222         {mso-footnote-separator:url(":t_coffee_technical_files:header.htm") fs;
5223         mso-footnote-continuation-separator:url(":t_coffee_technical_files:header.htm") fcs;
5224         mso-endnote-separator:url(":t_coffee_technical_files:header.htm") es;
5225         mso-endnote-continuation-separator:url(":t_coffee_technical_files:header.htm") ecs;}
5226 @page Section1
5227         {size:21.0cm 842.0pt;
5228         margin:48.0pt 48.0pt 48.0pt 48.0pt;
5229         mso-header-margin:0cm;
5230         mso-footer-margin:0cm;
5231         mso-page-numbers:0;
5232         mso-title-page:yes;
5233         mso-footer:url(":t_coffee_technical_files:header.htm") f1;
5234         mso-paper-source:0;}
5235 div.Section1
5236         {page:Section1;}
5237 @page Section2
5238         {size:21.0cm 842.0pt;
5239         margin:90.0pt 60.0pt 90.0pt 60.0pt;
5240         mso-header-margin:48.0pt;
5241         mso-footer-margin:48.0pt;
5242         mso-page-numbers:roman-lower 1;
5243         mso-title-page:yes;
5244         mso-footer:url(":t_coffee_technical_files:header.htm") f1;
5245         mso-first-footer:url(":t_coffee_technical_files:header.htm") ff2;
5246         mso-paper-source:0;}
5247 div.Section2
5248         {page:Section2;}
5249 @page Section3
5250         {size:21.0cm 842.0pt;
5251         margin:90.0pt 60.0pt 90.0pt 60.0pt;
5252         mso-header-margin:48.0pt;
5253         mso-footer-margin:48.0pt;
5254         mso-page-numbers:1;
5255         mso-header:url(":t_coffee_technical_files:header.htm") h3;
5256         mso-footer:url(":t_coffee_technical_files:header.htm") f3;
5257         mso-first-header:url(":t_coffee_technical_files:header.htm") fh3;
5258         mso-first-footer:url(":t_coffee_technical_files:header.htm") ff3;
5259         mso-paper-source:0;}
5260 div.Section3
5261         {page:Section3;}
5262 @page Section4
5263         {size:21.0cm 842.0pt;
5264         margin:72.0pt 90.0pt 72.0pt 90.0pt;
5265         mso-header-margin:36.0pt;
5266         mso-footer-margin:36.0pt;
5267         mso-header:url(":t_coffee_technical_files:header.htm") h4;
5268         mso-footer:url(":t_coffee_technical_files:header.htm") f4;
5269         mso-first-header:url(":t_coffee_technical_files:header.htm") fh4;
5270         mso-first-footer:url(":t_coffee_technical_files:header.htm") ff3;
5271         mso-paper-source:0;}
5272 div.Section4
5273         {page:Section4;}
5274  /* List Definitions */
5275 @list l0
5276         {mso-list-id:-132;
5277         mso-list-type:simple;
5278         mso-list-template-ids:243462170;}
5279 @list l0:level1
5280         {mso-level-style-link:"List Number 3";
5281         mso-level-tab-stop:90.0pt;
5282         mso-level-number-position:left;
5283         margin-left:90.0pt;
5284         text-indent:-18.0pt;}
5285 @list l1
5286         {mso-list-id:-131;
5287         mso-list-type:simple;
5288         mso-list-template-ids:579796312;}
5289 @list l1:level1
5290         {mso-level-style-link:"List Number 2";
5291         mso-level-tab-stop:72.0pt;
5292         mso-level-number-position:left;
5293         margin-left:72.0pt;
5294         text-indent:-18.0pt;}
5295 @list l2
5296         {mso-list-id:-130;
5297         mso-list-type:simple;
5298         mso-list-template-ids:-525153058;}
5299 @list l2:level1
5300         {mso-level-style-link:"List Bullet 5";
5301         mso-level-tab-stop:54.0pt;
5302         mso-level-number-position:left;
5303         margin-left:54.0pt;
5304         text-indent:-18.0pt;}
5305 @list l3
5306         {mso-list-id:-129;
5307         mso-list-type:simple;
5308         mso-list-template-ids:1970563230;}
5309 @list l3:level1
5310         {mso-level-style-link:"List Bullet 4";
5311         mso-level-tab-stop:36.0pt;
5312         mso-level-number-position:left;
5313         text-indent:-18.0pt;}
5314 @list l4
5315         {mso-list-id:-128;
5316         mso-list-type:simple;
5317         mso-list-template-ids:-118980482;}
5318 @list l4:level1
5319         {mso-level-number-format:bullet;
5320         mso-level-style-link:"List Bullet 3";
5321         mso-level-text:\F0B7;
5322         mso-level-tab-stop:90.0pt;
5323         mso-level-number-position:left;
5324         margin-left:90.0pt;
5325         text-indent:-18.0pt;
5326         font-family:Symbol;}
5327 @list l5
5328         {mso-list-id:-127;
5329         mso-list-type:simple;
5330         mso-list-template-ids:-1465100272;}
5331 @list l5:level1
5332         {mso-level-number-format:bullet;
5333         mso-level-style-link:"List Bullet 2";
5334         mso-level-text:\F0B7;
5335         mso-level-tab-stop:72.0pt;
5336         mso-level-number-position:left;
5337         margin-left:72.0pt;
5338         text-indent:-18.0pt;
5339         font-family:Symbol;}
5340 @list l6
5341         {mso-list-id:-126;
5342         mso-list-type:simple;
5343         mso-list-template-ids:-368430812;}
5344 @list l6:level1
5345         {mso-level-number-format:bullet;
5346         mso-level-style-link:"List 5";
5347         mso-level-text:\F0B7;
5348         mso-level-tab-stop:54.0pt;
5349         mso-level-number-position:left;
5350         margin-left:54.0pt;
5351         text-indent:-18.0pt;
5352         font-family:Symbol;}
5353 @list l7
5354         {mso-list-id:-125;
5355         mso-list-type:simple;
5356         mso-list-template-ids:-706941758;}
5357 @list l7:level1
5358         {mso-level-number-format:bullet;
5359         mso-level-style-link:"List 4";
5360         mso-level-text:\F0B7;
5361         mso-level-tab-stop:36.0pt;
5362         mso-level-number-position:left;
5363         text-indent:-18.0pt;
5364         font-family:Symbol;}
5365 @list l8
5366         {mso-list-id:-120;
5367         mso-list-type:simple;
5368         mso-list-template-ids:1576020400;}
5369 @list l8:level1
5370         {mso-level-style-link:"Plain Text";
5371         mso-level-tab-stop:18.0pt;
5372         mso-level-number-position:left;
5373         margin-left:18.0pt;
5374         text-indent:-18.0pt;}
5375 @list l9
5376         {mso-list-id:-119;
5377         mso-list-type:simple;
5378         mso-list-template-ids:96769246;}
5379 @list l9:level1
5380         {mso-level-number-format:bullet;
5381         mso-level-style-link:"Text body Char";
5382         mso-level-text:\F0B7;
5383         mso-level-tab-stop:18.0pt;
5384         mso-level-number-position:left;
5385         margin-left:18.0pt;
5386         text-indent:-18.0pt;
5387         font-family:Symbol;}
5388 @list l10
5389         {mso-list-id:-5;
5390         mso-list-template-ids:-1557078836;}
5391 @list l10:level1
5392         {mso-level-number-format:none;
5393         mso-level-suffix:none;
5394         mso-level-text:"";
5395         mso-level-tab-stop:none;
5396         mso-level-number-position:left;
5397         margin-left:0cm;
5398         text-indent:0cm;}
5399 @list l10:level2
5400         {mso-level-number-format:none;
5401         mso-level-text:"";
5402         mso-level-tab-stop:none;
5403         mso-level-number-position:left;
5404         mso-level-legacy:yes;
5405         mso-level-legacy-indent:0cm;
5406         mso-level-legacy-space:0cm;
5407         margin-left:0cm;
5408         text-indent:0cm;}
5409 @list l10:level3
5410         {mso-level-number-format:none;
5411         mso-level-text:"";
5412         mso-level-tab-stop:none;
5413         mso-level-number-position:left;
5414         mso-level-legacy:yes;
5415         mso-level-legacy-indent:0cm;
5416         mso-level-legacy-space:0cm;
5417         margin-left:0cm;
5418         text-indent:0cm;}
5419 @list l10:level4
5420         {mso-level-number-format:none;
5421         mso-level-text:"";
5422         mso-level-tab-stop:none;
5423         mso-level-number-position:left;
5424         mso-level-legacy:yes;
5425         mso-level-legacy-indent:0cm;
5426         mso-level-legacy-space:0cm;
5427         margin-left:0cm;
5428         text-indent:0cm;
5429         mso-ansi-language:EN-GB;}
5430 @list l10:level5
5431         {mso-level-start-at:0;
5432         mso-level-number-format:none;
5433         mso-level-text:"";
5434         mso-level-tab-stop:none;
5435         mso-level-number-position:left;
5436         margin-left:0cm;
5437         text-indent:0cm;}
5438 @list l10:level6
5439         {mso-level-start-at:0;
5440         mso-level-number-format:none;
5441         mso-level-text:"";
5442         mso-level-tab-stop:none;
5443         mso-level-number-position:left;
5444         margin-left:0cm;
5445         text-indent:0cm;}
5446 @list l10:level7
5447         {mso-level-start-at:0;
5448         mso-level-number-format:none;
5449         mso-level-text:"";
5450         mso-level-tab-stop:none;
5451         mso-level-number-position:left;
5452         margin-left:0cm;
5453         text-indent:0cm;}
5454 @list l10:level8
5455         {mso-level-start-at:0;
5456         mso-level-number-format:none;
5457         mso-level-text:"";
5458         mso-level-tab-stop:none;
5459         mso-level-number-position:left;
5460         margin-left:0cm;
5461         text-indent:0cm;}
5462 @list l10:level9
5463         {mso-level-start-at:0;
5464         mso-level-number-format:none;
5465         mso-level-text:"";
5466         mso-level-tab-stop:none;
5467         mso-level-number-position:left;
5468         margin-left:0cm;
5469         text-indent:0cm;}
5470 @list l11
5471         {mso-list-id:-2;
5472         mso-list-type:simple;
5473         mso-list-template-ids:-1;}
5474 @list l11:level1
5475         {mso-level-start-at:0;
5476         mso-level-text:*;
5477         mso-level-tab-stop:none;
5478         mso-level-number-position:left;
5479         margin-left:0cm;
5480         text-indent:0cm;}
5481 @list l12
5482         {mso-list-id:16198800;
5483         mso-list-type:hybrid;
5484         mso-list-template-ids:-1589361750 67895311 67895321 67895323 67895311 67895321 67895323 67895311 67895321 67895323;}
5485 @list l12:level1
5486         {mso-level-tab-stop:78.55pt;
5487         mso-level-number-position:left;
5488         margin-left:78.55pt;
5489         text-indent:-18.0pt;}
5490 @list l12:level2
5491         {mso-level-number-format:alpha-lower;
5492         mso-level-tab-stop:114.55pt;
5493         mso-level-number-position:left;
5494         margin-left:114.55pt;
5495         text-indent:-18.0pt;}
5496 @list l13
5497         {mso-list-id:31855817;
5498         mso-list-type:hybrid;
5499         mso-list-template-ids:1137623166 -1 -1 -1 -1 -1 -1 -1 -1 -1;}
5500 @list l13:level1
5501         {mso-level-number-format:bullet;
5502         mso-level-text:\F0A7;
5503         mso-level-tab-stop:108.0pt;
5504         mso-level-number-position:left;
5505         margin-left:108.0pt;
5506         text-indent:-18.0pt;
5507         font-family:Wingdings;}
5508 @list l14
5509         {mso-list-id:351080084;
5510         mso-list-template-ids:1670832864;}
5511 @list l14:level1
5512         {mso-level-number-format:bullet;
5513         mso-level-text:\F0B7;
5514         mso-level-tab-stop:36.0pt;
5515         mso-level-number-position:left;
5516         text-indent:-18.0pt;
5517         mso-ansi-font-size:10.0pt;
5518         font-family:Symbol;}
5519 @list l14:level2
5520         {mso-level-tab-stop:72.0pt;
5521         mso-level-number-position:left;
5522         text-indent:-18.0pt;}
5523 @list l15
5524         {mso-list-id:429860257;
5525         mso-list-type:simple;
5526         mso-list-template-ids:-1193904264;}
5527 @list l15:level1
5528         {mso-level-tab-stop:none;
5529         mso-level-number-position:left;
5530         mso-level-legacy:yes;
5531         mso-level-legacy-indent:18.0pt;
5532         mso-level-legacy-space:0cm;
5533         margin-right:36.0pt;
5534         text-indent:-18.0pt;
5535         mso-ansi-font-size:10.0pt;
5536         mso-ascii-font-family:"Arial Black";
5537         mso-hansi-font-family:"Arial Black";}
5538 @list l16
5539         {mso-list-id:873344605;
5540         mso-list-template-ids:1828727762;}
5541 @list l16:level1
5542         {mso-level-number-format:bullet;
5543         mso-level-text:\F0A7;
5544         mso-level-tab-stop:18.0pt;
5545         mso-level-number-position:left;
5546         margin-left:18.0pt;
5547         text-indent:-18.0pt;
5548         font-family:Wingdings;}
5549 @list l16:level2
5550         {mso-level-number-format:none;
5551         mso-level-text:"";
5552         mso-level-tab-stop:none;
5553         mso-level-number-position:left;
5554         mso-level-legacy:yes;
5555         mso-level-legacy-indent:0cm;
5556         mso-level-legacy-space:0cm;
5557         margin-left:0cm;
5558         text-indent:0cm;}
5559 @list l16:level3
5560         {mso-level-number-format:none;
5561         mso-level-text:"";
5562         mso-level-tab-stop:none;
5563         mso-level-number-position:left;
5564         mso-level-legacy:yes;
5565         mso-level-legacy-indent:0cm;
5566         mso-level-legacy-space:0cm;
5567         margin-left:0cm;
5568         text-indent:0cm;}
5569 @list l16:level4
5570         {mso-level-number-format:none;
5571         mso-level-text:"";
5572         mso-level-tab-stop:none;
5573         mso-level-number-position:left;
5574         mso-level-legacy:yes;
5575         mso-level-legacy-indent:0cm;
5576         mso-level-legacy-space:0cm;
5577         margin-left:0cm;
5578         text-indent:0cm;}
5579 @list l16:level5
5580         {mso-level-start-at:0;
5581         mso-level-number-format:none;
5582         mso-level-text:"";
5583         mso-level-tab-stop:none;
5584         mso-level-number-position:left;
5585         margin-left:0cm;
5586         text-indent:0cm;}
5587 @list l16:level6
5588         {mso-level-start-at:0;
5589         mso-level-number-format:none;
5590         mso-level-text:"";
5591         mso-level-tab-stop:none;
5592         mso-level-number-position:left;
5593         margin-left:0cm;
5594         text-indent:0cm;}
5595 @list l16:level7
5596         {mso-level-start-at:0;
5597         mso-level-number-format:none;
5598         mso-level-text:"";
5599         mso-level-tab-stop:none;
5600         mso-level-number-position:left;
5601         margin-left:0cm;
5602         text-indent:0cm;}
5603 @list l16:level8
5604         {mso-level-start-at:0;
5605         mso-level-number-format:none;
5606         mso-level-text:"";
5607         mso-level-tab-stop:none;
5608         mso-level-number-position:left;
5609         margin-left:0cm;
5610         text-indent:0cm;}
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5882 -->
5883 </style>
5884 <!--[if gte mso 10]>
5885 <style>
5886  /* Style Definitions */
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5900 <![endif]--><!--[if gte mso 9]><xml>
5901  <o:shapedefaults v:ext="edit" spidmax="2050"/>
5902 </xml><![endif]--><!--[if gte mso 9]><xml>
5903  <o:shapelayout v:ext="edit">
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5906 </head>
5907
5908 <body lang=EN-US link=blue vlink=purple style='tab-interval:35.4pt'>
5909
5910 <div class=Section1>
5911
5912 <div style='mso-element:frame;mso-element-wrap:no-wrap-beside;mso-height-rule:
5913 exactly'>
5914
5915 <table cellspacing=0 cellpadding=0 hspace=0 vspace=0 width=112 align=right>
5916  <tr>
5917   <td valign=top style='padding-top:9.35pt;padding-right:9.35pt;padding-bottom:
5918   9.35pt;padding-left:9.35pt'>
5919   <p class=PartTitle>Technical</p>
5920   </td>
5921  </tr>
5922 </table>
5923
5924 </div>
5925
5926 <![if !supportTextWrap]><br clear=ALL>
5927 <![endif]>
5928
5929 <p class=CompanyName><span style='font-size:14.0pt'>Centre National De LA
5930 Recherche scientifique (France)<br>
5931 CeNTRO De REGULACIO GENOMICA (SPAIN)<o:p></o:p></span></p>
5932
5933 <div style='mso-element:para-border-div;border:none;border-top:solid windowtext 1.0pt;
5934 mso-border-top-alt:solid windowtext .75pt;padding:1.0pt 0cm 0cm 0cm'>
5935
5936 <p class=SubtitleCover>Cédric Notredame<br>
5937 www.tcoffee.org</p>
5938
5939 </div>
5940
5941 <div style='mso-element:para-border-div;border:solid white 1.0pt;mso-border-alt:
5942 solid white .75pt;padding:31.0pt 31.0pt 31.0pt 31.0pt;background:#E5E5E5;
5943 mso-shading:windowtext;mso-pattern:gray-10 auto'>
5944
5945 <p class=TitleCover style='margin:0cm;margin-bottom:.0001pt;background:#E5E5E5;
5946 mso-shading:windowtext;mso-pattern:gray-10 auto'>T-Coffee:<br>
5947 Technical Documentation</p>
5948
5949 </div>
5950
5951 <div style='mso-element:para-border-div;border:none;border-top:solid windowtext 1.0pt;
5952 mso-border-top-alt:solid windowtext .75pt;padding:1.0pt 0cm 0cm 0cm'>
5953
5954 <p class=SubtitleCover><o:p>&nbsp;</o:p></p>
5955
5956 </div>
5957
5958 </div>
5959
5960 <span style='font-size:72.0pt;mso-bidi-font-size:10.0pt;font-family:Garamond;
5961 mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:"Times New Roman";
5962 letter-spacing:-3.5pt;mso-font-kerning:14.0pt;mso-ansi-language:EN-US;
5963 mso-fareast-language:EN-US'><br clear=ALL style='page-break-before:always;
5964 mso-break-type:section-break'>
5965 </span>
5966
5967 <div class=Section2>
5968
5969 <div style='mso-element:para-border-div;border:none;border-bottom:solid gray 1.0pt;
5970 mso-border-bottom-alt:solid gray .75pt;padding:0cm 0cm 14.0pt 0cm'>
5971
5972 <p class=MsoTitle>T-Coffee Technical Documentation<br>
5973 (Version 8.96, July 2010)<br>
5974 www.tcoffee.org<br>
5975 <br>
5976 T-Coffee, seq_reformat<br>
5977 <span style="mso-spacerun: yes">&nbsp;</span>PSI-Coffee, 3D-Coffee, Expresso, M-Coffee,
5978 R-Coffee, APDB, iRMSD, T-RMSD</p>
5979
5980 </div>
5981
5982 <p class=ReturnAddress><span style='font-family:Symbol;mso-ascii-font-family:
5983 Garamond;mso-hansi-font-family:Garamond;mso-char-type:symbol;mso-symbol-font-family:
5984 Symbol'><span style='mso-char-type:symbol;mso-symbol-font-family:Symbol'>ã</span></span>
5985 Cédric Notredame, Centro de Regulacio Genomica, Centre National de la Recherche
5986 Scientifique, France<span style='letter-spacing:0pt'><o:p></o:p></span></p>
5987
5988 </div>
5989
5990 <span style='font-size:8.0pt;mso-bidi-font-size:10.0pt;font-family:Garamond;
5991 mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:"Times New Roman";
5992 mso-ansi-language:EN-US;mso-fareast-language:EN-US'><br clear=ALL
5993 style='page-break-before:always;mso-break-type:section-break'>
5994 </span>
5995
5996 <div class=Section3>
5997
5998 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><!--[if supportFields]><span
5999 style='mso-element:field-begin'></span><span style="mso-spacerun:
6000 yes">&nbsp;</span>TOC <span style='mso-element:field-separator'></span><![endif]--><span
6001 style='mso-no-proof:yes'>T-Coffee is distributed under the Gnu Public License<span
6002 style='mso-tab-count:1 dotted'>................................................................. </span></span><!--[if supportFields]><span
6003 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732187
6004 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6005 style='mso-no-proof:yes'>6<!--[if gte mso 9]><xml>
6006  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003100380037000000</w:data>
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6008 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6009 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6010 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6011 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
6012
6013 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
6014 style='mso-no-proof:yes'>T-Coffee code can be re-used freely<span
6015 style='mso-tab-count:1 dotted'>............................................................................................. </span></span><!--[if supportFields]><span
6016 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732188
6017 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6018 style='mso-no-proof:yes'>6<!--[if gte mso 9]><xml>
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6021 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6022 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6023 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6024 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
6025
6026 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
6027 style='mso-no-proof:yes'>T-Coffee can be incorporated in most pipelines:
6028 Plug-in/Plug-out\85<span style='mso-tab-count:1 dotted'>......................................... </span></span><!--[if supportFields]><span
6029 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732189
6030 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6031 style='mso-no-proof:yes'>6<!--[if gte mso 9]><xml>
6032  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003100380039000000</w:data>
6033 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6034 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6035 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6036 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6037 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
6038
6039 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
6040 style='mso-no-proof:yes'>Contributors<span style='mso-tab-count:1 dotted'>................................................................................................................................... </span></span><!--[if supportFields]><span
6041 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732190
6042 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6043 style='mso-no-proof:yes'>7<!--[if gte mso 9]><xml>
6044  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003100390030000000</w:data>
6045 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6046 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6047 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6048 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6049 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
6050
6051 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
6052 style='mso-no-proof:yes'>Addresses<span style='mso-tab-count:1 dotted'>....................................................................................................................................... </span></span><!--[if supportFields]><span
6053 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732191
6054 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6055 style='mso-no-proof:yes'>7<!--[if gte mso 9]><xml>
6056  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003100390031000000</w:data>
6057 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6058 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6059 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6060 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6061 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
6062
6063 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
6064 style='mso-no-proof:yes'>T-Coffee<span style='mso-tab-count:1 dotted'>.......................................................................................................................................... </span></span><!--[if supportFields]><span
6065 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732192
6066 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6067 style='mso-no-proof:yes'>8<!--[if gte mso 9]><xml>
6068  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003100390032000000</w:data>
6069 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6070 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6071 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6072 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6073 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
6074
6075 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
6076 style='mso-no-proof:yes'>Mocca<span style='mso-tab-count:1 dotted'>............................................................................................................................................ </span></span><!--[if supportFields]><span
6077 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732193
6078 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6079 style='mso-no-proof:yes'>10<!--[if gte mso 9]><xml>
6080  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003100390033000000</w:data>
6081 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6082 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6083 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6084 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6085 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
6086
6087 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
6088 style='mso-no-proof:yes'>CORE<span style='mso-tab-count:1 dotted'>............................................................................................................................................. </span></span><!--[if supportFields]><span
6089 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732194
6090 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6091 style='mso-no-proof:yes'>10<!--[if gte mso 9]><xml>
6092  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003100390034000000</w:data>
6093 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6094 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6095 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6096 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6097 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
6098
6099 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
6100 style='mso-no-proof:yes'>Other Contributions<span style='mso-tab-count:1 dotted'>.................................................................................................................... </span></span><!--[if supportFields]><span
6101 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732195
6102 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6103 style='mso-no-proof:yes'>10<!--[if gte mso 9]><xml>
6104  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003100390035000000</w:data>
6105 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6106 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6107 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6108 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6109 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
6110
6111 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
6112 style='mso-no-proof:yes'>Bug Reports and Feedback<span style='mso-tab-count:
6113 1 dotted'>......................................................................................................... </span></span><!--[if supportFields]><span
6114 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732196
6115 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6116 style='mso-no-proof:yes'>10<!--[if gte mso 9]><xml>
6117  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003100390036000000</w:data>
6118 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6119 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6120 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6121 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6122 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
6123
6124 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
6125 style='mso-no-proof:yes'>Third Party Packages and On Demand Installations<span
6126 style='mso-tab-count:1 dotted'>................................................................ </span></span><!--[if supportFields]><span
6127 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732197
6128 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6129 style='mso-no-proof:yes'>11<!--[if gte mso 9]><xml>
6130  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003100390037000000</w:data>
6131 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6132 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6133 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6134 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6135 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
6136
6137 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
6138 style='mso-no-proof:yes'>Standard Installation of T-Coffee<span
6139 style='mso-tab-count:1 dotted'>............................................................................................... </span></span><!--[if supportFields]><span
6140 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732198
6141 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6142 style='mso-no-proof:yes'>11<!--[if gte mso 9]><xml>
6143  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003100390038000000</w:data>
6144 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6145 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6146 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6147 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6148 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
6149
6150 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
6151 style='mso-hansi-font-family:"Arial Black";mso-no-proof:yes'>Automated
6152 Installation</span><span style='mso-no-proof:yes'><span style='mso-tab-count:
6153 1 dotted'>......................................................................................................................................................................... </span></span><!--[if supportFields]><span
6154 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732199
6155 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6156 style='mso-no-proof:yes'>11<!--[if gte mso 9]><xml>
6157  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003100390039000000</w:data>
6158 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6159 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6160 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6161 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6162 mso-no-proof:yes'><o:p></o:p></span></p>
6163
6164 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
6165 style='mso-no-proof:yes'>Mac-OsX<span style='mso-tab-count:1 dotted'>........................................................................................................................................................................................................ </span></span><!--[if supportFields]><span
6166 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732200
6167 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6168 style='mso-no-proof:yes'>11<!--[if gte mso 9]><xml>
6169  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200300030000000</w:data>
6170 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6171 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6172 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6173 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6174 mso-no-proof:yes'><o:p></o:p></span></p>
6175
6176 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
6177 style='mso-no-proof:yes'>Unix<span style='mso-tab-count:1 dotted'>................................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
6178 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732201
6179 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6180 style='mso-no-proof:yes'>11<!--[if gte mso 9]><xml>
6181  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200300031000000</w:data>
6182 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6183 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6184 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6185 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6186 mso-no-proof:yes'><o:p></o:p></span></p>
6187
6188 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
6189 style='mso-hansi-font-family:"Arial Black";mso-no-proof:yes'>Unix</span><span
6190 style='mso-no-proof:yes'><span style='mso-tab-count:1 dotted'>.................................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
6191 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732202
6192 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6193 style='mso-no-proof:yes'>12<!--[if gte mso 9]><xml>
6194  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200300032000000</w:data>
6195 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6196 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6197 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6198 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6199 mso-no-proof:yes'><o:p></o:p></span></p>
6200
6201 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
6202 style='mso-no-proof:yes'>Microsoft Windows/Cygwin<span style='mso-tab-count:
6203 1 dotted'>............................................................................................................................................................ </span></span><!--[if supportFields]><span
6204 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732203
6205 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6206 style='mso-no-proof:yes'>13<!--[if gte mso 9]><xml>
6207  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200300033000000</w:data>
6208 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6209 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6210 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6211 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6212 mso-no-proof:yes'><o:p></o:p></span></p>
6213
6214 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
6215 style='mso-no-proof:yes'>MAC osX, Linux<span style='mso-tab-count:1 dotted'>........................................................................................................................................................................................... </span></span><!--[if supportFields]><span
6216 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732204
6217 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6218 style='mso-no-proof:yes'>13<!--[if gte mso 9]><xml>
6219  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200300034000000</w:data>
6220 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6221 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6222 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6223 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6224 mso-no-proof:yes'><o:p></o:p></span></p>
6225
6226 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
6227 style='mso-no-proof:yes'>CLUSTER Installation<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................. </span></span><!--[if supportFields]><span
6228 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732205
6229 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6230 style='mso-no-proof:yes'>13<!--[if gte mso 9]><xml>
6231  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200300035000000</w:data>
6232 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6233 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6234 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6235 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6236 mso-no-proof:yes'><o:p></o:p></span></p>
6237
6238 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
6239 style='mso-no-proof:yes'>If you have PDB installed:<span style='mso-tab-count:
6240 1 dotted'>.................................................................................................................................................................... </span></span><!--[if supportFields]><span
6241 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732206
6242 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6243 style='mso-no-proof:yes'>14<!--[if gte mso 9]><xml>
6244  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200300036000000</w:data>
6245 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6246 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6247 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6248 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6249 mso-no-proof:yes'><o:p></o:p></span></p>
6250
6251 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
6252 style='mso-no-proof:yes'>Installing BLAST for T-Coffee<span style='mso-tab-count:
6253 1 dotted'>...................................................................................................... </span></span><!--[if supportFields]><span
6254 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732207
6255 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6256 style='mso-no-proof:yes'>14<!--[if gte mso 9]><xml>
6257  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200300037000000</w:data>
6258 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6259 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6260 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6261 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6262 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
6263
6264 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
6265 style='mso-no-proof:yes'>Why Do I need BLAST with T-Coffee?<span
6266 style='mso-tab-count:1 dotted'>......................................................................................................................................... </span></span><!--[if supportFields]><span
6267 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732208
6268 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6269 style='mso-no-proof:yes'>14<!--[if gte mso 9]><xml>
6270  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200300038000000</w:data>
6271 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6272 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6273 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6274 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6275 mso-no-proof:yes'><o:p></o:p></span></p>
6276
6277 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
6278 style='mso-no-proof:yes'>Using the EBI BLAST Client<span style='mso-tab-count:
6279 1 dotted'>................................................................................................................................................................ </span></span><!--[if supportFields]><span
6280 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732209
6281 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6282 style='mso-no-proof:yes'>15<!--[if gte mso 9]><xml>
6283  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200300039000000</w:data>
6284 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6285 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6286 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6287 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6288 mso-no-proof:yes'><o:p></o:p></span></p>
6289
6290 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
6291 style='mso-no-proof:yes'>Using the NCBI BLAST Client<span style='mso-tab-count:
6292 1 dotted'>............................................................................................................................................................. </span></span><!--[if supportFields]><span
6293 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732210
6294 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6295 style='mso-no-proof:yes'>15<!--[if gte mso 9]><xml>
6296  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200310030000000</w:data>
6297 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6298 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6299 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6300 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6301 mso-no-proof:yes'><o:p></o:p></span></p>
6302
6303 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
6304 style='mso-no-proof:yes'>Using another Client<span style='mso-tab-count:1 dotted'>................................................................................................................................................................................ </span></span><!--[if supportFields]><span
6305 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732211
6306 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6307 style='mso-no-proof:yes'>16<!--[if gte mso 9]><xml>
6308  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200310031000000</w:data>
6309 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6310 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6311 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6312 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6313 mso-no-proof:yes'><o:p></o:p></span></p>
6314
6315 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
6316 style='mso-no-proof:yes'>Using a BLAST local version on UNIX<span
6317 style='mso-tab-count:1 dotted'>.......................................................................................................................................... </span></span><!--[if supportFields]><span
6318 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732212
6319 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6320 style='mso-no-proof:yes'>16<!--[if gte mso 9]><xml>
6321  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200310032000000</w:data>
6322 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6323 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6324 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6325 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6326 mso-no-proof:yes'><o:p></o:p></span></p>
6327
6328 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
6329 style='mso-no-proof:yes'>Using a BLAST local version on Windows/cygwin<span
6330 style='mso-tab-count:1 dotted'>............................................................................................................ </span></span><!--[if supportFields]><span
6331 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732213
6332 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6333 style='mso-no-proof:yes'>17<!--[if gte mso 9]><xml>
6334  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200310033000000</w:data>
6335 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6336 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6337 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6338 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6339 mso-no-proof:yes'><o:p></o:p></span></p>
6340
6341 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
6342 style='mso-no-proof:yes'>BLAST+<span style='mso-tab-count:1 dotted'>.......................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
6343 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732214
6344 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6345 style='mso-no-proof:yes'>17<!--[if gte mso 9]><xml>
6346  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200310034000000</w:data>
6347 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6348 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6349 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6350 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6351 mso-no-proof:yes'><o:p></o:p></span></p>
6352
6353 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
6354 style='mso-no-proof:yes'>ORIGINAL NCBI BLAST<span style='mso-tab-count:1 dotted'>.......................................................................................................................................................................... </span></span><!--[if supportFields]><span
6355 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732215
6356 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6357 style='mso-no-proof:yes'>17<!--[if gte mso 9]><xml>
6358  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200310035000000</w:data>
6359 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6360 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6361 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6362 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6363 mso-no-proof:yes'><o:p></o:p></span></p>
6364
6365 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
6366 style='mso-no-proof:yes'>Installing Other Companion Packages<span
6367 style='mso-tab-count:1 dotted'>....................................................................................... </span></span><!--[if supportFields]><span
6368 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732216
6369 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6370 style='mso-no-proof:yes'>17<!--[if gte mso 9]><xml>
6371  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200310036000000</w:data>
6372 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6373 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6374 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6375 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6376 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
6377
6378 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
6379 style='mso-no-proof:yes'>Installation of PSI-Coffee and Expresso<span
6380 style='mso-tab-count:1 dotted'>..................................................................................... </span></span><!--[if supportFields]><span
6381 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732217
6382 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6383 style='mso-no-proof:yes'>19<!--[if gte mso 9]><xml>
6384  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200310037000000</w:data>
6385 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6386 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6387 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6388 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6389 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
6390
6391 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
6392 style='mso-no-proof:yes'>Installation of M-Coffee<span style='mso-tab-count:
6393 1 dotted'>............................................................................................................... </span></span><!--[if supportFields]><span
6394 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732218
6395 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6396 style='mso-no-proof:yes'>19<!--[if gte mso 9]><xml>
6397  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200310038000000</w:data>
6398 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6399 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6400 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6401 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6402 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
6403
6404 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
6405 style='mso-no-proof:yes'>Automated Installation<span style='mso-tab-count:1 dotted'>......................................................................................................................................................................... </span></span><!--[if supportFields]><span
6406 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732219
6407 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6408 style='mso-no-proof:yes'>20<!--[if gte mso 9]><xml>
6409  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200310039000000</w:data>
6410 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6411 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6412 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6413 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6414 mso-no-proof:yes'><o:p></o:p></span></p>
6415
6416 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
6417 style='mso-no-proof:yes'>Manual Installation<span style='mso-tab-count:1 dotted'>.................................................................................................................................................................................. </span></span><!--[if supportFields]><span
6418 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732220
6419 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6420 style='mso-no-proof:yes'>20<!--[if gte mso 9]><xml>
6421  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200320030000000</w:data>
6422 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6423 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6424 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6425 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6426 mso-no-proof:yes'><o:p></o:p></span></p>
6427
6428 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
6429 style='mso-no-proof:yes'>Installation of APDB and iRMSD<span style='mso-tab-count:
6430 1 dotted'>.................................................................................................. </span></span><!--[if supportFields]><span
6431 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732221
6432 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6433 style='mso-no-proof:yes'>22<!--[if gte mso 9]><xml>
6434  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200320031000000</w:data>
6435 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6436 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6437 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6438 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6439 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
6440
6441 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
6442 style='mso-no-proof:yes'>Installation of tRMSD<span style='mso-tab-count:1 dotted'>................................................................................................................... </span></span><!--[if supportFields]><span
6443 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732222
6444 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6445 style='mso-no-proof:yes'>22<!--[if gte mso 9]><xml>
6446  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200320032000000</w:data>
6447 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6448 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6449 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6450 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6451 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
6452
6453 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
6454 style='mso-no-proof:yes'>Installation of seq_reformat<span style='mso-tab-count:
6455 1 dotted'>........................................................................................................ </span></span><!--[if supportFields]><span
6456 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732223
6457 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6458 style='mso-no-proof:yes'>23<!--[if gte mso 9]><xml>
6459  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200320033000000</w:data>
6460 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6461 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6462 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6463 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6464 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
6465
6466 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
6467 style='mso-no-proof:yes'>Installation of extract_from_pdb<span
6468 style='mso-tab-count:1 dotted'>................................................................................................ </span></span><!--[if supportFields]><span
6469 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732224
6470 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6471 style='mso-no-proof:yes'>23<!--[if gte mso 9]><xml>
6472  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200320034000000</w:data>
6473 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6474 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6475 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6476 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6477 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
6478
6479 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
6480 style='mso-no-proof:yes'>Installation of 3D-Coffee/Expresso<span
6481 style='mso-tab-count:1 dotted'>............................................................................................ </span></span><!--[if supportFields]><span
6482 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732225
6483 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6484 style='mso-no-proof:yes'>23<!--[if gte mso 9]><xml>
6485  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200320035000000</w:data>
6486 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6487 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6488 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6489 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6490 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
6491
6492 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
6493 style='mso-no-proof:yes'>Automated Installation<span style='mso-tab-count:1 dotted'>......................................................................................................................................................................... </span></span><!--[if supportFields]><span
6494 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732226
6495 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6496 style='mso-no-proof:yes'>23<!--[if gte mso 9]><xml>
6497  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200320036000000</w:data>
6498 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6499 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6500 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6501 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6502 mso-no-proof:yes'><o:p></o:p></span></p>
6503
6504 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
6505 style='mso-no-proof:yes'>Manual Installation<span style='mso-tab-count:1 dotted'>.................................................................................................................................................................................. </span></span><!--[if supportFields]><span
6506 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732227
6507 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6508 style='mso-no-proof:yes'>23<!--[if gte mso 9]><xml>
6509  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200320037000000</w:data>
6510 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6511 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6512 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6513 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6514 mso-no-proof:yes'><o:p></o:p></span></p>
6515
6516 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
6517 style='mso-no-proof:yes'>Installing Fugue for T-Coffee<span style='mso-tab-count:
6518 1 dotted'>............................................................................................................................................................. </span></span><!--[if supportFields]><span
6519 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732228
6520 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6521 style='mso-no-proof:yes'>24<!--[if gte mso 9]><xml>
6522  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200320038000000</w:data>
6523 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6524 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6525 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6526 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6527 mso-no-proof:yes'><o:p></o:p></span></p>
6528
6529 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
6530 style='mso-no-proof:yes'>Installation of R-Coffee<span style='mso-tab-count:
6531 1 dotted'>................................................................................................................ </span></span><!--[if supportFields]><span
6532 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732229
6533 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6534 style='mso-no-proof:yes'>24<!--[if gte mso 9]><xml>
6535  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200320039000000</w:data>
6536 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6537 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6538 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6539 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6540 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
6541
6542 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
6543 style='mso-no-proof:yes'>Automated Installation<span style='mso-tab-count:1 dotted'>......................................................................................................................................................................... </span></span><!--[if supportFields]><span
6544 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732230
6545 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6546 style='mso-no-proof:yes'>24<!--[if gte mso 9]><xml>
6547  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200330030000000</w:data>
6548 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6549 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6550 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6551 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6552 mso-no-proof:yes'><o:p></o:p></span></p>
6553
6554 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
6555 style='mso-no-proof:yes'>Manual Installation<span style='mso-tab-count:1 dotted'>.................................................................................................................................................................................. </span></span><!--[if supportFields]><span
6556 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732231
6557 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6558 style='mso-no-proof:yes'>25<!--[if gte mso 9]><xml>
6559  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200330031000000</w:data>
6560 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6561 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6562 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6563 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6564 mso-no-proof:yes'><o:p></o:p></span></p>
6565
6566 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
6567 style='mso-no-proof:yes'>Installing ProbbonsRNA for R-Coffee<span
6568 style='mso-tab-count:1 dotted'>.......................................................................................................................................... </span></span><!--[if supportFields]><span
6569 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732232
6570 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6571 style='mso-no-proof:yes'>25<!--[if gte mso 9]><xml>
6572  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200330032000000</w:data>
6573 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6574 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6575 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6576 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6577 mso-no-proof:yes'><o:p></o:p></span></p>
6578
6579 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
6580 style='mso-no-proof:yes'>Installing Consan for R-Coffee<span style='mso-tab-count:
6581 1 dotted'>.......................................................................................................................................................... </span></span><!--[if supportFields]><span
6582 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732233
6583 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6584 style='mso-no-proof:yes'>25<!--[if gte mso 9]><xml>
6585  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200330033000000</w:data>
6586 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6587 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6588 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6589 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6590 mso-no-proof:yes'><o:p></o:p></span></p>
6591
6592 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
6593 style='mso-no-proof:yes'>T-COFFEE<span style='mso-tab-count:1 dotted'>...................................................................................................................................... </span></span><!--[if supportFields]><span
6594 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732234
6595 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6596 style='mso-no-proof:yes'>26<!--[if gte mso 9]><xml>
6597  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200330034000000</w:data>
6598 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6599 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6600 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6601 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6602 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
6603
6604 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
6605 style='mso-no-proof:yes'>M-Coffee<span style='mso-tab-count:1 dotted'>....................................................................................................................................... </span></span><!--[if supportFields]><span
6606 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732235
6607 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6608 style='mso-no-proof:yes'>26<!--[if gte mso 9]><xml>
6609  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200330035000000</w:data>
6610 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6611 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6612 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6613 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6614 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
6615
6616 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
6617 style='mso-no-proof:yes'>Expresso<span style='mso-tab-count:1 dotted'>....................................................................................................................................... </span></span><!--[if supportFields]><span
6618 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732236
6619 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6620 style='mso-no-proof:yes'>27<!--[if gte mso 9]><xml>
6621  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200330036000000</w:data>
6622 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6623 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6624 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6625 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6626 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
6627
6628 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
6629 style='mso-no-proof:yes'>R-Coffee<span style='mso-tab-count:1 dotted'>........................................................................................................................................ </span></span><!--[if supportFields]><span
6630 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732237
6631 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6632 style='mso-no-proof:yes'>27<!--[if gte mso 9]><xml>
6633  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200330037000000</w:data>
6634 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6635 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6636 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6637 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6638 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
6639
6640 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
6641 style='mso-no-proof:yes'>iRMSD and APDB<span style='mso-tab-count:1 dotted'>.......................................................................................................................... </span></span><!--[if supportFields]><span
6642 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732238
6643 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6644 style='mso-no-proof:yes'>28<!--[if gte mso 9]><xml>
6645  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200330038000000</w:data>
6646 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6647 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6648 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6649 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6650 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
6651
6652 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
6653 style='mso-no-proof:yes'>tRMSD<span style='mso-tab-count:1 dotted'>........................................................................................................................................... </span></span><!--[if supportFields]><span
6654 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732239
6655 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6656 style='mso-no-proof:yes'>28<!--[if gte mso 9]><xml>
6657  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200330039000000</w:data>
6658 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6659 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6660 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6661 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6662 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
6663
6664 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
6665 style='mso-no-proof:yes'>MOCCA<span style='mso-tab-count:1 dotted'>.......................................................................................................................................... </span></span><!--[if supportFields]><span
6666 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732240
6667 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6668 style='mso-no-proof:yes'>29<!--[if gte mso 9]><xml>
6669  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200340030000000</w:data>
6670 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6671 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6672 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6673 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6674 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
6675
6676 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
6677 style='mso-no-proof:yes'>Environment Variables<span style='mso-tab-count:1 dotted'>............................................................................................................... </span></span><!--[if supportFields]><span
6678 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732241
6679 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6680 style='mso-no-proof:yes'>31<!--[if gte mso 9]><xml>
6681  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200340031000000</w:data>
6682 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6683 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6684 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6685 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6686 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
6687
6688 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
6689 style='mso-no-proof:yes'>http_proxy_4_TCOFFEE<span style='mso-tab-count:1 dotted'>........................................................................................................................................................................ </span></span><!--[if supportFields]><span
6690 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732242
6691 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6692 style='mso-no-proof:yes'>31<!--[if gte mso 9]><xml>
6693  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200340032000000</w:data>
6694 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6695 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6696 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6697 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6698 mso-no-proof:yes'><o:p></o:p></span></p>
6699
6700 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
6701 style='mso-no-proof:yes'>email_4_TCOFFEE<span style='mso-tab-count:1 dotted'>..................................................................................................................................................................................... </span></span><!--[if supportFields]><span
6702 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732243
6703 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6704 style='mso-no-proof:yes'>32<!--[if gte mso 9]><xml>
6705  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200340033000000</w:data>
6706 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6707 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6708 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6709 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6710 mso-no-proof:yes'><o:p></o:p></span></p>
6711
6712 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
6713 style='mso-no-proof:yes'>DIR_4_TCOFFEE<span style='mso-tab-count:1 dotted'>......................................................................................................................................................................................... </span></span><!--[if supportFields]><span
6714 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732244
6715 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6716 style='mso-no-proof:yes'>32<!--[if gte mso 9]><xml>
6717  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200340034000000</w:data>
6718 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6719 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6720 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6721 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6722 mso-no-proof:yes'><o:p></o:p></span></p>
6723
6724 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
6725 style='mso-no-proof:yes'>TMP_4_TCOFFEE<span style='mso-tab-count:1 dotted'>....................................................................................................................................................................................... </span></span><!--[if supportFields]><span
6726 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732245
6727 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6728 style='mso-no-proof:yes'>32<!--[if gte mso 9]><xml>
6729  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200340035000000</w:data>
6730 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6731 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6732 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6733 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6734 mso-no-proof:yes'><o:p></o:p></span></p>
6735
6736 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
6737 style='mso-no-proof:yes'>CACHE_4_TCOFFEE<span style='mso-tab-count:1 dotted'>................................................................................................................................................................................. </span></span><!--[if supportFields]><span
6738 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732246
6739 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6740 style='mso-no-proof:yes'>32<!--[if gte mso 9]><xml>
6741  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200340036000000</w:data>
6742 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6743 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6744 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6745 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6746 mso-no-proof:yes'><o:p></o:p></span></p>
6747
6748 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
6749 style='mso-no-proof:yes'>PLUGINS_4_TCOFFEE<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................. </span></span><!--[if supportFields]><span
6750 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732247
6751 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6752 style='mso-no-proof:yes'>32<!--[if gte mso 9]><xml>
6753  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200340037000000</w:data>
6754 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6755 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6756 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6757 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6758 mso-no-proof:yes'><o:p></o:p></span></p>
6759
6760 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
6761 style='mso-no-proof:yes'>NO_ERROR_REPORT_4_TCOFFEE<span style='mso-tab-count:
6762 1 dotted'>.................................................................................................................................................. </span></span><!--[if supportFields]><span
6763 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732248
6764 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6765 style='mso-no-proof:yes'>32<!--[if gte mso 9]><xml>
6766  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200340038000000</w:data>
6767 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6768 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6769 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6770 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6771 mso-no-proof:yes'><o:p></o:p></span></p>
6772
6773 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
6774 style='mso-no-proof:yes'>PDB_DIR<span style='mso-tab-count:1 dotted'>.......................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
6775 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732249
6776 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6777 style='mso-no-proof:yes'>32<!--[if gte mso 9]><xml>
6778  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200340039000000</w:data>
6779 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6780 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6781 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6782 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6783 mso-no-proof:yes'><o:p></o:p></span></p>
6784
6785 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
6786 style='mso-no-proof:yes'>NO_WARNING_4_TCOFFEE<span style='mso-tab-count:1 dotted'>................................................................................................................................................................ </span></span><!--[if supportFields]><span
6787 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732250
6788 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6789 style='mso-no-proof:yes'>32<!--[if gte mso 9]><xml>
6790  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200350030000000</w:data>
6791 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6792 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6793 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6794 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6795 mso-no-proof:yes'><o:p></o:p></span></p>
6796
6797 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
6798 style='mso-no-proof:yes'>UNIQUE_DIR_4_TCOFFEE<span style='mso-tab-count:1 dotted'>.................................................................................................................................................................... </span></span><!--[if supportFields]><span
6799 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732251
6800 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6801 style='mso-no-proof:yes'>32<!--[if gte mso 9]><xml>
6802  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200350031000000</w:data>
6803 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6804 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6805 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6806 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6807 mso-no-proof:yes'><o:p></o:p></span></p>
6808
6809 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
6810 style='mso-no-proof:yes'>Setting up the T-Coffee environment variables<span
6811 style='mso-tab-count:1 dotted'>........................................................................ </span></span><!--[if supportFields]><span
6812 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732252
6813 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6814 style='mso-no-proof:yes'>32<!--[if gte mso 9]><xml>
6815  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200350032000000</w:data>
6816 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6817 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6818 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6819 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6820 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
6821
6822 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
6823 style='mso-no-proof:yes'>Well Behaved Parameters<span style='mso-tab-count:
6824 1 dotted'>.......................................................................................................... </span></span><!--[if supportFields]><span
6825 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732253
6826 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6827 style='mso-no-proof:yes'>33<!--[if gte mso 9]><xml>
6828  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200350033000000</w:data>
6829 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6830 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6831 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6832 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6833 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
6834
6835 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
6836 style='mso-no-proof:yes'>Separation<span style='mso-tab-count:1 dotted'>...................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
6837 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732254
6838 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6839 style='mso-no-proof:yes'>33<!--[if gte mso 9]><xml>
6840  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200350034000000</w:data>
6841 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6842 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6843 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6844 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6845 mso-no-proof:yes'><o:p></o:p></span></p>
6846
6847 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
6848 style='mso-no-proof:yes'>Posix<span style='mso-tab-count:1 dotted'>.................................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
6849 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732255
6850 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6851 style='mso-no-proof:yes'>33<!--[if gte mso 9]><xml>
6852  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200350035000000</w:data>
6853 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6854 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6855 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6856 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6857 mso-no-proof:yes'><o:p></o:p></span></p>
6858
6859 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
6860 style='mso-no-proof:yes'>Entering the right parameters<span style='mso-tab-count:
6861 1 dotted'>.......................................................................................................................................................... </span></span><!--[if supportFields]><span
6862 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732256
6863 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6864 style='mso-no-proof:yes'>33<!--[if gte mso 9]><xml>
6865  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200350036000000</w:data>
6866 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6867 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6868 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6869 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6870 mso-no-proof:yes'><o:p></o:p></span></p>
6871
6872 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
6873 style='mso-no-proof:yes'>Parameters Syntax<span style='mso-tab-count:1 dotted'>...................................................................................................................... </span></span><!--[if supportFields]><span
6874 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732257
6875 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6876 style='mso-no-proof:yes'>34<!--[if gte mso 9]><xml>
6877  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200350037000000</w:data>
6878 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6879 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6880 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6881 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6882 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
6883
6884 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
6885 style='mso-no-proof:yes'>No Flag<span style='mso-tab-count:1 dotted'>........................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
6886 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732258
6887 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6888 style='mso-no-proof:yes'>34<!--[if gte mso 9]><xml>
6889  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200350038000000</w:data>
6890 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6891 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6892 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6893 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6894 mso-no-proof:yes'><o:p></o:p></span></p>
6895
6896 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
6897 style='mso-no-proof:yes'>-parameters<span style='mso-tab-count:1 dotted'>................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
6898 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732259
6899 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6900 style='mso-no-proof:yes'>34<!--[if gte mso 9]><xml>
6901  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200350039000000</w:data>
6902 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6903 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6904 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6905 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6906 mso-no-proof:yes'><o:p></o:p></span></p>
6907
6908 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
6909 style='mso-no-proof:yes'>-t_coffee_defaults<span style='mso-tab-count:1 dotted'>...................................................................................................................................................................................... </span></span><!--[if supportFields]><span
6910 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732260
6911 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6912 style='mso-no-proof:yes'>35<!--[if gte mso 9]><xml>
6913  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200360030000000</w:data>
6914 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6915 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6916 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6917 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6918 mso-no-proof:yes'><o:p></o:p></span></p>
6919
6920 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
6921 style='mso-no-proof:yes'>-mode<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
6922 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732261
6923 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6924 style='mso-no-proof:yes'>35<!--[if gte mso 9]><xml>
6925  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200360031000000</w:data>
6926 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6927 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6928 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6929 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6930 mso-no-proof:yes'><o:p></o:p></span></p>
6931
6932 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
6933 style='mso-no-proof:yes'>-score [Deprecated]<span style='mso-tab-count:1 dotted'>................................................................................................................................................................................ </span></span><!--[if supportFields]><span
6934 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732262
6935 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6936 style='mso-no-proof:yes'>35<!--[if gte mso 9]><xml>
6937  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200360032000000</w:data>
6938 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6939 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6940 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6941 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6942 mso-no-proof:yes'><o:p></o:p></span></p>
6943
6944 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
6945 style='mso-no-proof:yes'>-evaluate<span style='mso-tab-count:1 dotted'>....................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
6946 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732263
6947 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6948 style='mso-no-proof:yes'>35<!--[if gte mso 9]><xml>
6949  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200360033000000</w:data>
6950 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6951 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6952 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6953 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6954 mso-no-proof:yes'><o:p></o:p></span></p>
6955
6956 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
6957 style='mso-no-proof:yes'>-convert [cw]<span style='mso-tab-count:1 dotted'>.............................................................................................................................................................................................. </span></span><!--[if supportFields]><span
6958 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732264
6959 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6960 style='mso-no-proof:yes'>36<!--[if gte mso 9]><xml>
6961  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200360034000000</w:data>
6962 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6963 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6964 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6965 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6966 mso-no-proof:yes'><o:p></o:p></span></p>
6967
6968 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
6969 style='mso-no-proof:yes'>-do_align [cw]<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................ </span></span><!--[if supportFields]><span
6970 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732265
6971 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6972 style='mso-no-proof:yes'>36<!--[if gte mso 9]><xml>
6973  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200360035000000</w:data>
6974 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6975 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6976 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6977 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6978 mso-no-proof:yes'><o:p></o:p></span></p>
6979
6980 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
6981 style='mso-no-proof:yes'>Special Parameters<span style='mso-tab-count:1 dotted'>...................................................................................................................... </span></span><!--[if supportFields]><span
6982 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732266
6983 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6984 style='mso-no-proof:yes'>36<!--[if gte mso 9]><xml>
6985  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200360036000000</w:data>
6986 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6987 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
6988 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
6989 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
6990 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
6991
6992 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
6993 style='mso-no-proof:yes'>-version<span style='mso-tab-count:1 dotted'>......................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
6994 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732267
6995 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
6996 style='mso-no-proof:yes'>36<!--[if gte mso 9]><xml>
6997  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200360037000000</w:data>
6998 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
6999 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7000 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7001 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7002 mso-no-proof:yes'><o:p></o:p></span></p>
7003
7004 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7005 style='mso-no-proof:yes'>-proxy<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
7006 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732268
7007 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7008 style='mso-no-proof:yes'>36<!--[if gte mso 9]><xml>
7009  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200360038000000</w:data>
7010 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7011 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7012 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7013 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7014 mso-no-proof:yes'><o:p></o:p></span></p>
7015
7016 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7017 style='mso-no-proof:yes'>-email<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
7018 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732269
7019 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7020 style='mso-no-proof:yes'>36<!--[if gte mso 9]><xml>
7021  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200360039000000</w:data>
7022 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7023 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7024 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7025 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7026 mso-no-proof:yes'><o:p></o:p></span></p>
7027
7028 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7029 style='mso-no-proof:yes'>-check_configuration<span style='mso-tab-count:1 dotted'>.............................................................................................................................................................................. </span></span><!--[if supportFields]><span
7030 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732270
7031 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7032 style='mso-no-proof:yes'>37<!--[if gte mso 9]><xml>
7033  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200370030000000</w:data>
7034 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7035 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7036 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7037 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7038 mso-no-proof:yes'><o:p></o:p></span></p>
7039
7040 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7041 style='mso-no-proof:yes'>-cache<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
7042 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732271
7043 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7044 style='mso-no-proof:yes'>37<!--[if gte mso 9]><xml>
7045  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200370031000000</w:data>
7046 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7047 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7048 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7049 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7050 mso-no-proof:yes'><o:p></o:p></span></p>
7051
7052 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7053 style='mso-no-proof:yes'>-update<span style='mso-tab-count:1 dotted'>.......................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
7054 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732272
7055 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7056 style='mso-no-proof:yes'>37<!--[if gte mso 9]><xml>
7057  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200370032000000</w:data>
7058 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7059 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7060 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7061 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7062 mso-no-proof:yes'><o:p></o:p></span></p>
7063
7064 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7065 style='mso-no-proof:yes'>-full_log<span style='mso-tab-count:1 dotted'>......................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
7066 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732273
7067 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7068 style='mso-no-proof:yes'>37<!--[if gte mso 9]><xml>
7069  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200370033000000</w:data>
7070 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7071 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7072 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7073 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7074 mso-no-proof:yes'><o:p></o:p></span></p>
7075
7076 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7077 style='mso-no-proof:yes'>-plugins<span style='mso-tab-count:1 dotted'>......................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
7078 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732274
7079 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7080 style='mso-no-proof:yes'>37<!--[if gte mso 9]><xml>
7081  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200370034000000</w:data>
7082 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7083 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7084 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7085 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7086 mso-no-proof:yes'><o:p></o:p></span></p>
7087
7088 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7089 style='mso-no-proof:yes'>-other_pg<span style='mso-tab-count:1 dotted'>...................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
7090 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732275
7091 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7092 style='mso-no-proof:yes'>37<!--[if gte mso 9]><xml>
7093  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200370035000000</w:data>
7094 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7095 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7096 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7097 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7098 mso-no-proof:yes'><o:p></o:p></span></p>
7099
7100 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
7101 style='mso-no-proof:yes'>Input<span style='mso-tab-count:1 dotted'>............................................................................................................................................. </span></span><!--[if supportFields]><span
7102 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732276
7103 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7104 style='mso-no-proof:yes'>38<!--[if gte mso 9]><xml>
7105  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200370036000000</w:data>
7106 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7107 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7108 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7109 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7110 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
7111
7112 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
7113 style='mso-no-proof:yes'>Sequence Input<span style='mso-tab-count:1 dotted'>........................................................................................................................................................................................... </span></span><!--[if supportFields]><span
7114 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732277
7115 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7116 style='mso-no-proof:yes'>38<!--[if gte mso 9]><xml>
7117  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200370037000000</w:data>
7118 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7119 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7120 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7121 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7122 mso-no-proof:yes'><o:p></o:p></span></p>
7123
7124 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7125 style='mso-no-proof:yes'>-infile [cw]<span style='mso-tab-count:1 dotted'>................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
7126 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732278
7127 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7128 style='mso-no-proof:yes'>38<!--[if gte mso 9]><xml>
7129  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200370038000000</w:data>
7130 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7131 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7132 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7133 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7134 mso-no-proof:yes'><o:p></o:p></span></p>
7135
7136 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7137 style='mso-no-proof:yes'>-in (Cf &#8211;in from the Method and Library Input
7138 section)<span style='mso-tab-count:1 dotted'>........................................................................................................ </span></span><!--[if supportFields]><span
7139 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732279
7140 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7141 style='mso-no-proof:yes'>38<!--[if gte mso 9]><xml>
7142  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200370039000000</w:data>
7143 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7144 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7145 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7146 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7147 mso-no-proof:yes'><o:p></o:p></span></p>
7148
7149 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7150 style='mso-no-proof:yes'>-get_type<span style='mso-tab-count:1 dotted'>....................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
7151 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732280
7152 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7153 style='mso-no-proof:yes'>38<!--[if gte mso 9]><xml>
7154  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200380030000000</w:data>
7155 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7156 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7157 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7158 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7159 mso-no-proof:yes'><o:p></o:p></span></p>
7160
7161 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7162 style='mso-no-proof:yes'>-type [cw]<span style='mso-tab-count:1 dotted'>..................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
7163 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732281
7164 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7165 style='mso-no-proof:yes'>38<!--[if gte mso 9]><xml>
7166  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200380031000000</w:data>
7167 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7168 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7169 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7170 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7171 mso-no-proof:yes'><o:p></o:p></span></p>
7172
7173 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7174 style='mso-no-proof:yes'>-seq<span style='mso-tab-count:1 dotted'>.................................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
7175 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732282
7176 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7177 style='mso-no-proof:yes'>38<!--[if gte mso 9]><xml>
7178  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200380032000000</w:data>
7179 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7180 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7181 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7182 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7183 mso-no-proof:yes'><o:p></o:p></span></p>
7184
7185 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7186 style='mso-no-proof:yes'>-seq_source<span style='mso-tab-count:1 dotted'>.................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
7187 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732283
7188 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7189 style='mso-no-proof:yes'>38<!--[if gte mso 9]><xml>
7190  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200380033000000</w:data>
7191 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7192 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7193 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7194 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7195 mso-no-proof:yes'><o:p></o:p></span></p>
7196
7197 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
7198 style='mso-no-proof:yes'>Structure Input<span style='mso-tab-count:1 dotted'>.......................................................................................................................................................................................... </span></span><!--[if supportFields]><span
7199 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732284
7200 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7201 style='mso-no-proof:yes'>39<!--[if gte mso 9]><xml>
7202  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200380034000000</w:data>
7203 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7204 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7205 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7206 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7207 mso-no-proof:yes'><o:p></o:p></span></p>
7208
7209 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7210 style='mso-no-proof:yes'>-pdb<span style='mso-tab-count:1 dotted'>................................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
7211 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732285
7212 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7213 style='mso-no-proof:yes'>39<!--[if gte mso 9]><xml>
7214  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200380035000000</w:data>
7215 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7216 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7217 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7218 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7219 mso-no-proof:yes'><o:p></o:p></span></p>
7220
7221 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
7222 style='mso-no-proof:yes'>Tree Input<span style='mso-tab-count:1 dotted'>...................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
7223 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732286
7224 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7225 style='mso-no-proof:yes'>39<!--[if gte mso 9]><xml>
7226  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200380036000000</w:data>
7227 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7228 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7229 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7230 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7231 mso-no-proof:yes'><o:p></o:p></span></p>
7232
7233 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7234 style='mso-no-proof:yes'>-usetree<span style='mso-tab-count:1 dotted'>......................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
7235 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732287
7236 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7237 style='mso-no-proof:yes'>39<!--[if gte mso 9]><xml>
7238  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200380037000000</w:data>
7239 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7240 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7241 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7242 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7243 mso-no-proof:yes'><o:p></o:p></span></p>
7244
7245 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
7246 style='mso-no-proof:yes'>Structures, Sequences Methods and Library Input via
7247 the -in Flag<span style='mso-tab-count:1 dotted'>......................................................................... </span></span><!--[if supportFields]><span
7248 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732288
7249 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7250 style='mso-no-proof:yes'>39<!--[if gte mso 9]><xml>
7251  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200380038000000</w:data>
7252 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7253 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7254 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7255 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7256 mso-no-proof:yes'><o:p></o:p></span></p>
7257
7258 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7259 style='mso-no-proof:yes'>-in<span style='mso-tab-count:1 dotted'>..................................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
7260 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732289
7261 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7262 style='mso-no-proof:yes'>40<!--[if gte mso 9]><xml>
7263  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200380039000000</w:data>
7264 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7265 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7266 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7267 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7268 mso-no-proof:yes'><o:p></o:p></span></p>
7269
7270 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
7271 style='mso-no-proof:yes'>Profile Input<span style='mso-tab-count:1 dotted'>................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
7272 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732290
7273 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7274 style='mso-no-proof:yes'>41<!--[if gte mso 9]><xml>
7275  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200390030000000</w:data>
7276 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7277 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7278 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7279 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7280 mso-no-proof:yes'><o:p></o:p></span></p>
7281
7282 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7283 style='mso-no-proof:yes'>-profile<span style='mso-tab-count:1 dotted'>........................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
7284 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732291
7285 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7286 style='mso-no-proof:yes'>41<!--[if gte mso 9]><xml>
7287  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200390031000000</w:data>
7288 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7289 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7290 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7291 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7292 mso-no-proof:yes'><o:p></o:p></span></p>
7293
7294 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7295 style='mso-no-proof:yes'>-profile1 [cw]<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................. </span></span><!--[if supportFields]><span
7296 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732292
7297 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7298 style='mso-no-proof:yes'>42<!--[if gte mso 9]><xml>
7299  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200390032000000</w:data>
7300 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7301 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7302 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7303 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7304 mso-no-proof:yes'><o:p></o:p></span></p>
7305
7306 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7307 style='mso-no-proof:yes'>-profile2 [cw]<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................. </span></span><!--[if supportFields]><span
7308 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732293
7309 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7310 style='mso-no-proof:yes'>42<!--[if gte mso 9]><xml>
7311  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200390033000000</w:data>
7312 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7313 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7314 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7315 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7316 mso-no-proof:yes'><o:p></o:p></span></p>
7317
7318 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
7319 style='mso-no-proof:yes'>Alignment Computation<span style='mso-tab-count:1 dotted'>.............................................................................................................. </span></span><!--[if supportFields]><span
7320 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732294
7321 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7322 style='mso-no-proof:yes'>42<!--[if gte mso 9]><xml>
7323  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200390034000000</w:data>
7324 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7325 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7326 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7327 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7328 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
7329
7330 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
7331 style='mso-no-proof:yes'>Library Computation: Methods<span style='mso-tab-count:
7332 1 dotted'>...................................................................................................................................................... </span></span><!--[if supportFields]><span
7333 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732295
7334 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7335 style='mso-no-proof:yes'>42<!--[if gte mso 9]><xml>
7336  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200390035000000</w:data>
7337 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7338 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7339 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7340 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7341 mso-no-proof:yes'><o:p></o:p></span></p>
7342
7343 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7344 style='mso-no-proof:yes'>-lalign_n_top<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................... </span></span><!--[if supportFields]><span
7345 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732296
7346 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7347 style='mso-no-proof:yes'>42<!--[if gte mso 9]><xml>
7348  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200390036000000</w:data>
7349 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7350 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7351 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7352 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7353 mso-no-proof:yes'><o:p></o:p></span></p>
7354
7355 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7356 style='mso-no-proof:yes'>-align_pdb_param_file<span style='mso-tab-count:1 dotted'>........................................................................................................................................................................... </span></span><!--[if supportFields]><span
7357 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732297
7358 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7359 style='mso-no-proof:yes'>42<!--[if gte mso 9]><xml>
7360  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200390037000000</w:data>
7361 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7362 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7363 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7364 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7365 mso-no-proof:yes'><o:p></o:p></span></p>
7366
7367 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7368 style='mso-no-proof:yes'>-align_pdb_hasch_mode<span style='mso-tab-count:1 dotted'>....................................................................................................................................................................... </span></span><!--[if supportFields]><span
7369 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732298
7370 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7371 style='mso-no-proof:yes'>42<!--[if gte mso 9]><xml>
7372  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200390038000000</w:data>
7373 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7374 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7375 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7376 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7377 mso-no-proof:yes'><o:p></o:p></span></p>
7378
7379 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
7380 style='mso-no-proof:yes'>Library Computation: Extension<span style='mso-tab-count:
7381 1 dotted'>.................................................................................................................................................... </span></span><!--[if supportFields]><span
7382 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732299
7383 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7384 style='mso-no-proof:yes'>43<!--[if gte mso 9]><xml>
7385  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003200390039000000</w:data>
7386 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7387 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7388 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7389 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7390 mso-no-proof:yes'><o:p></o:p></span></p>
7391
7392 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7393 style='mso-no-proof:yes'>-lib_list [Unsupported]<span style='mso-tab-count:
7394 1 dotted'>.......................................................................................................................................................................... </span></span><!--[if supportFields]><span
7395 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732300
7396 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7397 style='mso-no-proof:yes'>43<!--[if gte mso 9]><xml>
7398  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300300030000000</w:data>
7399 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7400 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7401 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7402 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7403 mso-no-proof:yes'><o:p></o:p></span></p>
7404
7405 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7406 style='mso-no-proof:yes'>-do_normalise<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................ </span></span><!--[if supportFields]><span
7407 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732301
7408 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7409 style='mso-no-proof:yes'>43<!--[if gte mso 9]><xml>
7410  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300300031000000</w:data>
7411 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7412 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7413 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7414 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7415 mso-no-proof:yes'><o:p></o:p></span></p>
7416
7417 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7418 style='mso-no-proof:yes'>-extend<span style='mso-tab-count:1 dotted'>.......................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
7419 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732302
7420 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7421 style='mso-no-proof:yes'>43<!--[if gte mso 9]><xml>
7422  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300300032000000</w:data>
7423 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7424 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7425 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7426 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7427 mso-no-proof:yes'><o:p></o:p></span></p>
7428
7429 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7430 style='mso-no-proof:yes'>-extend_mode<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................ </span></span><!--[if supportFields]><span
7431 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732303
7432 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7433 style='mso-no-proof:yes'>43<!--[if gte mso 9]><xml>
7434  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300300033000000</w:data>
7435 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7436 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7437 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7438 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7439 mso-no-proof:yes'><o:p></o:p></span></p>
7440
7441 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7442 style='mso-no-proof:yes'>-max_n_pair<span style='mso-tab-count:1 dotted'>................................................................................................................................................................................................ </span></span><!--[if supportFields]><span
7443 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732304
7444 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7445 style='mso-no-proof:yes'>44<!--[if gte mso 9]><xml>
7446  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300300034000000</w:data>
7447 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7448 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7449 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7450 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7451 mso-no-proof:yes'><o:p></o:p></span></p>
7452
7453 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7454 style='mso-no-proof:yes'>-seq_name_for_quadruplet<span style='mso-tab-count:
7455 1 dotted'>.................................................................................................................................................................. </span></span><!--[if supportFields]><span
7456 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732305
7457 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7458 style='mso-no-proof:yes'>44<!--[if gte mso 9]><xml>
7459  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300300035000000</w:data>
7460 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7461 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7462 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7463 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7464 mso-no-proof:yes'><o:p></o:p></span></p>
7465
7466 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7467 style='mso-no-proof:yes'>-compact<span style='mso-tab-count:1 dotted'>........................................................................................................................................................................................................ </span></span><!--[if supportFields]><span
7468 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732306
7469 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7470 style='mso-no-proof:yes'>44<!--[if gte mso 9]><xml>
7471  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300300036000000</w:data>
7472 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7473 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7474 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7475 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7476 mso-no-proof:yes'><o:p></o:p></span></p>
7477
7478 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7479 style='mso-no-proof:yes'>-clean<span style='mso-tab-count:1 dotted'>.............................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
7480 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732307
7481 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7482 style='mso-no-proof:yes'>44<!--[if gte mso 9]><xml>
7483  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300300037000000</w:data>
7484 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7485 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7486 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7487 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7488 mso-no-proof:yes'><o:p></o:p></span></p>
7489
7490 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7491 style='mso-no-proof:yes'>-maximise<span style='mso-tab-count:1 dotted'>..................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
7492 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732308
7493 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7494 style='mso-no-proof:yes'>44<!--[if gte mso 9]><xml>
7495  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300300038000000</w:data>
7496 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7497 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7498 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7499 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7500 mso-no-proof:yes'><o:p></o:p></span></p>
7501
7502 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7503 style='mso-no-proof:yes'>-do_self<span style='mso-tab-count:1 dotted'>.......................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
7504 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732309
7505 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7506 style='mso-no-proof:yes'>44<!--[if gte mso 9]><xml>
7507  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300300039000000</w:data>
7508 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7509 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7510 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7511 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7512 mso-no-proof:yes'><o:p></o:p></span></p>
7513
7514 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7515 style='mso-no-proof:yes'>-seq_name_for_quadruplet<span style='mso-tab-count:
7516 1 dotted'>.................................................................................................................................................................. </span></span><!--[if supportFields]><span
7517 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732310
7518 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7519 style='mso-no-proof:yes'>44<!--[if gte mso 9]><xml>
7520  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300310030000000</w:data>
7521 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7522 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7523 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7524 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7525 mso-no-proof:yes'><o:p></o:p></span></p>
7526
7527 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7528 style='mso-no-proof:yes'>-weight<span style='mso-tab-count:1 dotted'>.......................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
7529 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732311
7530 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7531 style='mso-no-proof:yes'>44<!--[if gte mso 9]><xml>
7532  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300310031000000</w:data>
7533 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7534 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7535 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7536 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7537 mso-no-proof:yes'><o:p></o:p></span></p>
7538
7539 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
7540 style='mso-no-proof:yes'>Tree Computation<span style='mso-tab-count:1 dotted'>.................................................................................................................................................................................... </span></span><!--[if supportFields]><span
7541 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732312
7542 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7543 style='mso-no-proof:yes'>45<!--[if gte mso 9]><xml>
7544  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300310032000000</w:data>
7545 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7546 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7547 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7548 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7549 mso-no-proof:yes'><o:p></o:p></span></p>
7550
7551 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7552 style='mso-no-proof:yes'>-distance_matrix_mode<span style='mso-tab-count:1 dotted'>......................................................................................................................................................................... </span></span><!--[if supportFields]><span
7553 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732313
7554 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7555 style='mso-no-proof:yes'>45<!--[if gte mso 9]><xml>
7556  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300310033000000</w:data>
7557 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7558 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7559 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7560 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7561 mso-no-proof:yes'><o:p></o:p></span></p>
7562
7563 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7564 style='mso-no-proof:yes'>-quicktree [CW]<span style='mso-tab-count:1 dotted'>......................................................................................................................................................................................... </span></span><!--[if supportFields]><span
7565 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732314
7566 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7567 style='mso-no-proof:yes'>45<!--[if gte mso 9]><xml>
7568  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300310034000000</w:data>
7569 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7570 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7571 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7572 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7573 mso-no-proof:yes'><o:p></o:p></span></p>
7574
7575 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
7576 style='mso-no-proof:yes'>Pair-wise Alignment Computation<span style='mso-tab-count:
7577 1 dotted'>................................................................................................................................................ </span></span><!--[if supportFields]><span
7578 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732315
7579 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7580 style='mso-no-proof:yes'>46<!--[if gte mso 9]><xml>
7581  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300310035000000</w:data>
7582 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7583 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7584 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7585 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7586 mso-no-proof:yes'><o:p></o:p></span></p>
7587
7588 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7589 style='mso-no-proof:yes'>-dp_mode<span style='mso-tab-count:1 dotted'>..................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
7590 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732316
7591 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7592 style='mso-no-proof:yes'>46<!--[if gte mso 9]><xml>
7593  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300310036000000</w:data>
7594 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7595 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7596 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7597 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7598 mso-no-proof:yes'><o:p></o:p></span></p>
7599
7600 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7601 style='mso-no-proof:yes'>-ktuple<span style='mso-tab-count:1 dotted'>........................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
7602 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732317
7603 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7604 style='mso-no-proof:yes'>47<!--[if gte mso 9]><xml>
7605  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300310037000000</w:data>
7606 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7607 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7608 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7609 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7610 mso-no-proof:yes'><o:p></o:p></span></p>
7611
7612 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7613 style='mso-no-proof:yes'>-ndiag<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
7614 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732318
7615 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7616 style='mso-no-proof:yes'>47<!--[if gte mso 9]><xml>
7617  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300310038000000</w:data>
7618 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7619 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7620 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7621 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7622 mso-no-proof:yes'><o:p></o:p></span></p>
7623
7624 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7625 style='mso-no-proof:yes'>-diag_mode<span style='mso-tab-count:1 dotted'>.................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
7626 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732319
7627 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7628 style='mso-no-proof:yes'>47<!--[if gte mso 9]><xml>
7629  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300310039000000</w:data>
7630 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7631 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7632 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7633 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7634 mso-no-proof:yes'><o:p></o:p></span></p>
7635
7636 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7637 style='mso-no-proof:yes'>-diag_threshold<span style='mso-tab-count:1 dotted'>......................................................................................................................................................................................... </span></span><!--[if supportFields]><span
7638 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732320
7639 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7640 style='mso-no-proof:yes'>47<!--[if gte mso 9]><xml>
7641  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300320030000000</w:data>
7642 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7643 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7644 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7645 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7646 mso-no-proof:yes'><o:p></o:p></span></p>
7647
7648 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7649 style='mso-no-proof:yes'>-sim_matrix<span style='mso-tab-count:1 dotted'>.................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
7650 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732321
7651 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7652 style='mso-no-proof:yes'>47<!--[if gte mso 9]><xml>
7653  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300320031000000</w:data>
7654 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7655 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7656 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7657 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7658 mso-no-proof:yes'><o:p></o:p></span></p>
7659
7660 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7661 style='mso-no-proof:yes'>-matrix [CW]<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................... </span></span><!--[if supportFields]><span
7662 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732322
7663 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7664 style='mso-no-proof:yes'>48<!--[if gte mso 9]><xml>
7665  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300320032000000</w:data>
7666 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7667 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7668 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7669 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7670 mso-no-proof:yes'><o:p></o:p></span></p>
7671
7672 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7673 style='mso-no-proof:yes'>-nomatch<span style='mso-tab-count:1 dotted'>....................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
7674 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732323
7675 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7676 style='mso-no-proof:yes'>48<!--[if gte mso 9]><xml>
7677  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300320033000000</w:data>
7678 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7679 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7680 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7681 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7682 mso-no-proof:yes'><o:p></o:p></span></p>
7683
7684 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7685 style='mso-no-proof:yes'>-gapopen<span style='mso-tab-count:1 dotted'>...................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
7686 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732324
7687 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7688 style='mso-no-proof:yes'>48<!--[if gte mso 9]><xml>
7689  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300320034000000</w:data>
7690 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7691 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7692 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7693 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7694 mso-no-proof:yes'><o:p></o:p></span></p>
7695
7696 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7697 style='mso-no-proof:yes'>-gapext<span style='mso-tab-count:1 dotted'>........................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
7698 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732325
7699 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7700 style='mso-no-proof:yes'>48<!--[if gte mso 9]><xml>
7701  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300320035000000</w:data>
7702 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7703 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7704 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7705 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7706 mso-no-proof:yes'><o:p></o:p></span></p>
7707
7708 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7709 style='mso-no-proof:yes'>-fgapopen<span style='mso-tab-count:1 dotted'>..................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
7710 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732326
7711 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7712 style='mso-no-proof:yes'>48<!--[if gte mso 9]><xml>
7713  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300320036000000</w:data>
7714 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7715 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7716 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7717 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7718 mso-no-proof:yes'><o:p></o:p></span></p>
7719
7720 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7721 style='mso-no-proof:yes'>-fgapext<span style='mso-tab-count:1 dotted'>......................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
7722 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732327
7723 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7724 style='mso-no-proof:yes'>49<!--[if gte mso 9]><xml>
7725  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300320037000000</w:data>
7726 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7727 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7728 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7729 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7730 mso-no-proof:yes'><o:p></o:p></span></p>
7731
7732 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7733 style='mso-no-proof:yes'>-cosmetic_penalty<span style='mso-tab-count:1 dotted'>..................................................................................................................................................................................... </span></span><!--[if supportFields]><span
7734 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732328
7735 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7736 style='mso-no-proof:yes'>49<!--[if gte mso 9]><xml>
7737  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300320038000000</w:data>
7738 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7739 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7740 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7741 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7742 mso-no-proof:yes'><o:p></o:p></span></p>
7743
7744 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7745 style='mso-no-proof:yes'>-tg_mode<span style='mso-tab-count:1 dotted'>....................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
7746 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732329
7747 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7748 style='mso-no-proof:yes'>49<!--[if gte mso 9]><xml>
7749  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300320039000000</w:data>
7750 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7751 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7752 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7753 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7754 mso-no-proof:yes'><o:p></o:p></span></p>
7755
7756 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
7757 style='mso-no-proof:yes'>Weighting Schemes<span style='mso-tab-count:1 dotted'>.................................................................................................................................................................................. </span></span><!--[if supportFields]><span
7758 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732330
7759 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7760 style='mso-no-proof:yes'>49<!--[if gte mso 9]><xml>
7761  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300330030000000</w:data>
7762 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7763 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7764 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7765 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7766 mso-no-proof:yes'><o:p></o:p></span></p>
7767
7768 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7769 style='mso-no-proof:yes'>-seq_weight<span style='mso-tab-count:1 dotted'>................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
7770 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732331
7771 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7772 style='mso-no-proof:yes'>49<!--[if gte mso 9]><xml>
7773  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300330031000000</w:data>
7774 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7775 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7776 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7777 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7778 mso-no-proof:yes'><o:p></o:p></span></p>
7779
7780 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
7781 style='mso-no-proof:yes'>Multiple Alignment Computation<span style='mso-tab-count:
7782 1 dotted'>................................................................................................................................................... </span></span><!--[if supportFields]><span
7783 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732332
7784 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7785 style='mso-no-proof:yes'>50<!--[if gte mso 9]><xml>
7786  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300330032000000</w:data>
7787 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7788 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7789 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7790 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7791 mso-no-proof:yes'><o:p></o:p></span></p>
7792
7793 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7794 style='mso-no-proof:yes'>-msa_mode<span style='mso-tab-count:1 dotted'>................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
7795 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732333
7796 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7797 style='mso-no-proof:yes'>50<!--[if gte mso 9]><xml>
7798  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300330033000000</w:data>
7799 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7800 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7801 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7802 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7803 mso-no-proof:yes'><o:p></o:p></span></p>
7804
7805 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7806 style='mso-no-proof:yes'>-one2all<span style='mso-tab-count:1 dotted'>......................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
7807 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732334
7808 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7809 style='mso-no-proof:yes'>50<!--[if gte mso 9]><xml>
7810  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300330034000000</w:data>
7811 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7812 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7813 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7814 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7815 mso-no-proof:yes'><o:p></o:p></span></p>
7816
7817 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7818 style='mso-no-proof:yes'>-profile_comparison<span style='mso-tab-count:1 dotted'>................................................................................................................................................................................ </span></span><!--[if supportFields]><span
7819 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732335
7820 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7821 style='mso-no-proof:yes'>50<!--[if gte mso 9]><xml>
7822  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300330035000000</w:data>
7823 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7824 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7825 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7826 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7827 mso-no-proof:yes'><o:p></o:p></span></p>
7828
7829 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7830 style='mso-no-proof:yes'>-profile_mode<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................. </span></span><!--[if supportFields]><span
7831 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732336
7832 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7833 style='mso-no-proof:yes'>50<!--[if gte mso 9]><xml>
7834  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300330036000000</w:data>
7835 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7836 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7837 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7838 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7839 mso-no-proof:yes'><o:p></o:p></span></p>
7840
7841 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
7842 style='mso-no-proof:yes'>Alignment Post-Processing<span style='mso-tab-count:
7843 1 dotted'>................................................................................................................................................................ </span></span><!--[if supportFields]><span
7844 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732337
7845 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7846 style='mso-no-proof:yes'>51<!--[if gte mso 9]><xml>
7847  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300330037000000</w:data>
7848 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7849 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7850 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7851 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7852 mso-no-proof:yes'><o:p></o:p></span></p>
7853
7854 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7855 style='mso-no-proof:yes'>-clean_aln<span style='mso-tab-count:1 dotted'>..................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
7856 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732338
7857 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7858 style='mso-no-proof:yes'>51<!--[if gte mso 9]><xml>
7859  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300330038000000</w:data>
7860 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7861 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7862 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7863 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7864 mso-no-proof:yes'><o:p></o:p></span></p>
7865
7866 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7867 style='mso-no-proof:yes'>-clean_threshold<span style='mso-tab-count:1 dotted'>....................................................................................................................................................................................... </span></span><!--[if supportFields]><span
7868 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732339
7869 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7870 style='mso-no-proof:yes'>51<!--[if gte mso 9]><xml>
7871  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300330039000000</w:data>
7872 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7873 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7874 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7875 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7876 mso-no-proof:yes'><o:p></o:p></span></p>
7877
7878 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7879 style='mso-no-proof:yes'>-clean_iteration<span style='mso-tab-count:1 dotted'>......................................................................................................................................................................................... </span></span><!--[if supportFields]><span
7880 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732340
7881 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7882 style='mso-no-proof:yes'>51<!--[if gte mso 9]><xml>
7883  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300340030000000</w:data>
7884 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7885 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7886 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7887 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7888 mso-no-proof:yes'><o:p></o:p></span></p>
7889
7890 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7891 style='mso-no-proof:yes'>-clean_evaluation_mode<span style='mso-tab-count:1 dotted'>....................................................................................................................................................................... </span></span><!--[if supportFields]><span
7892 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732341
7893 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7894 style='mso-no-proof:yes'>51<!--[if gte mso 9]><xml>
7895  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300340031000000</w:data>
7896 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7897 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7898 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7899 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7900 mso-no-proof:yes'><o:p></o:p></span></p>
7901
7902 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7903 style='mso-no-proof:yes'>-iterate<span style='mso-tab-count:1 dotted'>........................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
7904 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732342
7905 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7906 style='mso-no-proof:yes'>51<!--[if gte mso 9]><xml>
7907  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300340032000000</w:data>
7908 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7909 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7910 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7911 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7912 mso-no-proof:yes'><o:p></o:p></span></p>
7913
7914 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
7915 style='mso-no-proof:yes'>BLAST Template Selection Parameters<span
7916 style='mso-tab-count:1 dotted'>...................................................................................... </span></span><!--[if supportFields]><span
7917 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732343
7918 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7919 style='mso-no-proof:yes'>51<!--[if gte mso 9]><xml>
7920  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300340033000000</w:data>
7921 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7922 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7923 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7924 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7925 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
7926
7927 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7928 style='mso-no-proof:yes'>-blast_server<span style='mso-tab-count:1 dotted'>................................................................................................................................................................................................ </span></span><!--[if supportFields]><span
7929 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732344
7930 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7931 style='mso-no-proof:yes'>52<!--[if gte mso 9]><xml>
7932  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300340034000000</w:data>
7933 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7934 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7935 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7936 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7937 mso-no-proof:yes'><o:p></o:p></span></p>
7938
7939 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7940 style='mso-no-proof:yes'>-prot_min_sim<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................ </span></span><!--[if supportFields]><span
7941 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732345
7942 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7943 style='mso-no-proof:yes'>52<!--[if gte mso 9]><xml>
7944  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300340035000000</w:data>
7945 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7946 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7947 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7948 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7949 mso-no-proof:yes'><o:p></o:p></span></p>
7950
7951 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7952 style='mso-no-proof:yes'>-prot_max_sim<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................ </span></span><!--[if supportFields]><span
7953 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732346
7954 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7955 style='mso-no-proof:yes'>52<!--[if gte mso 9]><xml>
7956  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300340036000000</w:data>
7957 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7958 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7959 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7960 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7961 mso-no-proof:yes'><o:p></o:p></span></p>
7962
7963 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7964 style='mso-no-proof:yes'>-prot_min_cov<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................. </span></span><!--[if supportFields]><span
7965 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732347
7966 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7967 style='mso-no-proof:yes'>52<!--[if gte mso 9]><xml>
7968  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300340037000000</w:data>
7969 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7970 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7971 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7972 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7973 mso-no-proof:yes'><o:p></o:p></span></p>
7974
7975 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7976 style='mso-no-proof:yes'>-protein_db<span style='mso-tab-count:1 dotted'>.................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
7977 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732348
7978 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7979 style='mso-no-proof:yes'>52<!--[if gte mso 9]><xml>
7980  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300340038000000</w:data>
7981 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7982 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7983 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7984 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7985 mso-no-proof:yes'><o:p></o:p></span></p>
7986
7987 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
7988 style='mso-no-proof:yes'>-pdb_min_sim<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................. </span></span><!--[if supportFields]><span
7989 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732349
7990 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
7991 style='mso-no-proof:yes'>52<!--[if gte mso 9]><xml>
7992  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300340039000000</w:data>
7993 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
7994 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
7995 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
7996 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
7997 mso-no-proof:yes'><o:p></o:p></span></p>
7998
7999 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8000 style='mso-no-proof:yes'>-pdb_max_sim<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................ </span></span><!--[if supportFields]><span
8001 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732350
8002 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8003 style='mso-no-proof:yes'>52<!--[if gte mso 9]><xml>
8004  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300350030000000</w:data>
8005 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8006 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8007 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8008 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8009 mso-no-proof:yes'><o:p></o:p></span></p>
8010
8011 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8012 style='mso-no-proof:yes'>-pdb_min_cov<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................. </span></span><!--[if supportFields]><span
8013 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732351
8014 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8015 style='mso-no-proof:yes'>53<!--[if gte mso 9]><xml>
8016  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300350031000000</w:data>
8017 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8018 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8019 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8020 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8021 mso-no-proof:yes'><o:p></o:p></span></p>
8022
8023 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8024 style='mso-no-proof:yes'>-pdb_db<span style='mso-tab-count:1 dotted'>......................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
8025 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732352
8026 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8027 style='mso-no-proof:yes'>53<!--[if gte mso 9]><xml>
8028  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300350032000000</w:data>
8029 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8030 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8031 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8032 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8033 mso-no-proof:yes'><o:p></o:p></span></p>
8034
8035 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8036 style='mso-no-proof:yes'>-pdb_type<span style='mso-tab-count:1 dotted'>..................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
8037 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732353
8038 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8039 style='mso-no-proof:yes'>53<!--[if gte mso 9]><xml>
8040  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300350033000000</w:data>
8041 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8042 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8043 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8044 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8045 mso-no-proof:yes'><o:p></o:p></span></p>
8046
8047 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
8048 style='mso-no-proof:yes'>CPU Control<span style='mso-tab-count:1 dotted'>................................................................................................................................... </span></span><!--[if supportFields]><span
8049 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732354
8050 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8051 style='mso-no-proof:yes'>53<!--[if gte mso 9]><xml>
8052  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300350034000000</w:data>
8053 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8054 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8055 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8056 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8057 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
8058
8059 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
8060 style='mso-no-proof:yes'>Multithreading<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................ </span></span><!--[if supportFields]><span
8061 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732355
8062 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8063 style='mso-no-proof:yes'>53<!--[if gte mso 9]><xml>
8064  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300350035000000</w:data>
8065 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8066 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8067 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8068 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8069 mso-no-proof:yes'><o:p></o:p></span></p>
8070
8071 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8072 style='mso-no-proof:yes'>-multi_core<span style='mso-tab-count:1 dotted'>................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
8073 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732356
8074 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8075 style='mso-no-proof:yes'>53<!--[if gte mso 9]><xml>
8076  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300350036000000</w:data>
8077 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8078 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8079 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8080 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8081 mso-no-proof:yes'><o:p></o:p></span></p>
8082
8083 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8084 style='mso-no-proof:yes'>-n_core<span style='mso-tab-count:1 dotted'>........................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
8085 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732357
8086 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8087 style='mso-no-proof:yes'>54<!--[if gte mso 9]><xml>
8088  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300350037000000</w:data>
8089 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8090 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8091 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8092 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8093 mso-no-proof:yes'><o:p></o:p></span></p>
8094
8095 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
8096 style='mso-no-proof:yes'>Limits<span style='mso-tab-count:1 dotted'>................................................................................................................................................................................................................ </span></span><!--[if supportFields]><span
8097 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732358
8098 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8099 style='mso-no-proof:yes'>54<!--[if gte mso 9]><xml>
8100  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300350038000000</w:data>
8101 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8102 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8103 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8104 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8105 mso-no-proof:yes'><o:p></o:p></span></p>
8106
8107 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8108 style='mso-no-proof:yes'>-mem_mode<span style='mso-tab-count:1 dotted'>................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
8109 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732359
8110 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8111 style='mso-no-proof:yes'>54<!--[if gte mso 9]><xml>
8112  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300350039000000</w:data>
8113 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8114 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8115 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8116 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8117 mso-no-proof:yes'><o:p></o:p></span></p>
8118
8119 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8120 style='mso-no-proof:yes'>-ulimit<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................................ </span></span><!--[if supportFields]><span
8121 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732360
8122 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8123 style='mso-no-proof:yes'>54<!--[if gte mso 9]><xml>
8124  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300360030000000</w:data>
8125 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8126 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8127 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8128 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8129 mso-no-proof:yes'><o:p></o:p></span></p>
8130
8131 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8132 style='mso-no-proof:yes'>-maxlen<span style='mso-tab-count:1 dotted'>......................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
8133 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732361
8134 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8135 style='mso-no-proof:yes'>54<!--[if gte mso 9]><xml>
8136  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300360031000000</w:data>
8137 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8138 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8139 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8140 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8141 mso-no-proof:yes'><o:p></o:p></span></p>
8142
8143 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
8144 style='mso-no-proof:yes'>Aligning more than 100 sequences with DPA<span
8145 style='mso-tab-count:1 dotted'>......................................................................................................................... </span></span><!--[if supportFields]><span
8146 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732362
8147 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8148 style='mso-no-proof:yes'>54<!--[if gte mso 9]><xml>
8149  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300360032000000</w:data>
8150 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8151 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8152 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8153 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8154 mso-no-proof:yes'><o:p></o:p></span></p>
8155
8156 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8157 style='mso-no-proof:yes'>-maxnseq<span style='mso-tab-count:1 dotted'>...................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
8158 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732363
8159 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8160 style='mso-no-proof:yes'>54<!--[if gte mso 9]><xml>
8161  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300360033000000</w:data>
8162 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8163 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8164 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8165 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8166 mso-no-proof:yes'><o:p></o:p></span></p>
8167
8168 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8169 style='mso-no-proof:yes'>-dpa_master_aln<span style='mso-tab-count:1 dotted'>....................................................................................................................................................................................... </span></span><!--[if supportFields]><span
8170 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732364
8171 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8172 style='mso-no-proof:yes'>55<!--[if gte mso 9]><xml>
8173  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300360034000000</w:data>
8174 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8175 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8176 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8177 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8178 mso-no-proof:yes'><o:p></o:p></span></p>
8179
8180 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8181 style='mso-no-proof:yes'>-dpa_maxnseq<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................ </span></span><!--[if supportFields]><span
8182 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732365
8183 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8184 style='mso-no-proof:yes'>55<!--[if gte mso 9]><xml>
8185  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300360035000000</w:data>
8186 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8187 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8188 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8189 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8190 mso-no-proof:yes'><o:p></o:p></span></p>
8191
8192 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8193 style='mso-no-proof:yes'>-dpa_min_score1<span style='mso-tab-count:1 dotted'>...................................................................................................................................................................................... </span></span><!--[if supportFields]><span
8194 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732366
8195 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8196 style='mso-no-proof:yes'>55<!--[if gte mso 9]><xml>
8197  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300360036000000</w:data>
8198 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8199 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8200 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8201 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8202 mso-no-proof:yes'><o:p></o:p></span></p>
8203
8204 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8205 style='mso-no-proof:yes'>-dpa_min_score2<span style='mso-tab-count:1 dotted'>...................................................................................................................................................................................... </span></span><!--[if supportFields]><span
8206 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732367
8207 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8208 style='mso-no-proof:yes'>55<!--[if gte mso 9]><xml>
8209  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300360037000000</w:data>
8210 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8211 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8212 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8213 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8214 mso-no-proof:yes'><o:p></o:p></span></p>
8215
8216 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8217 style='mso-no-proof:yes'>-dap_tree [NOT IMPLEMENTED]<span style='mso-tab-count:
8218 1 dotted'>.................................................................................................................................................... </span></span><!--[if supportFields]><span
8219 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732368
8220 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8221 style='mso-no-proof:yes'>55<!--[if gte mso 9]><xml>
8222  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300360038000000</w:data>
8223 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8224 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8225 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8226 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8227 mso-no-proof:yes'><o:p></o:p></span></p>
8228
8229 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
8230 style='mso-no-proof:yes'>Using Structures<span style='mso-tab-count:1 dotted'>.......................................................................................................................... </span></span><!--[if supportFields]><span
8231 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732369
8232 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8233 style='mso-no-proof:yes'>56<!--[if gte mso 9]><xml>
8234  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300360039000000</w:data>
8235 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8236 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8237 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8238 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8239 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
8240
8241 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
8242 style='mso-no-proof:yes'>Generic<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
8243 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732370
8244 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8245 style='mso-no-proof:yes'>56<!--[if gte mso 9]><xml>
8246  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300370030000000</w:data>
8247 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8248 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8249 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8250 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8251 mso-no-proof:yes'><o:p></o:p></span></p>
8252
8253 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8254 style='mso-no-proof:yes'>-mode<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
8255 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732371
8256 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8257 style='mso-no-proof:yes'>56<!--[if gte mso 9]><xml>
8258  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300370031000000</w:data>
8259 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8260 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8261 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8262 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8263 mso-no-proof:yes'><o:p></o:p></span></p>
8264
8265 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8266 style='mso-no-proof:yes'>-check_pdb_status<span style='mso-tab-count:1 dotted'>.................................................................................................................................................................................... </span></span><!--[if supportFields]><span
8267 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732372
8268 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8269 style='mso-no-proof:yes'>56<!--[if gte mso 9]><xml>
8270  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300370032000000</w:data>
8271 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8272 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8273 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8274 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8275 mso-no-proof:yes'><o:p></o:p></span></p>
8276
8277 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
8278 style='mso-no-proof:yes'>3D Coffee: Using SAP<span style='mso-tab-count:1 dotted'>................................................................................................................................................................................ </span></span><!--[if supportFields]><span
8279 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732373
8280 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8281 style='mso-no-proof:yes'>56<!--[if gte mso 9]><xml>
8282  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300370033000000</w:data>
8283 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8284 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8285 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8286 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8287 mso-no-proof:yes'><o:p></o:p></span></p>
8288
8289 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
8290 style='mso-no-proof:yes'>Using/finding PDB templates for the Sequences<span
8291 style='mso-tab-count:1 dotted'>................................................................................................................... </span></span><!--[if supportFields]><span
8292 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732374
8293 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8294 style='mso-no-proof:yes'>57<!--[if gte mso 9]><xml>
8295  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300370034000000</w:data>
8296 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8297 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8298 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8299 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8300 mso-no-proof:yes'><o:p></o:p></span></p>
8301
8302 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8303 style='mso-no-proof:yes'>-template_file<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................. </span></span><!--[if supportFields]><span
8304 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732375
8305 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8306 style='mso-no-proof:yes'>57<!--[if gte mso 9]><xml>
8307  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300370035000000</w:data>
8308 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8309 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8310 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8311 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8312 mso-no-proof:yes'><o:p></o:p></span></p>
8313
8314 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8315 style='mso-no-proof:yes'>-struc_to_use<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................... </span></span><!--[if supportFields]><span
8316 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732376
8317 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8318 style='mso-no-proof:yes'>59<!--[if gte mso 9]><xml>
8319  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300370036000000</w:data>
8320 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8321 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8322 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8323 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8324 mso-no-proof:yes'><o:p></o:p></span></p>
8325
8326 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
8327 style='mso-no-proof:yes'>Multiple Local Alignments<span style='mso-tab-count:
8328 1 dotted'>........................................................................................................... </span></span><!--[if supportFields]><span
8329 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732377
8330 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8331 style='mso-no-proof:yes'>59<!--[if gte mso 9]><xml>
8332  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300370037000000</w:data>
8333 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8334 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8335 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8336 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8337 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
8338
8339 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8340 style='mso-no-proof:yes'>-domain/-mocca<span style='mso-tab-count:1 dotted'>........................................................................................................................................................................................ </span></span><!--[if supportFields]><span
8341 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732378
8342 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8343 style='mso-no-proof:yes'>59<!--[if gte mso 9]><xml>
8344  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300370038000000</w:data>
8345 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8346 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8347 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8348 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8349 mso-no-proof:yes'><o:p></o:p></span></p>
8350
8351 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8352 style='mso-no-proof:yes'>-start<span style='mso-tab-count:1 dotted'>................................................................................................................................................................................................................ </span></span><!--[if supportFields]><span
8353 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732379
8354 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8355 style='mso-no-proof:yes'>59<!--[if gte mso 9]><xml>
8356  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300370039000000</w:data>
8357 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8358 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8359 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8360 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8361 mso-no-proof:yes'><o:p></o:p></span></p>
8362
8363 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8364 style='mso-no-proof:yes'>-len<span style='mso-tab-count:1 dotted'>.................................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
8365 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732380
8366 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8367 style='mso-no-proof:yes'>60<!--[if gte mso 9]><xml>
8368  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300380030000000</w:data>
8369 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8370 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8371 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8372 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8373 mso-no-proof:yes'><o:p></o:p></span></p>
8374
8375 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8376 style='mso-no-proof:yes'>-scale<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
8377 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732381
8378 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8379 style='mso-no-proof:yes'>60<!--[if gte mso 9]><xml>
8380  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300380031000000</w:data>
8381 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8382 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8383 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8384 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8385 mso-no-proof:yes'><o:p></o:p></span></p>
8386
8387 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8388 style='mso-no-proof:yes'>-domain_interactive [Examples]<span style='mso-tab-count:
8389 1 dotted'>...................................................................................................................................................... </span></span><!--[if supportFields]><span
8390 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732382
8391 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8392 style='mso-no-proof:yes'>60<!--[if gte mso 9]><xml>
8393  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300380032000000</w:data>
8394 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8395 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8396 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8397 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8398 mso-no-proof:yes'><o:p></o:p></span></p>
8399
8400 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
8401 style='mso-no-proof:yes'>Output Control<span style='mso-tab-count:1 dotted'>............................................................................................................................. </span></span><!--[if supportFields]><span
8402 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732383
8403 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8404 style='mso-no-proof:yes'>61<!--[if gte mso 9]><xml>
8405  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300380033000000</w:data>
8406 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8407 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8408 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8409 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8410 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
8411
8412 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
8413 style='mso-no-proof:yes'>Generic<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
8414 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732384
8415 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8416 style='mso-no-proof:yes'>61<!--[if gte mso 9]><xml>
8417  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300380034000000</w:data>
8418 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8419 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8420 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8421 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8422 mso-no-proof:yes'><o:p></o:p></span></p>
8423
8424 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8425 style='mso-no-proof:yes'>Conventions Regarding Filenames<span style='mso-tab-count:
8426 1 dotted'>................................................................................................................................................. </span></span><!--[if supportFields]><span
8427 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732385
8428 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8429 style='mso-no-proof:yes'>61<!--[if gte mso 9]><xml>
8430  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300380035000000</w:data>
8431 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8432 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8433 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8434 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8435 mso-no-proof:yes'><o:p></o:p></span></p>
8436
8437 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8438 style='mso-no-proof:yes'>Identifying the Output files automatically<span
8439 style='mso-tab-count:1 dotted'>.................................................................................................................................. </span></span><!--[if supportFields]><span
8440 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732386
8441 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8442 style='mso-no-proof:yes'>61<!--[if gte mso 9]><xml>
8443  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300380036000000</w:data>
8444 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8445 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8446 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8447 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8448 mso-no-proof:yes'><o:p></o:p></span></p>
8449
8450 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8451 style='mso-no-proof:yes'>-no_warning<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................... </span></span><!--[if supportFields]><span
8452 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732387
8453 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8454 style='mso-no-proof:yes'>61<!--[if gte mso 9]><xml>
8455  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300380037000000</w:data>
8456 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8457 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8458 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8459 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8460 mso-no-proof:yes'><o:p></o:p></span></p>
8461
8462 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
8463 style='mso-no-proof:yes'>Alignments<span style='mso-tab-count:1 dotted'>.................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
8464 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732388
8465 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8466 style='mso-no-proof:yes'>61<!--[if gte mso 9]><xml>
8467  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300380038000000</w:data>
8468 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8469 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8470 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8471 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8472 mso-no-proof:yes'><o:p></o:p></span></p>
8473
8474 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8475 style='mso-no-proof:yes'>-outfile<span style='mso-tab-count:1 dotted'>........................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
8476 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732389
8477 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8478 style='mso-no-proof:yes'>61<!--[if gte mso 9]><xml>
8479  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300380039000000</w:data>
8480 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8481 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8482 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8483 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8484 mso-no-proof:yes'><o:p></o:p></span></p>
8485
8486 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8487 style='mso-no-proof:yes'>-output<span style='mso-tab-count:1 dotted'>........................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
8488 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732390
8489 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8490 style='mso-no-proof:yes'>61<!--[if gte mso 9]><xml>
8491  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300390030000000</w:data>
8492 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8493 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8494 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8495 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8496 mso-no-proof:yes'><o:p></o:p></span></p>
8497
8498 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8499 style='mso-no-proof:yes'>-outseqweight<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................ </span></span><!--[if supportFields]><span
8500 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732391
8501 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8502 style='mso-no-proof:yes'>62<!--[if gte mso 9]><xml>
8503  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300390031000000</w:data>
8504 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8505 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8506 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8507 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8508 mso-no-proof:yes'><o:p></o:p></span></p>
8509
8510 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8511 style='mso-no-proof:yes'>-case<span style='mso-tab-count:1 dotted'>................................................................................................................................................................................................................ </span></span><!--[if supportFields]><span
8512 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732392
8513 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8514 style='mso-no-proof:yes'>62<!--[if gte mso 9]><xml>
8515  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300390032000000</w:data>
8516 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8517 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8518 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8519 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8520 mso-no-proof:yes'><o:p></o:p></span></p>
8521
8522 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8523 style='mso-no-proof:yes'>-cpu<span style='mso-tab-count:1 dotted'>................................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
8524 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732393
8525 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8526 style='mso-no-proof:yes'>63<!--[if gte mso 9]><xml>
8527  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300390033000000</w:data>
8528 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8529 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8530 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8531 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8532 mso-no-proof:yes'><o:p></o:p></span></p>
8533
8534 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8535 style='mso-no-proof:yes'>-outseqweight<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................ </span></span><!--[if supportFields]><span
8536 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732394
8537 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8538 style='mso-no-proof:yes'>63<!--[if gte mso 9]><xml>
8539  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300390034000000</w:data>
8540 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8541 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8542 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8543 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8544 mso-no-proof:yes'><o:p></o:p></span></p>
8545
8546 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8547 style='mso-no-proof:yes'>-outorder [cw]<span style='mso-tab-count:1 dotted'>........................................................................................................................................................................................... </span></span><!--[if supportFields]><span
8548 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732395
8549 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8550 style='mso-no-proof:yes'>63<!--[if gte mso 9]><xml>
8551  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300390035000000</w:data>
8552 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8553 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8554 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8555 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8556 mso-no-proof:yes'><o:p></o:p></span></p>
8557
8558 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8559 style='mso-no-proof:yes'>-inorder [cw]<span style='mso-tab-count:1 dotted'>.............................................................................................................................................................................................. </span></span><!--[if supportFields]><span
8560 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732396
8561 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8562 style='mso-no-proof:yes'>63<!--[if gte mso 9]><xml>
8563  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300390036000000</w:data>
8564 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8565 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8566 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8567 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8568 mso-no-proof:yes'><o:p></o:p></span></p>
8569
8570 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8571 style='mso-no-proof:yes'>-seqnos<span style='mso-tab-count:1 dotted'>........................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
8572 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732397
8573 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8574 style='mso-no-proof:yes'>63<!--[if gte mso 9]><xml>
8575  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300390037000000</w:data>
8576 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8577 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8578 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8579 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8580 mso-no-proof:yes'><o:p></o:p></span></p>
8581
8582 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
8583 style='mso-no-proof:yes'>Libraries<span style='mso-tab-count:1 dotted'>......................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
8584 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732398
8585 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8586 style='mso-no-proof:yes'>63<!--[if gte mso 9]><xml>
8587  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300390038000000</w:data>
8588 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8589 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8590 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8591 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8592 mso-no-proof:yes'><o:p></o:p></span></p>
8593
8594 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8595 style='mso-no-proof:yes'>-out_lib<span style='mso-tab-count:1 dotted'>........................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
8596 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732399
8597 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8598 style='mso-no-proof:yes'>64<!--[if gte mso 9]><xml>
8599  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003300390039000000</w:data>
8600 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8601 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8602 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8603 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8604 mso-no-proof:yes'><o:p></o:p></span></p>
8605
8606 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8607 style='mso-no-proof:yes'>-lib_only<span style='mso-tab-count:1 dotted'>........................................................................................................................................................................................................ </span></span><!--[if supportFields]><span
8608 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732400
8609 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8610 style='mso-no-proof:yes'>64<!--[if gte mso 9]><xml>
8611  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400300030000000</w:data>
8612 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8613 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8614 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8615 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8616 mso-no-proof:yes'><o:p></o:p></span></p>
8617
8618 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
8619 style='mso-no-proof:yes'>Trees<span style='mso-tab-count:1 dotted'>................................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
8620 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732401
8621 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8622 style='mso-no-proof:yes'>64<!--[if gte mso 9]><xml>
8623  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400300031000000</w:data>
8624 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8625 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8626 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8627 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8628 mso-no-proof:yes'><o:p></o:p></span></p>
8629
8630 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8631 style='mso-no-proof:yes'>-newtree<span style='mso-tab-count:1 dotted'>....................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
8632 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732402
8633 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8634 style='mso-no-proof:yes'>64<!--[if gte mso 9]><xml>
8635  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400300032000000</w:data>
8636 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8637 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8638 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8639 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8640 mso-no-proof:yes'><o:p></o:p></span></p>
8641
8642 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
8643 style='mso-no-proof:yes'>Reliability Estimation<span style='mso-tab-count:1 dotted'>................................................................................................................... </span></span><!--[if supportFields]><span
8644 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732403
8645 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8646 style='mso-no-proof:yes'>64<!--[if gte mso 9]><xml>
8647  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400300033000000</w:data>
8648 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8649 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8650 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8651 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8652 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
8653
8654 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
8655 style='mso-no-proof:yes'>CORE Computation<span style='mso-tab-count:1 dotted'>.................................................................................................................................................................................. </span></span><!--[if supportFields]><span
8656 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732404
8657 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8658 style='mso-no-proof:yes'>64<!--[if gte mso 9]><xml>
8659  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400300034000000</w:data>
8660 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8661 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8662 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8663 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8664 mso-no-proof:yes'><o:p></o:p></span></p>
8665
8666 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8667 style='mso-no-proof:yes'>-evaluate_mode<span style='mso-tab-count:1 dotted'>......................................................................................................................................................................................... </span></span><!--[if supportFields]><span
8668 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732405
8669 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8670 style='mso-no-proof:yes'>64<!--[if gte mso 9]><xml>
8671  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400300035000000</w:data>
8672 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8673 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8674 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8675 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8676 mso-no-proof:yes'><o:p></o:p></span></p>
8677
8678 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
8679 style='mso-no-proof:yes'>Generic Output<span style='mso-tab-count:1 dotted'>............................................................................................................................ </span></span><!--[if supportFields]><span
8680 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732406
8681 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8682 style='mso-no-proof:yes'>65<!--[if gte mso 9]><xml>
8683  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400300036000000</w:data>
8684 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8685 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8686 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8687 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8688 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
8689
8690 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8691 style='mso-no-proof:yes'>-run_name<span style='mso-tab-count:1 dotted'>................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
8692 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732407
8693 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8694 style='mso-no-proof:yes'>65<!--[if gte mso 9]><xml>
8695  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400300037000000</w:data>
8696 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8697 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8698 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8699 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8700 mso-no-proof:yes'><o:p></o:p></span></p>
8701
8702 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8703 style='mso-no-proof:yes'>-quiet<span style='mso-tab-count:1 dotted'>.............................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
8704 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732408
8705 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8706 style='mso-no-proof:yes'>65<!--[if gte mso 9]><xml>
8707  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400300038000000</w:data>
8708 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8709 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8710 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8711 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8712 mso-no-proof:yes'><o:p></o:p></span></p>
8713
8714 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8715 style='mso-no-proof:yes'>-align [CW]<span style='mso-tab-count:1 dotted'>.................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
8716 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732409
8717 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8718 style='mso-no-proof:yes'>65<!--[if gte mso 9]><xml>
8719  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400300039000000</w:data>
8720 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8721 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8722 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8723 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8724 mso-no-proof:yes'><o:p></o:p></span></p>
8725
8726 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
8727 style='mso-no-proof:yes'>APDB, iRMSD and tRMSD Parameters<span
8728 style='mso-tab-count:1 dotted'>........................................................................................ </span></span><!--[if supportFields]><span
8729 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732410
8730 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8731 style='mso-no-proof:yes'>65<!--[if gte mso 9]><xml>
8732  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400310030000000</w:data>
8733 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8734 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8735 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8736 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8737 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
8738
8739 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8740 style='mso-no-proof:yes'>-quiet [Same as T-Coffee]<span style='mso-tab-count:
8741 1 dotted'>..................................................................................................................................................................... </span></span><!--[if supportFields]><span
8742 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732411
8743 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8744 style='mso-no-proof:yes'>66<!--[if gte mso 9]><xml>
8745  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400310031000000</w:data>
8746 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8747 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8748 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8749 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8750 mso-no-proof:yes'><o:p></o:p></span></p>
8751
8752 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8753 style='mso-no-proof:yes'>-run_name [Same as T-Coffee]<span style='mso-tab-count:
8754 1 dotted'>.......................................................................................................................................................... </span></span><!--[if supportFields]><span
8755 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732412
8756 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8757 style='mso-no-proof:yes'>66<!--[if gte mso 9]><xml>
8758  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400310032000000</w:data>
8759 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8760 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8761 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8762 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8763 mso-no-proof:yes'><o:p></o:p></span></p>
8764
8765 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8766 style='mso-no-proof:yes'>-aln<span style='mso-tab-count:1 dotted'>.................................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
8767 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732413
8768 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8769 style='mso-no-proof:yes'>66<!--[if gte mso 9]><xml>
8770  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400310033000000</w:data>
8771 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8772 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8773 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8774 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8775 mso-no-proof:yes'><o:p></o:p></span></p>
8776
8777 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8778 style='mso-no-proof:yes'>-n_excluded_nb<span style='mso-tab-count:1 dotted'>......................................................................................................................................................................................... </span></span><!--[if supportFields]><span
8779 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732414
8780 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8781 style='mso-no-proof:yes'>66<!--[if gte mso 9]><xml>
8782  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400310034000000</w:data>
8783 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8784 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8785 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8786 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8787 mso-no-proof:yes'><o:p></o:p></span></p>
8788
8789 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8790 style='mso-no-proof:yes'>-maximum_distance<span style='mso-tab-count:1 dotted'>................................................................................................................................................................................ </span></span><!--[if supportFields]><span
8791 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732415
8792 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8793 style='mso-no-proof:yes'>66<!--[if gte mso 9]><xml>
8794  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400310035000000</w:data>
8795 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8796 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8797 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8798 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8799 mso-no-proof:yes'><o:p></o:p></span></p>
8800
8801 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8802 style='mso-no-proof:yes'>-similarity_threshold<span style='mso-tab-count:1 dotted'>.............................................................................................................................................................................. </span></span><!--[if supportFields]><span
8803 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732416
8804 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8805 style='mso-no-proof:yes'>66<!--[if gte mso 9]><xml>
8806  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400310036000000</w:data>
8807 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8808 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8809 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8810 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8811 mso-no-proof:yes'><o:p></o:p></span></p>
8812
8813 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8814 style='mso-no-proof:yes'>-local_mode<span style='mso-tab-count:1 dotted'>................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
8815 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732417
8816 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8817 style='mso-no-proof:yes'>67<!--[if gte mso 9]><xml>
8818  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400310037000000</w:data>
8819 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8820 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8821 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8822 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8823 mso-no-proof:yes'><o:p></o:p></span></p>
8824
8825 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8826 style='mso-no-proof:yes'>-filter<span style='mso-tab-count:1 dotted'>............................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
8827 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732418
8828 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8829 style='mso-no-proof:yes'>67<!--[if gte mso 9]><xml>
8830  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400310038000000</w:data>
8831 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8832 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8833 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8834 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8835 mso-no-proof:yes'><o:p></o:p></span></p>
8836
8837 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8838 style='mso-no-proof:yes'>-print_rapdb [Unsupported]<span style='mso-tab-count:
8839 1 dotted'>.............................................................................................................................................................. </span></span><!--[if supportFields]><span
8840 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732419
8841 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8842 style='mso-no-proof:yes'>67<!--[if gte mso 9]><xml>
8843  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400310039000000</w:data>
8844 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8845 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8846 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8847 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8848 mso-no-proof:yes'><o:p></o:p></span></p>
8849
8850 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8851 style='mso-no-proof:yes'>-outfile [Same as T-Coffee]<span style='mso-tab-count:
8852 1 dotted'>.................................................................................................................................................................. </span></span><!--[if supportFields]><span
8853 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732420
8854 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8855 style='mso-no-proof:yes'>67<!--[if gte mso 9]><xml>
8856  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400320030000000</w:data>
8857 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8858 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8859 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8860 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8861 mso-no-proof:yes'><o:p></o:p></span></p>
8862
8863 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
8864 style='mso-no-proof:yes'>-color_mode<span style='mso-tab-count:1 dotted'>................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
8865 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732421
8866 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8867 style='mso-no-proof:yes'>67<!--[if gte mso 9]><xml>
8868  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400320031000000</w:data>
8869 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8870 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8871 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8872 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8873 mso-no-proof:yes'><o:p></o:p></span></p>
8874
8875 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
8876 style='mso-no-proof:yes'>Environment Variables<span style='mso-tab-count:1 dotted'>......................................................................................................................................................................... </span></span><!--[if supportFields]><span
8877 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732422
8878 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8879 style='mso-no-proof:yes'>68<!--[if gte mso 9]><xml>
8880  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400320032000000</w:data>
8881 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8882 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8883 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8884 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8885 mso-no-proof:yes'><o:p></o:p></span></p>
8886
8887 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
8888 style='mso-no-proof:yes'>Output of the .dnd file.<span style='mso-tab-count:
8889 1 dotted'>............................................................................................................................................................................ </span></span><!--[if supportFields]><span
8890 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732423
8891 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8892 style='mso-no-proof:yes'>69<!--[if gte mso 9]><xml>
8893  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400320033000000</w:data>
8894 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8895 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8896 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8897 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8898 mso-no-proof:yes'><o:p></o:p></span></p>
8899
8900 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
8901 style='mso-no-proof:yes'>Permissions<span style='mso-tab-count:1 dotted'>.................................................................................................................................................................................................. </span></span><!--[if supportFields]><span
8902 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732424
8903 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8904 style='mso-no-proof:yes'>69<!--[if gte mso 9]><xml>
8905  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400320034000000</w:data>
8906 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8907 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8908 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8909 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8910 mso-no-proof:yes'><o:p></o:p></span></p>
8911
8912 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
8913 style='mso-no-proof:yes'>Other Programs<span style='mso-tab-count:1 dotted'>......................................................................................................................................................................................... </span></span><!--[if supportFields]><span
8914 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732425
8915 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8916 style='mso-no-proof:yes'>69<!--[if gte mso 9]><xml>
8917  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400320035000000</w:data>
8918 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8919 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8920 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8921 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8922 mso-no-proof:yes'><o:p></o:p></span></p>
8923
8924 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
8925 style='mso-no-proof:yes'>Parameter files<span style='mso-tab-count:1 dotted'>............................................................................................................................ </span></span><!--[if supportFields]><span
8926 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732426
8927 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8928 style='mso-no-proof:yes'>70<!--[if gte mso 9]><xml>
8929  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400320036000000</w:data>
8930 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8931 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8932 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8933 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8934 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
8935
8936 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
8937 style='mso-no-proof:yes'>Sequence Name Handling<span style='mso-tab-count:1 dotted'>........................................................................................................... </span></span><!--[if supportFields]><span
8938 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732427
8939 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8940 style='mso-no-proof:yes'>70<!--[if gte mso 9]><xml>
8941  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400320037000000</w:data>
8942 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8943 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8944 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8945 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8946 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
8947
8948 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
8949 style='mso-no-proof:yes'>Automatic Format Recognition<span style='mso-tab-count:
8950 1 dotted'>................................................................................................... </span></span><!--[if supportFields]><span
8951 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732428
8952 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8953 style='mso-no-proof:yes'>71<!--[if gte mso 9]><xml>
8954  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400320038000000</w:data>
8955 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8956 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8957 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8958 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8959 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
8960
8961 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
8962 style='mso-no-proof:yes'>Structures<span style='mso-tab-count:1 dotted'>.................................................................................................................................... </span></span><!--[if supportFields]><span
8963 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732429
8964 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8965 style='mso-no-proof:yes'>71<!--[if gte mso 9]><xml>
8966  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400320039000000</w:data>
8967 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8968 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8969 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8970 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8971 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
8972
8973 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
8974 style='mso-no-proof:yes'>RNA Structures<span style='mso-tab-count:1 dotted'>............................................................................................................................. </span></span><!--[if supportFields]><span
8975 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732430
8976 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8977 style='mso-no-proof:yes'>71<!--[if gte mso 9]><xml>
8978  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400330030000000</w:data>
8979 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8980 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8981 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8982 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8983 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
8984
8985 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
8986 style='mso-no-proof:yes'>Sequences<span style='mso-tab-count:1 dotted'>.................................................................................................................................... </span></span><!--[if supportFields]><span
8987 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732431
8988 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
8989 style='mso-no-proof:yes'>71<!--[if gte mso 9]><xml>
8990  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400330031000000</w:data>
8991 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
8992 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
8993 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
8994 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
8995 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
8996
8997 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
8998 style='mso-no-proof:yes'>Alignments<span style='mso-tab-count:1 dotted'>................................................................................................................................... </span></span><!--[if supportFields]><span
8999 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732432
9000 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
9001 style='mso-no-proof:yes'>71<!--[if gte mso 9]><xml>
9002  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400330032000000</w:data>
9003 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
9004 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
9005 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
9006 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
9007 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
9008
9009 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
9010 style='mso-no-proof:yes'>Libraries<span style='mso-tab-count:1 dotted'>....................................................................................................................................... </span></span><!--[if supportFields]><span
9011 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732433
9012 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
9013 style='mso-no-proof:yes'>72<!--[if gte mso 9]><xml>
9014  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400330033000000</w:data>
9015 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
9016 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
9017 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
9018 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
9019 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
9020
9021 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
9022 style='mso-no-proof:yes'>T-COFFEE_LIB_FORMAT_01<span style='mso-tab-count:1 dotted'>............................................................................................................................................................. </span></span><!--[if supportFields]><span
9023 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732434
9024 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
9025 style='mso-no-proof:yes'>72<!--[if gte mso 9]><xml>
9026  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400330034000000</w:data>
9027 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
9028 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
9029 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
9030 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
9031 mso-no-proof:yes'><o:p></o:p></span></p>
9032
9033 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
9034 style='mso-no-proof:yes'>T-COFFEE_LIB_FORMAT_02<span style='mso-tab-count:1 dotted'>............................................................................................................................................................. </span></span><!--[if supportFields]><span
9035 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732435
9036 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
9037 style='mso-no-proof:yes'>73<!--[if gte mso 9]><xml>
9038  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400330035000000</w:data>
9039 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
9040 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
9041 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
9042 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
9043 mso-no-proof:yes'><o:p></o:p></span></p>
9044
9045 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
9046 style='mso-no-proof:yes'>Library List<span style='mso-tab-count:1 dotted'>................................................................................................................................... </span></span><!--[if supportFields]><span
9047 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732436
9048 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
9049 style='mso-no-proof:yes'>73<!--[if gte mso 9]><xml>
9050  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400330036000000</w:data>
9051 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
9052 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
9053 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
9054 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
9055 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
9056
9057 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
9058 style='mso-no-proof:yes'>Substitution matrices.<span style='mso-tab-count:1 dotted'>................................................................................................................. </span></span><!--[if supportFields]><span
9059 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732437
9060 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
9061 style='mso-no-proof:yes'>73<!--[if gte mso 9]><xml>
9062  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400330037000000</w:data>
9063 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
9064 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
9065 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
9066 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
9067 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
9068
9069 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
9070 style='mso-no-proof:yes'>ClustalW Style [Deprecated]<span style='mso-tab-count:
9071 1 dotted'>.............................................................................................................................................................. </span></span><!--[if supportFields]><span
9072 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732438
9073 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
9074 style='mso-no-proof:yes'>73<!--[if gte mso 9]><xml>
9075  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400330038000000</w:data>
9076 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
9077 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
9078 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
9079 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
9080 mso-no-proof:yes'><o:p></o:p></span></p>
9081
9082 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
9083 style='mso-no-proof:yes'>BLAST Format [Recommended]<span style='mso-tab-count:
9084 1 dotted'>..................................................................................................................................................... </span></span><!--[if supportFields]><span
9085 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732439
9086 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
9087 style='mso-no-proof:yes'>74<!--[if gte mso 9]><xml>
9088  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400330039000000</w:data>
9089 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
9090 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
9091 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
9092 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
9093 mso-no-proof:yes'><o:p></o:p></span></p>
9094
9095 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
9096 style='mso-no-proof:yes'>Sequences Weights<span style='mso-tab-count:1 dotted'>..................................................................................................................... </span></span><!--[if supportFields]><span
9097 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732440
9098 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
9099 style='mso-no-proof:yes'>74<!--[if gte mso 9]><xml>
9100  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400340030000000</w:data>
9101 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
9102 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
9103 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
9104 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
9105 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
9106
9107 <p class=MsoToc2 style='tab-stops:right dotted 474.85pt'><span
9108 style='mso-no-proof:yes'>Development<span style='mso-tab-count:1 dotted'>............................................................................................................................... </span></span><!--[if supportFields]><span
9109 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732441
9110 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
9111 style='mso-no-proof:yes'>76<!--[if gte mso 9]><xml>
9112  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400340031000000</w:data>
9113 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
9114 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
9115 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
9116 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
9117 font-weight:normal;mso-no-proof:yes'><o:p></o:p></span></p>
9118
9119 <p class=MsoToc4 style='tab-stops:right dotted 474.85pt'><span
9120 style='mso-no-proof:yes'>profile2list<span style='mso-tab-count:1 dotted'>................................................................................................................................................................................................... </span></span><!--[if supportFields]><span
9121 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732442
9122 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
9123 style='mso-no-proof:yes'>76<!--[if gte mso 9]><xml>
9124  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400340032000000</w:data>
9125 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
9126 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
9127 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
9128 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
9129 mso-no-proof:yes'><o:p></o:p></span></p>
9130
9131 <p class=MsoToc3 style='tab-stops:right dotted 474.85pt'><span
9132 style='mso-no-proof:yes'>Command Line List<span style='mso-tab-count:1 dotted'>.................................................................................................................................................................................. </span></span><!--[if supportFields]><span
9133 style='mso-no-proof:yes'><span style='mso-element:field-begin'></span> PAGEREF _Toc151732443
9134 \h <span style='mso-element:field-separator'></span></span><![endif]--><span
9135 style='mso-no-proof:yes'>76<!--[if gte mso 9]><xml>
9136  <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100350031003700330032003400340033000000</w:data>
9137 </xml><![endif]--></span><!--[if supportFields]><span style='mso-no-proof:yes'><span
9138 style='mso-element:field-end'></span></span><![endif]--><span style='font-size:
9139 12.0pt;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:minor-fareast;
9140 mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:minor-bidi;
9141 mso-no-proof:yes'><o:p></o:p></span></p>
9142
9143 <p class=FAQ><!--[if supportFields]><span lang=EN-GB><span style='mso-element:
9144 field-end'></span></span><![endif]--></p>
9145
9146 </div>
9147
9148 <b style='mso-bidi-font-weight:normal'><span lang=EN-GB style='font-size:11.0pt;
9149 mso-bidi-font-size:14.0pt;font-family:"Comic Sans MS";mso-fareast-font-family:
9150 "Times New Roman";mso-bidi-font-family:"Courier New";mso-ansi-language:EN-GB;
9151 mso-fareast-language:EN-US'><br clear=ALL style='page-break-before:auto;
9152 mso-break-type:section-break'>
9153 </span></b>
9154
9155 <div class=Section4>
9156
9157 <div style='mso-element:para-border-div;border:solid windowtext 3.0pt;
9158 padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#CCCCCC;margin-left:0cm;margin-right:
9159 4.25pt'>
9160
9161 <p class=ChapterTitle><a name="_Toc101065185"></a><a name="_Toc102494650"><span
9162 style='mso-bookmark:_Toc101065185'>License and Terms of Use</span></a></p>
9163
9164 </div>
9165
9166 <p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>
9167
9168 <h2><a name="_Toc102494275"></a><a name="_Toc102494651"></a><a
9169 name="_Toc151732187"><span style='mso-bookmark:_Toc102494651'><span
9170 style='mso-bookmark:_Toc102494275'>T-Coffee is distributed under the Gnu Public
9171 License</span></span></a></h2>
9172
9173 <p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>
9174
9175 <p class=MyNormal><span lang=AF>Please make sure you have agreed with the terms
9176 of the license attached to the package before using the T-Coffee package or its
9177 documentation. T-Coffee is a freeware open source distributed under a GPL
9178 license. This means that there are very little restrictions to its use, either
9179 in an academic or a non academic environment.</span></p>
9180
9181 <h2><a name="_Toc102494276"></a><a name="_Toc102494652"></a><a
9182 name="_Toc151732188"><span style='mso-bookmark:_Toc102494652'><span
9183 style='mso-bookmark:_Toc102494276'>T-Coffee code can be re-used freely</span></span></a></h2>
9184
9185 <p class=MyNormal><span lang=AF>Our philosophy is that code is meant to be
9186 re-used, including ours. No permission is needed for the cut and paste of a few
9187 functions, although we are always happy to receive pieces of improved code.</span></p>
9188
9189 <h2><a name="_Toc101065186"></a><a name="_Toc102494653"></a><a
9190 name="_Toc151732189"><span style='mso-bookmark:_Toc102494653'><span
9191 style='mso-bookmark:_Toc101065186'>T-Coffee can be incorporated in most
9192 pipelines: Plug-in/Plug-out\85</span></span></a><span style='mso-bookmark:_Toc102494653'><span
9193 style='mso-bookmark:_Toc101065186'></span></span></h2>
9194
9195 <p class=MyNormal><span style='mso-bookmark:_Toc102494653'><span
9196 style='mso-bookmark:_Toc101065186'><span lang=AF>Our philosophy is to insure
9197 that as many methods as possible can be used as plug-ins within T-Coffee.
9198 Likewise, we will give as much support as possible to anyone wishing to turn
9199 T-Coffee into a plug-in for another method. For more details on how to do this,
9200 see the plug-in and the plug-out sections of the Tutorial Manual.</span></span></span></p>
9201
9202 <p class=MyNormal><span style='mso-bookmark:_Toc102494653'><span
9203 style='mso-bookmark:_Toc101065186'><span lang=AF>Again, you do not need our
9204 permission to either use T-Coffee (or your method as a plug-in/out) but if you
9205 let us know, we will insure the stability of T-Coffee within your system
9206 through future releases. </span></span></span></p>
9207
9208 <p class=MyNormal><span style='mso-bookmark:_Toc102494653'><span
9209 style='mso-bookmark:_Toc101065186'><span lang=AF>The current license only
9210 allows for the incorporation of T-Coffee in non-commercial pipelines (i.e.
9211 where you do not sell the pipeline, or access to it). If your pipeline is
9212 commercial, please get in touch with us. </span></span></span></p>
9213
9214 <p class=MyNormal><span style='mso-bookmark:_Toc102494653'><span
9215 style='mso-bookmark:_Toc101065186'><span lang=AF><o:p>&nbsp;</o:p></span></span></span></p>
9216
9217 <div style='mso-element:para-border-div;border:solid windowtext 3.0pt;
9218 padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#CCCCCC;margin-left:0cm;margin-right:
9219 4.25pt'>
9220
9221 <p class=ChapterTitle><span style='mso-bookmark:_Toc102494653'><span
9222 style='mso-bookmark:_Toc101065186'>Addresses and Contacts</span></span><span
9223 style='mso-bookmark:_Toc101065186'></span><span style='mso-bookmark:_Toc102494653'></span><span
9224 style='font-size:98.0pt;mso-bidi-font-size:48.0pt'><o:p></o:p></span></p>
9225
9226 </div>
9227
9228 <h2><a name="_Toc151732190">Contributors</a></h2>
9229
9230 <p class=MsoBodyText>T-coffee is developed, maintained, monitored, used and
9231 debugged by a dedicated team that include or have included:</p>
9232
9233 <p class=MsoBodyText><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Cédric
9234 Notredame, Paolo di Tomasso, Jean-François Taly, Cedrik Magis, Fabrice
9235 Armougom, Des Higgins, Sebastien Moretti, Orla O\92Sullivan. Eamon O\92Toole,
9236 Olivier Poirot, Karsten Suhre, Iain Wallace, Andreas Wilm</p>
9237
9238 <h2><a name="_Toc151732191">Addresses</a></h2>
9239
9240 <p class=MyNormal><span lang=AF>We are always very eager to get some user
9241 feedback. Please do not hesitate to drop us a line<span style="mso-spacerun:
9242 yes">&nbsp; </span>at: <a href="mailto:cedric.notredame@europe.com"><span
9243 lang=EN-US style='mso-ansi-language:EN-US'>cedric.notredame@europe.com</span></a>
9244 The latest updates of T-Coffee are always available<span style="mso-spacerun:
9245 yes">&nbsp; </span>on: www.tcoffee.org . On this address you will also find a
9246 link to some of the online T-Coffee servers, including Tcoffee@igs </span></p>
9247
9248 <p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>
9249
9250 <p class=MyNormal><span lang=AF>T-Coffee can be used to automatically check if
9251 an updated version is available, however the program will not update
9252 automatically, as this can cause endless reproducibility problems.</span></p>
9253
9254 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
9255 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
9256 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
9257 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
9258
9259 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
9260 &#8211;update</p>
9261
9262 </div>
9263
9264 <p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>
9265
9266 <div style='mso-element:para-border-div;border:solid windowtext 3.0pt;
9267 padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#CCCCCC;margin-left:0cm;margin-right:
9268 4.25pt'>
9269
9270 <p class=ChapterTitle><a name="_Toc101065187"></a><a name="_Toc102494654"><span
9271 style='mso-bookmark:_Toc101065187'>Citations</span></a></p>
9272
9273 </div>
9274
9275 <p class=MyNormal><span lang=AF>It is important that you cite T-Coffee when you
9276 use it. Citing us is (almost) like giving us money: it helps us convincing our
9277 institutions that what we do is useful and that they should keep paying our
9278 salaries and deliver Donuts to our offices from time to time (Not that they
9279 ever did it, but it would be nice anyway). </span></p>
9280
9281 <p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>
9282
9283 <p class=MyNormal><span lang=AF>Cite the server if you used it, otherwise, cite
9284 the original paper from 2000 (No, it was never named &quot;T-Coffee
9285 2000&quot;).</span></p>
9286
9287 <table class=MsoNormalTable border=0 cellspacing=4 cellpadding=0 width="81%"
9288  style='width:81.78%;mso-cellspacing:3.7pt;mso-padding-alt:0cm 0cm 0cm 0cm'>
9289  <tr style='mso-yfti-irow:0;mso-yfti-firstrow:yes'>
9290   <td width="53%" style='width:53.48%;padding:0cm 0cm 0cm 0cm'>
9291   <p class=MyNormalJustified><a
9292   href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=pubmed&amp;dopt=Abstract&amp;list_uids=10964570">Notredame
9293   C, Higgins DG, Heringa J.</a><span style='mso-bidi-font-size:12.0pt;
9294   color:black'><o:p></o:p></span></p>
9295   </td>
9296   <td width="43%" nowrap valign=top style='width:43.3%;padding:0cm 0cm 0cm 0cm'>
9297   <p class=MyNormalJustified><a
9298   href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Display&amp;dopt=pubmed_pubmed&amp;from_uid=10964570"><span
9299   style='mso-bidi-font-size:9.0pt;color:#336699'>Related Articles,</span></a> <!--[if gte vml 1]><v:shapetype
9300    id="_x0000_t75" coordsize="21600,21600" o:spt="75" o:preferrelative="t"
9301    path="m@4@5l@4@11@9@11@9@5xe" filled="f" stroked="f">
9302    <v:stroke joinstyle="miter"/>
9303    <v:formulas>
9304     <v:f eqn="if lineDrawn pixelLineWidth 0"/>
9305     <v:f eqn="sum @0 1 0"/>
9306     <v:f eqn="sum 0 0 @1"/>
9307     <v:f eqn="prod @2 1 2"/>
9308     <v:f eqn="prod @3 21600 pixelWidth"/>
9309     <v:f eqn="prod @3 21600 pixelHeight"/>
9310     <v:f eqn="sum @0 0 1"/>
9311     <v:f eqn="prod @6 1 2"/>
9312     <v:f eqn="prod @7 21600 pixelWidth"/>
9313     <v:f eqn="sum @8 21600 0"/>
9314     <v:f eqn="prod @7 21600 pixelHeight"/>
9315     <v:f eqn="sum @10 21600 0"/>
9316    </v:formulas>
9317    <v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/>
9318    <o:lock v:ext="edit" aspectratio="t"/>
9319   </v:shapetype><v:shape id="_x0000_i1025" type="#_x0000_t75" style='width:15pt;
9320    height:11pt;visibility:hidden' print="f">
9321    <v:imagedata src="t_coffee_technical_files/image001.png" o:title="&#37008;&#28494;&#28018;&#27745;&#36864;&#24902;x0&#37008;1"/>
9322    <o:lock v:ext="edit" grouping="t"/>
9323   </v:shape><![endif]--><!--[if gte vml 1]><v:shape id="_x0000_i1026" type="#_x0000_t75"
9324    style='width:15pt;height:11pt;visibility:hidden' print="f">
9325    <v:imagedata src="t_coffee_technical_files/image002.png" o:title="&#37008;&#28494;&#28018;&#27745;&#36864;&#24902;x0&#37008;1"/>
9326    <o:lock v:ext="edit" grouping="t"/>
9327   </v:shape><![endif]--><span style='mso-field-code:"HYPERLINK \0022javascript\:PopUpMenu2_Set\(Menu10964570\)\;\0022 \\t \0022_self\0022"'><span
9328   class=MsoHyperlink><span style='mso-bidi-font-size:9.0pt;color:#336699'>Links</span></span></span>
9329   <span style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>
9330   </td>
9331  </tr>
9332  <tr style='mso-yfti-irow:1;mso-yfti-lastrow:yes'>
9333   <td width="97%" colspan=2 style='width:97.86%;padding:0cm 0cm 0cm 0cm'>
9334   <p class=MyNormalJustified>T-Coffee: A novel method for fast and accurate
9335   multiple sequence alignment.<br>
9336   J Mol Biol. 2000 Sep 8;302(1):205-17. <br>
9337   PMID: 10964570 [PubMed - indexed for MEDLINE]<span style='mso-bidi-font-size:
9338   12.0pt;color:black'><o:p></o:p></span></p>
9339   </td>
9340  </tr>
9341 </table>
9342
9343 <p class=MyNormal><span lang=AF>Other useful publications include:</span></p>
9344
9345 <h2><a name="_Toc101065188"></a><a name="_Toc102494277"></a><a
9346 name="_Toc102494655"></a><a name="_Toc151732192"><span style='mso-bookmark:
9347 _Toc102494655'><span style='mso-bookmark:_Toc102494277'><span style='mso-bookmark:
9348 _Toc101065188'>T-Coffee</span></span></span></a></h2>
9349
9350 <table class=MsoNormalTable border=0 cellspacing=4 cellpadding=0 width="81%"
9351  style='width:81.78%;mso-cellspacing:3.7pt;mso-padding-alt:0cm 0cm 0cm 0cm'>
9352  <tr style='mso-yfti-irow:0;mso-yfti-firstrow:yes'>
9353   <td width="53%" style='width:53.48%;padding:0cm 0cm 0cm 0cm'>
9354   <p class=MyNormalJustified><a
9355   href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=pubmed&amp;dopt=Abstract&amp;list_uids=15215460">Claude
9356   JB, Suhre K, Notredame C, Claverie JM, Abergel C.</a><span style='mso-bidi-font-size:
9357   12.0pt;color:black'><o:p></o:p></span></p>
9358   </td>
9359   <td width="43%" nowrap valign=top style='width:43.3%;padding:0cm 0cm 0cm 0cm'>
9360   <p class=MyNormalJustified><a
9361   href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Display&amp;dopt=pubmed_pubmed&amp;from_uid=15215460"><span
9362   style='mso-bidi-font-size:9.0pt;color:#336699'>Related Articles,</span></a> <!--[if gte vml 1]><v:shape
9363    id="_x0000_i1027" type="#_x0000_t75" style='width:15pt;height:11pt;
9364    visibility:hidden' print="f">
9365    <v:imagedata src="t_coffee_technical_files/image003.png" o:title="&#37008;&#28494;&#28018;&#27745;&#36864;&#24902;x0&#37008;1"/>
9366    <o:lock v:ext="edit" grouping="t"/>
9367   </v:shape><![endif]--><!--[if gte vml 1]><v:shape id="_x0000_i1028" type="#_x0000_t75"
9368    style='width:15pt;height:11pt;visibility:hidden' print="f">
9369    <v:imagedata src="t_coffee_technical_files/image004.png" o:title="&#37008;&#28494;&#28018;&#27745;&#36864;&#24902;x0&#37008;1"/>
9370    <o:lock v:ext="edit" grouping="t"/>
9371   </v:shape><![endif]--><span style='mso-field-code:"HYPERLINK \0022javascript\:PopUpMenu2_Set\(Menu15215460\)\;\0022 \\t \0022_self\0022"'><span
9372   class=MsoHyperlink><span style='mso-bidi-font-size:9.0pt;color:#336699'>Links</span></span></span>
9373   <span style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>
9374   </td>
9375  </tr>
9376  <tr style='mso-yfti-irow:1;mso-yfti-lastrow:yes'>
9377   <td width="97%" colspan=2 style='width:97.86%;padding:0cm 0cm 0cm 0cm'>
9378   <p class=MyNormalJustified>CaspR: a web server for automated molecular
9379   replacement using homology modelling.<br>
9380   Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W606-9. <br>
9381   PMID: 15215460 [PubMed - indexed for MEDLINE]<span style='mso-bidi-font-size:
9382   12.0pt;color:black'><o:p></o:p></span></p>
9383   </td>
9384  </tr>
9385 </table>
9386
9387 <p class=MyNormalJustified><o:p>&nbsp;</o:p></p>
9388
9389 <table class=MsoNormalTable border=0 cellspacing=4 cellpadding=0 width="81%"
9390  style='width:81.98%;mso-cellspacing:3.7pt;mso-padding-alt:0cm 0cm 0cm 0cm'>
9391  <tr style='mso-yfti-irow:0;mso-yfti-firstrow:yes'>
9392   <td width="53%" style='width:53.5%;padding:0cm 0cm 0cm 0cm'>
9393   <p class=MyNormalJustified><a
9394   href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=pubmed&amp;dopt=Abstract&amp;list_uids=15215345">Poirot
9395   O, Suhre K, Abergel C, O'Toole E, Notredame C.</a><span style='mso-bidi-font-size:
9396   12.0pt;color:black'><o:p></o:p></span></p>
9397   </td>
9398   <td nowrap valign=top style='padding:0cm 0cm 0cm 0cm'>
9399   <p class=MyNormalJustified><a
9400   href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Display&amp;dopt=pubmed_pubmed&amp;from_uid=15215345"><span
9401   style='mso-bidi-font-size:9.0pt;color:#336699'>Related Articles,</span></a> <!--[if gte vml 1]><v:shape
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9403    visibility:hidden' print="f">
9404    <v:imagedata src="t_coffee_technical_files/image005.png" o:title="&#37008;&#28494;&#28018;&#27745;&#36864;&#24902;x0&#37008;1"/>
9405    <o:lock v:ext="edit" grouping="t"/>
9406   </v:shape><![endif]--><span style='mso-field-code:"HYPERLINK \0022javascript\:PopUpMenu2_Set\(Menu15215345\)\;\0022 \\t \0022_self\0022"'><span
9407   class=MsoHyperlink><span style='mso-bidi-font-size:9.0pt;color:#336699'>Links</span></span></span>
9408   <span style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>
9409   </td>
9410  </tr>
9411  <tr style='mso-yfti-irow:1;mso-yfti-lastrow:yes'>
9412   <td colspan=2 style='padding:0cm 0cm 0cm 0cm'>
9413   <p class=MyNormalJustified>3DCoffee@igs: a web server for combining sequences
9414   and structures into a multiple sequence alignment.<br>
9415   Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W37-40. <br>
9416   PMID: 15215345 [PubMed - indexed for MEDLINE]<span style='mso-bidi-font-size:
9417   12.0pt;color:black'><o:p></o:p></span></p>
9418   </td>
9419  </tr>
9420 </table>
9421
9422 <p class=MyNormalJustified><o:p>&nbsp;</o:p></p>
9423
9424 <table class=MsoNormalTable border=0 cellspacing=4 cellpadding=0 width="81%"
9425  style='width:81.98%;mso-cellspacing:3.7pt;mso-padding-alt:0cm 0cm 0cm 0cm'>
9426  <tr style='mso-yfti-irow:0;mso-yfti-firstrow:yes'>
9427   <td width="53%" style='width:53.5%;padding:0cm 0cm 0cm 0cm'>
9428   <p class=MyNormalJustified><a
9429   href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=pubmed&amp;dopt=Abstract&amp;list_uids=15201059">O'Sullivan
9430   O, Suhre K, Abergel C, Higgins DG, Notredame C.</a><span style='mso-bidi-font-size:
9431   12.0pt;color:black'><o:p></o:p></span></p>
9432   </td>
9433   <td nowrap valign=top style='padding:0cm 0cm 0cm 0cm'>
9434   <p class=MyNormalJustified><a
9435   href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Display&amp;dopt=pubmed_pubmed&amp;from_uid=15201059"><span
9436   style='mso-bidi-font-size:9.0pt;color:#336699'>Related Articles,</span></a> <!--[if gte vml 1]><v:shape
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9438    visibility:hidden' print="f">
9439    <v:imagedata src="t_coffee_technical_files/image006.png" o:title="&#37008;&#28494;&#28018;&#27745;&#36864;&#24902;x0&#37008;1"/>
9440    <o:lock v:ext="edit" grouping="t"/>
9441   </v:shape><![endif]--><span style='mso-field-code:"HYPERLINK \0022javascript\:PopUpMenu2_Set\(Menu15201059\)\;\0022 \\t \0022_self\0022"'><span
9442   class=MsoHyperlink><span style='mso-bidi-font-size:9.0pt;color:#336699'>Links</span></span></span>
9443   <span style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>
9444   </td>
9445  </tr>
9446  <tr style='mso-yfti-irow:1;mso-yfti-lastrow:yes'>
9447   <td colspan=2 style='padding:0cm 0cm 0cm 0cm'>
9448   <p class=MyNormalJustified>3DCoffee: combining protein sequences and
9449   structures within multiple sequence alignments.<br>
9450   J Mol Biol. 2004 Jul 2;340(2):385-95. <br>
9451   PMID: 15201059 [PubMed - indexed for MEDLINE]<span style='mso-bidi-font-size:
9452   12.0pt;color:black'><o:p></o:p></span></p>
9453   </td>
9454  </tr>
9455 </table>
9456
9457 <p class=MyNormalJustified><o:p>&nbsp;</o:p></p>
9458
9459 <table class=MsoNormalTable border=0 cellspacing=4 cellpadding=0 width="81%"
9460  style='width:81.98%;mso-cellspacing:3.7pt;mso-padding-alt:0cm 0cm 0cm 0cm'>
9461  <tr style='mso-yfti-irow:0;mso-yfti-firstrow:yes'>
9462   <td width="53%" style='width:53.5%;padding:0cm 0cm 0cm 0cm'>
9463   <p class=MyNormalJustified><a
9464   href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=pubmed&amp;dopt=Abstract&amp;list_uids=12824354">Poirot
9465   O, O'Toole E, Notredame C.</a><span style='mso-bidi-font-size:12.0pt;
9466   color:black'><o:p></o:p></span></p>
9467   </td>
9468   <td nowrap valign=top style='padding:0cm 0cm 0cm 0cm'>
9469   <p class=MyNormalJustified><a
9470   href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Display&amp;dopt=pubmed_pubmed&amp;from_uid=12824354"><span
9471   style='mso-bidi-font-size:9.0pt;color:#336699'>Related Articles,</span></a> <!--[if gte vml 1]><v:shape
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9473    visibility:hidden' print="f">
9474    <v:imagedata src="t_coffee_technical_files/image007.png" o:title="&#37008;&#28494;&#28018;&#27745;&#36864;&#24902;x0&#37008;1"/>
9475    <o:lock v:ext="edit" grouping="t"/>
9476   </v:shape><![endif]--><span style='mso-field-code:"HYPERLINK \0022javascript\:PopUpMenu2_Set\(Menu12824354\)\;\0022 \\t \0022_self\0022"'><span
9477   class=MsoHyperlink><span style='mso-bidi-font-size:9.0pt;color:#336699'>Links</span></span></span>
9478   <span style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>
9479   </td>
9480  </tr>
9481  <tr style='mso-yfti-irow:1;mso-yfti-lastrow:yes'>
9482   <td colspan=2 style='padding:0cm 0cm 0cm 0cm'>
9483   <p class=MyNormalJustified>Tcoffee@igs: A web server for computing,
9484   evaluating and combining multiple sequence alignments.<br>
9485   Nucleic Acids Res. 2003 Jul 1;31(13):3503-6. <br>
9486   PMID: 12824354 [PubMed - indexed for MEDLINE]<span style='mso-bidi-font-size:
9487   12.0pt;color:black'><o:p></o:p></span></p>
9488   </td>
9489  </tr>
9490 </table>
9491
9492 <p class=MyNormalJustified><o:p>&nbsp;</o:p></p>
9493
9494 <table class=MsoNormalTable border=0 cellspacing=4 cellpadding=0 width="81%"
9495  style='width:81.98%;mso-cellspacing:3.7pt;mso-padding-alt:0cm 0cm 0cm 0cm'>
9496  <tr style='mso-yfti-irow:0;mso-yfti-firstrow:yes'>
9497   <td width="53%" style='width:53.5%;padding:0cm 0cm 0cm 0cm'>
9498   <p class=MyNormalJustified><a
9499   href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=pubmed&amp;dopt=Abstract&amp;list_uids=11301309">Notredame
9500   C.</a><span style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>
9501   </td>
9502   <td nowrap valign=top style='padding:0cm 0cm 0cm 0cm'>
9503   <p class=MyNormalJustified><a
9504   href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Display&amp;dopt=pubmed_pubmed&amp;from_uid=11301309"><span
9505   style='mso-bidi-font-size:9.0pt;color:#336699'>Related Articles,</span></a> <!--[if gte vml 1]><v:shape
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9507    visibility:hidden' print="f">
9508    <v:imagedata src="t_coffee_technical_files/image008.png" o:title="&#37008;&#28494;&#28018;&#27745;&#36864;&#24902;x0&#37008;1"/>
9509    <o:lock v:ext="edit" grouping="t"/>
9510   </v:shape><![endif]--><span style='mso-field-code:"HYPERLINK \0022javascript\:PopUpMenu2_Set\(Menu11301309\)\;\0022 \\t \0022_self\0022"'><span
9511   class=MsoHyperlink><span style='mso-bidi-font-size:9.0pt;color:#336699'>Links</span></span></span>
9512   <span style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>
9513   </td>
9514  </tr>
9515  <tr style='mso-yfti-irow:1;mso-yfti-lastrow:yes'>
9516   <td colspan=2 style='padding:0cm 0cm 0cm 0cm'>
9517   <p class=MyNormalJustified>Mocca: semi-automatic method for domain hunting.<br>
9518   Bioinformatics. 2001 Apr;17(4):373-4. <br>
9519   PMID: 11301309 [PubMed - indexed for MEDLINE]<span style='mso-bidi-font-size:
9520   12.0pt;color:black'><o:p></o:p></span></p>
9521   </td>
9522  </tr>
9523 </table>
9524
9525 <p class=MyNormalJustified><o:p>&nbsp;</o:p></p>
9526
9527 <table class=MsoNormalTable border=0 cellspacing=4 cellpadding=0 width="81%"
9528  style='width:81.98%;mso-cellspacing:3.7pt;mso-padding-alt:0cm 0cm 0cm 0cm'>
9529  <tr style='mso-yfti-irow:0;mso-yfti-firstrow:yes'>
9530   <td width="53%" style='width:53.5%;padding:0cm 0cm 0cm 0cm'>
9531   <p class=MyNormalJustified><a
9532   href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=pubmed&amp;dopt=Abstract&amp;list_uids=10964570">Notredame
9533   C, Higgins DG, Heringa J.</a><span style='mso-bidi-font-size:12.0pt;
9534   color:black'><o:p></o:p></span></p>
9535   </td>
9536   <td nowrap valign=top style='padding:0cm 0cm 0cm 0cm'>
9537   <p class=MyNormalJustified><a
9538   href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Display&amp;dopt=pubmed_pubmed&amp;from_uid=10964570"><span
9539   style='mso-bidi-font-size:9.0pt;color:#336699'>Related Articles,</span></a> <!--[if gte vml 1]><v:shape
9540    id="_x0000_i1033" type="#_x0000_t75" style='width:15pt;height:11pt;
9541    visibility:hidden' print="f">
9542    <v:imagedata src="t_coffee_technical_files/image009.png" o:title="&#37008;&#28494;&#28018;&#27745;&#36864;&#24902;x0&#37008;1"/>
9543    <o:lock v:ext="edit" grouping="t"/>
9544   </v:shape><![endif]--><span style='mso-field-code:"HYPERLINK \0022javascript\:PopUpMenu2_Set\(Menu10964570\)\;\0022 \\t \0022_self\0022"'><span
9545   class=MsoHyperlink><span style='mso-bidi-font-size:9.0pt;color:#336699'>Links</span></span></span>
9546   <span style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>
9547   </td>
9548  </tr>
9549  <tr style='mso-yfti-irow:1;mso-yfti-lastrow:yes'>
9550   <td colspan=2 style='padding:0cm 0cm 0cm 0cm'>
9551   <p class=MyNormalJustified>T-Coffee: A novel method for fast and accurate
9552   multiple sequence alignment.<br>
9553   J Mol Biol. 2000 Sep 8;302(1):205-17. <br>
9554   PMID: 10964570 [PubMed - indexed for MEDLINE]<span style='mso-bidi-font-size:
9555   12.0pt;color:black'><o:p></o:p></span></p>
9556   </td>
9557  </tr>
9558 </table>
9559
9560 <p class=MyNormalJustified><o:p>&nbsp;</o:p></p>
9561
9562 <table class=MsoNormalTable border=0 cellspacing=4 cellpadding=0 width="81%"
9563  style='width:81.98%;mso-cellspacing:3.7pt;mso-padding-alt:0cm 0cm 0cm 0cm'>
9564  <tr style='mso-yfti-irow:0;mso-yfti-firstrow:yes'>
9565   <td width="53%" style='width:53.5%;padding:0cm 0cm 0cm 0cm'>
9566   <p class=MyNormalJustified><a
9567   href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=pubmed&amp;dopt=Abstract&amp;list_uids=9682054">Notredame
9568   C, Holm L, Higgins DG.</a><span style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>
9569   </td>
9570   <td nowrap valign=top style='padding:0cm 0cm 0cm 0cm'>
9571   <p class=MyNormalJustified><a
9572   href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Display&amp;dopt=pubmed_pubmed&amp;from_uid=9682054"><span
9573   style='mso-bidi-font-size:9.0pt;color:#336699'>Related Articles,</span></a> <!--[if gte vml 1]><v:shape
9574    id="_x0000_i1034" type="#_x0000_t75" style='width:15pt;height:11pt;
9575    visibility:hidden' print="f">
9576    <v:imagedata src="t_coffee_technical_files/image010.png" o:title="&#37008;&#28494;&#28018;&#27745;&#36864;&#24902;x0&#37008;1"/>
9577    <o:lock v:ext="edit" grouping="t"/>
9578   </v:shape><![endif]--><span style='mso-field-code:"HYPERLINK \0022javascript\:PopUpMenu2_Set\(Menu9682054\)\;\0022 \\t \0022_self\0022"'><span
9579   class=MsoHyperlink><span style='mso-bidi-font-size:9.0pt;color:#336699'>Links</span></span></span>
9580   <span style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>
9581   </td>
9582  </tr>
9583  <tr style='mso-yfti-irow:1;mso-yfti-lastrow:yes'>
9584   <td colspan=2 style='padding:0cm 0cm 0cm 0cm'>
9585   <p class=MyNormalJustified>COFFEE: an objective function for multiple
9586   sequence alignments.<br>
9587   Bioinformatics. 1998 Jun;14(5):407-22. <br>
9588   PMID: 9682054 [PubMed - indexed for MEDLINE]<span style='mso-bidi-font-size:
9589   12.0pt;color:black'><o:p></o:p></span></p>
9590   </td>
9591  </tr>
9592 </table>
9593
9594 <p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>
9595
9596 <h2><a name="_Toc101065189"></a><a name="_Toc102494278"></a><a
9597 name="_Toc102494656"></a><a name="_Toc151732193"><span style='mso-bookmark:
9598 _Toc102494656'><span style='mso-bookmark:_Toc102494278'><span style='mso-bookmark:
9599 _Toc101065189'>Mocca</span></span></span></a></h2>
9600
9601 <table class=MsoNormalTable border=0 cellspacing=4 cellpadding=0 width="81%"
9602  style='width:81.98%;mso-cellspacing:3.7pt;mso-padding-alt:0cm 0cm 0cm 0cm'>
9603  <tr style='mso-yfti-irow:0;mso-yfti-firstrow:yes'>
9604   <td width="53%" style='width:53.5%;padding:0cm 0cm 0cm 0cm'>
9605   <p class=MyNormal><span lang=AF><a
9606   href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=pubmed&amp;dopt=Abstract&amp;list_uids=11301309"><span
9607   lang=EN-US style='mso-ansi-language:EN-US'>Notredame C.</span></a></span><span
9608   lang=AF style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>
9609   </td>
9610   <td nowrap valign=top style='padding:0cm 0cm 0cm 0cm'>
9611   <p class=MyNormal><span lang=AF><a
9612   href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Display&amp;dopt=pubmed_pubmed&amp;from_uid=11301309&amp;tool=ExternalSearch"><span
9613   lang=EN-US style='mso-bidi-font-size:9.0pt;color:#336699;mso-ansi-language:
9614   EN-US'>Related Articles,</span></a> <!--[if gte vml 1]><v:shape id="_x0000_i1035"
9615    type="#_x0000_t75" style='width:15pt;height:11pt;visibility:hidden' print="f">
9616    <v:imagedata src="t_coffee_technical_files/image011.png" o:title="&#37008;&#28494;&#28018;&#27745;&#36864;&#24902;x0&#37008;1"/>
9617    <o:lock v:ext="edit" grouping="t"/>
9618   </v:shape><![endif]--><span style='mso-field-code:"HYPERLINK \0022javascript\:PopUpMenu2_Set\(Menu11301309\)\;\0022 \\t \0022_self\0022"'><span
9619   class=MsoHyperlink><span lang=EN-US style='mso-bidi-font-size:9.0pt;
9620   color:#336699;mso-ansi-language:EN-US'>Links</span></span></span> </span><span
9621   lang=AF style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>
9622   </td>
9623  </tr>
9624  <tr style='mso-yfti-irow:1;mso-yfti-lastrow:yes'>
9625   <td colspan=2 style='padding:0cm 0cm 0cm 0cm'>
9626   <p class=MyNormal><span lang=AF>Mocca: semi-automatic method for domain
9627   hunting.<br>
9628   Bioinformatics. 2001 Apr;17(4):373-4. <br>
9629   PMID: 11301309 [PubMed - indexed for MEDLINE]</span><span lang=AF
9630   style='mso-bidi-font-size:12.0pt;color:black'><o:p></o:p></span></p>
9631   </td>
9632  </tr>
9633 </table>
9634
9635 <h2><a name="_Toc102494279"></a><a name="_Toc102494657"></a><a
9636 name="_Toc151732194"><span style='mso-bookmark:_Toc102494657'><span
9637 style='mso-bookmark:_Toc102494279'>CORE</span></span></a></h2>
9638
9639 <p class=MyNormal><span lang=AF><a
9640 href="http://www.tcoffee.org/Publications/Pdf/core.pp.pdf"><span lang=EN-US
9641 style='mso-ansi-language:EN-US'>http://www.tcoffee.org/Publications/Pdf/core.pp.pdf<o:p></o:p></span></a></span></p>
9642
9643 <h2><a name="_Toc101065367"></a><a name="_Toc102494280"></a><a
9644 name="_Toc102494658"><span style='mso-bookmark:_Toc102494280'><span
9645 style='mso-bookmark:_Toc101065367'></span></span></a><a name="_Toc151732195"><span
9646 style='mso-bookmark:_Toc101065367'><span style='mso-bookmark:_Toc102494280'><span
9647 style='mso-bookmark:_Toc102494658'>Other Contributions</span></span></span></a></h2>
9648
9649 <p class=MyNormal><span lang=AF>We do not mean to steal code, but we will
9650 always try to re-use pre-existing code whenever that code exists, free of
9651 copyright, just like we expect people to do with our code. However, whenever
9652 this happens, we make a point at properly citing the source of the original
9653 contribution. If ever you recognize a piece of your code improperly cited,
9654 please drop us a note and we will be happy to correct that.</span></p>
9655
9656 <p class=MyNormal><span lang=AF>In the mean time, here are some important
9657 pieces of code from other packages that have been incorporated within the
9658 T-Coffee package. These include: </span></p>
9659
9660 <p class=MyNormal><span lang=AF><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>-The
9661 Sim algorithm of Huang and Miller that given two sequences computes the N best
9662 scoring local alignments.</span></p>
9663
9664 <p class=MyNormal><span lang=AF><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>-The
9665 tree reading/computing routines are taken from the ClustalW Package, courtesy
9666 of Julie Thompson, Des Higgins and Toby Gibson (Thompson, Higgins, Gibson,
9667 1994, 4673-4680,vol. 22, Nucleic Acid Research).</span></p>
9668
9669 <p class=MyNormal><span lang=AF><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>-The
9670 implementation of the algorithm for aligning two sequences in linear space was
9671 adapted from Myers and Miller, in CABIOS, 1988, 11-17, vol. 1)</span></p>
9672
9673 <p class=MyNormal><span lang=AF><span style="mso-spacerun: yes">&nbsp;</span><span
9674 style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>-Various
9675 techniques and algorithms have been implemented. Whenever relevant, the source
9676 of the code/algorithm/idea is indicated in the corresponding function.</span></p>
9677
9678 <p class=MyNormal><span lang=AF><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>-64
9679 Bits compliance was implemented by Benjamin Sohn, Performance Computing Center
9680 Stuttgart (HLRS), Germany</span></p>
9681
9682 <p class=MyNormal><span lang=AF><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>-David
9683 Mathog (Caltech) provided many fixes and useful feedback for improving the code
9684 and making the whole soft behaving more rationally</span></p>
9685
9686 <h2><a name="_Toc151732196">Bug Reports and Feedback</a></h2>
9687
9688 <p class=MyNormal><span lang=AF><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>-Prof
9689 David Jones (UCL) reported and corrected the PDB1K bug (now t_coffee/sap can
9690 align PDB sequences longer than 1000 AA).</span></p>
9691
9692 <p class=MyNormal><span lang=AF><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>-Johan
9693 Leckner reported several bugs related to the treatment of PDB structures,
9694 insuring a consistent behavior between version 1.37 and current ones.</span></p>
9695
9696 <p class=MyNormal><span lang=AF><span style="mso-spacerun: yes">&nbsp;</span></span></p>
9697
9698 <p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>
9699
9700 <div style='mso-element:para-border-div;border:solid windowtext 3.0pt;
9701 padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#CCCCCC;margin-left:0cm;margin-right:
9702 4.25pt'>
9703
9704 <p class=ChapterTitle><a name="_Toc101065204"></a><a name="_Toc102494673"><span
9705 style='mso-bookmark:_Toc101065204'>I</span></a>nstallation of The T-Coffee
9706 Packages</p>
9707
9708 </div>
9709
9710 <h2><a name="_Toc101065205"></a><a name="_Toc102494294"></a><a
9711 name="_Toc102494674"></a><a name="_Toc151732197"><span style='mso-bookmark:
9712 _Toc102494674'><span style='mso-bookmark:_Toc102494294'><span style='mso-bookmark:
9713 _Toc101065205'>Third Party Packages and On Demand Installations</span></span></span></a><span
9714 style='mso-bookmark:_Toc102494674'><span style='mso-bookmark:_Toc102494294'><span
9715 style='mso-bookmark:_Toc101065205'></span></span></span></h2>
9716
9717 <p class=MyNormaBoldl><span style='mso-bookmark:_Toc102494674'><span
9718 style='mso-bookmark:_Toc102494294'><span style='mso-bookmark:_Toc101065205'><span
9719 lang=AF>T-Coffee is a complex package that interacts with many other third part
9720 software. If you only want a standalone version of T-Coffee, you may install
9721 that package on its own. If you want to use a most sophisticated flavor
9722 (3dcoffee, expresso, rcofeee, etc...), the installer will try to install all
9723 the third party packages required.</span></span></span></span></p>
9724
9725 <p class=MyNormaBoldl><span style='mso-bookmark:_Toc102494674'><span
9726 style='mso-bookmark:_Toc102494294'><span style='mso-bookmark:_Toc101065205'><span
9727 lang=AF>Note that since version 7.56, T-Coffee will use 'on demand'
9728 installation and install the third party packages it needs *when* it needs
9729 them. This only works for packages not requiring specific licenses and that can
9730 be installed by the regular installer. Please let us know if you would like
9731 another third party package to be included. </span></span></span></span></p>
9732
9733 <p class=MyNormaBoldl><span style='mso-bookmark:_Toc102494674'><span
9734 style='mso-bookmark:_Toc102494294'><span style='mso-bookmark:_Toc101065205'><span
9735 lang=AF>Whenver on-demand installation or automated installation fails because
9736 of unforessen system specificities, users should install the third party package
9737 manually. This documentation gives some tips we have found useful, but users
9738 are encouraged to check the original documentation.</span></span></span></span></p>
9739
9740 <h2><span style='mso-bookmark:_Toc102494674'><span style='mso-bookmark:_Toc102494294'><span
9741 style='mso-bookmark:_Toc101065205'><a name="_Toc151732198">Standard
9742 Installation</a></span></span></span><span style='mso-bookmark:_Toc151732198'>
9743 of T-Coffee</span></h2>
9744
9745 <h3><a name="_Toc151732199"><span style='mso-hansi-font-family:"Arial Black"'>Automated
9746 Installation</span></a><span style='mso-hansi-font-family:"Arial Black"'><o:p></o:p></span></h3>
9747
9748 <p class=MyNormaBoldl><span lang=AF>We now recommend that you use the automated
9749 installer provided for UNIX or Linux platforms. </span></p>
9750
9751 <h4><a name="_Toc151732200"><span lang=AF>Mac-OsX</span></a></h4>
9752
9753 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
9754 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
9755 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
9756 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
9757
9758 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
9759 style='mso-tab-count:1'>&nbsp;&nbsp; </span>Click on tge .dmg file</p>
9760
9761 </div>
9762
9763 <h4><a name="_Toc151732201"><span lang=AF>Unix</span></a></h4>
9764
9765 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
9766 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
9767 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
9768 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
9769
9770 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
9771 style='mso-tab-count:1'>&nbsp;&nbsp; </span>rpm &#8211;i &lt;rmp&gt;</p>
9772
9773 </div>
9774
9775 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
9776
9777 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
9778
9779 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
9780
9781 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
9782
9783 <h3><a name="_Toc151732202"><span style='mso-hansi-font-family:"Arial Black"'>Unix</span></a></h3>
9784
9785 <p class=MyNormaBoldl><span lang=AF>You need to have: gcc, g77, CPAN and an
9786 internet connection and your root password. You will also need the two
9787 following perl modules: LWP and XML::Simple. These are needed if you want to
9788 use the web services provided by the EBI via REST (http://www.ebi.ac.uk/Tools/webservices/tutorials/02_rest)</span></p>
9789
9790 <p class=MsoNormal style='margin-left:72.0pt'><o:p>&nbsp;</o:p></p>
9791
9792 <p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
9793 margin-left:72.0pt;text-indent:-18.0pt;mso-list:l24 level2 lfo39;tab-stops:
9794 list 72.0pt'><![if !supportLists]><span style='font-family:Arial;mso-fareast-font-family:
9795 Arial;mso-bidi-font-family:Arial'><span style='mso-list:Ignore'>1.<span
9796 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><code><span
9797 style='font-size:10.0pt'>gunzip t_coffee.tar.gz</span></code><span
9798 style='font-family:Arial;mso-bidi-font-family:Arial'><o:p></o:p></span></p>
9799
9800 <p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
9801 margin-left:72.0pt;text-indent:-18.0pt;mso-list:l24 level2 lfo39;tab-stops:
9802 list 72.0pt'><![if !supportLists]><span style='font-family:Arial;mso-fareast-font-family:
9803 Arial;mso-bidi-font-family:Arial'><span style='mso-list:Ignore'>2.<span
9804 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><code><span
9805 style='font-size:10.0pt'>tar -xvf t_coffee.tar</span></code><span
9806 style='font-family:Arial;mso-bidi-font-family:Arial'><o:p></o:p></span></p>
9807
9808 <p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
9809 margin-left:72.0pt;text-indent:-18.0pt;mso-list:l24 level2 lfo39;tab-stops:
9810 list 72.0pt'><![if !supportLists]><span style='font-family:Arial;mso-fareast-font-family:
9811 Arial;mso-bidi-font-family:Arial'><span style='mso-list:Ignore'>3.<span
9812 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><code><span
9813 style='font-size:10.0pt'>cd t_coffee</span></code><span style='font-family:
9814 Arial;mso-bidi-font-family:Arial'><o:p></o:p></span></p>
9815
9816 <p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
9817 margin-left:72.0pt;text-indent:-18.0pt;mso-list:l24 level2 lfo39;tab-stops:
9818 list 72.0pt'><![if !supportLists]><span style='font-family:Arial;mso-fareast-font-family:
9819 Arial;mso-bidi-font-family:Arial'><span style='mso-list:Ignore'>4.<span
9820 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><code><span
9821 style='font-size:10.0pt'>./install t_coffee</span></code><span
9822 style='font-family:Arial;mso-bidi-font-family:Arial'><o:p></o:p></span></p>
9823
9824 <p class=MyNormal><span lang=AF>This installation will only install the stand
9825 alone T-Coffee. If you want to install a specific mode of T-Coffee, you may try
9826 the following commands that will try to gather all the necessary third party
9827 packages. Note that a package already found on your system will not be
9828 re-installed.</span></p>
9829
9830 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
9831 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
9832 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
9833 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
9834
9835 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
9836 style='mso-tab-count:1'>&nbsp;&nbsp; </span>./install t_coffee</p>
9837
9838 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
9839 style='mso-tab-count:1'>&nbsp;&nbsp; </span>./install mcoffee</p>
9840
9841 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
9842 style='mso-tab-count:1'>&nbsp;&nbsp; </span>./install 3dcoffee</p>
9843
9844 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
9845 style='mso-tab-count:1'>&nbsp;&nbsp; </span>./install rcoffee</p>
9846
9847 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
9848 style='mso-tab-count:1'>&nbsp;&nbsp; </span>./install psicoffee</p>
9849
9850 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><o:p>&nbsp;</o:p></p>
9851
9852 </div>
9853
9854 <p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>
9855
9856 <p class=MyNormal><span lang=AF>Or even</span></p>
9857
9858 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
9859 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
9860 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
9861 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
9862
9863 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
9864 style='mso-tab-count:1'>&nbsp;&nbsp; </span>./install all</p>
9865
9866 </div>
9867
9868 <p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>
9869
9870 <p class=MyNormal><span lang=AF>-All the corresponding executables will be
9871 downloaded automatically and installed in</span></p>
9872
9873 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
9874 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
9875 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
9876 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
9877
9878 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
9879 style='mso-tab-count:1'>&nbsp;&nbsp; </span>$HOME/.t_coffee/plugins</p>
9880
9881 </div>
9882
9883 <p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>
9884
9885 <p class=MyNormal><span lang=AF>-if you executables are in a different location,
9886 give it to T-Coffee using the -plugins flag.</span></p>
9887
9888 <p class=MyNormal><span lang=AF>-If the installation of any of the companion
9889 package fails, you should install it yourself using the provided link (see
9890 below) and following the authors instructions.<span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></p>
9891
9892 <p class=MyNormal><span lang=AF>-If you have not managed to install SOAP::Lite,
9893 you can re-install it later (from anywhere) following steps 1-2.</span></p>
9894
9895 <p class=MsoNormal style='margin-left:72.0pt'><o:p>&nbsp;</o:p></p>
9896
9897 <p class=MyNormaBoldl><span lang=AF>-This procedure attempts 3 things:
9898 installing and Compiling T-Coffee (C program), Installing and compiling <a
9899 href="http://zhang.bioinformatics.ku.edu/TM-align/"><span lang=EN-US
9900 style='mso-ansi-language:EN-US'>TMalign</span></a> (Fortran), Installing and
9901 compiling XML::Simple</span></p>
9902
9903 <p class=MyNormaBoldl><span lang=AF><o:p>&nbsp;</o:p></span></p>
9904
9905 <p class=MyNormaBoldl><span lang=AF>-If you have never installed a perl module
9906 before, CPAN will ask you many questions: say Yes to all </span></p>
9907
9908 <p class=MyNormaBoldl><span lang=AF>-If everything went well, the procedure has
9909 created in the <b>bin</b> directory two executables: t_coffee and TMalign (<b>Make
9910 sure these executables are on your $PATH!</b>)</span></p>
9911
9912 <p class=MyNormaBoldl><span lang=AF><o:p>&nbsp;</o:p></span></p>
9913
9914 <h3><a name="_Toc151732203">Microsoft Windows/Cygwin</a></h3>
9915
9916 <p class=MyNormaBoldl><span lang=AF>Install <a href="http://www.cygwin.com"><span
9917 lang=EN-US style='color:windowtext;mso-ansi-language:EN-US;text-decoration:
9918 none;text-underline:none'>Cygwin</span></a></span></p>
9919
9920 <p class=MyNormaBoldl><span lang=AF>Download The Installer (NOT Cygwin/X)</span></p>
9921
9922 <p class=MyNormaBoldl><span lang=AF>Click on view to list ALL the packages</span></p>
9923
9924 <p class=MyNormaBoldl><span lang=AF>Select: gcc-core, make, wget</span></p>
9925
9926 <p class=MyNormaBoldl><span lang=AF>Optional: ssh, xemacs, nano</span></p>
9927
9928 <p class=MyNormaBoldl><span lang=AF>Run mkpasswd in Cywin (as requested when
9929 you start cygwin)</span></p>
9930
9931 <p class=MyNormaBoldl><span lang=AF>Install T-Coffee within Cygwin using the
9932 Unix procedure</span></p>
9933
9934 <h3><a name="_Toc151732204">MAC osX, Linux</a></h3>
9935
9936 <p class=MyNormaBoldl><span lang=AF>Make sure you have the Developer's kit installed
9937 (compilers and makefile)</span></p>
9938
9939 <p class=MyNormaBoldl><span lang=AF>Follow the Unix Procedure</span></p>
9940
9941 <p class=Mylist><span lang=AF><o:p>&nbsp;</o:p></span></p>
9942
9943 <h3><a name="_Toc151732205">CLUSTER Installation</a></h3>
9944
9945 <p class=MyNormal><span lang=AF>In order to run, T-Coffee must have a value for
9946 the http_proxy and for the E-mail. In order to do so you can either:</span></p>
9947
9948 <p class=MyNormaBoldl><span lang=AF>export the following values:</span></p>
9949
9950 <p class=MyNormaBoldl><span lang=AF>export
9951 http_proxy_4_TCOFFEE=&quot;proxy&quot; or &quot;&quot; if no proxy</span></p>
9952
9953 <p class=MyNormaBoldl><span lang=AF>export EMAIL_4_TCOFFEE=&quot;your
9954 email&quot;</span></p>
9955
9956 <p class=MyNormaBoldl><span lang=AF>OR </span></p>
9957
9958 <p class=MyNormaBoldl><span lang=AF>modify the file ~/.t_coffee/t_coffee_env</span></p>
9959
9960 <p class=MyNormaBoldl><span lang=AF>OR</span></p>
9961
9962 <p class=MyNormaBoldl><span lang=AF>add to your command line: t_coffee \85.
9963 -proxy=&lt;proxy&gt; -email=&lt;email</span></p>
9964
9965 <p class=MyNormaBoldl><span lang=AF>if you have no proxy: t_coffee \85 -proxy
9966 -email=&lt;email&gt;</span></p>
9967
9968 <p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>
9969
9970 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
9971
9972 <h3><a name="_Toc151732206">If you have PDB installed:</a></h3>
9973
9974 <p class=MyNormal><span lang=AF>Assuming you have a standard PDB installation
9975 in your file system</span></p>
9976
9977 <p class=example2CxSpFirst>setenv (or export)<span style="mso-spacerun:
9978 yes">&nbsp; </span>PDB_DIR &lt;abs path&gt;/data/structures/all/pdb/</p>
9979
9980 <p class=example2CxSpMiddle>OR</p>
9981
9982 <p class=example2CxSpLast>setenv (or export)<span style="mso-spacerun:
9983 yes">&nbsp; </span>PDB_DIR &lt;abs path&gt;/structures/divided/pdb/</p>
9984
9985 <p class=MyNormal><span lang=AF>If you do not have PDB installed, don't worry,
9986 t_coffee will go and fetch any structure it needs directly from the PDB
9987 repository. It will simply be a bit slower than if you had PDB locally. </span></p>
9988
9989 <h2><a name="_Toc101065206"></a><a name="_Toc102494295"></a><a
9990 name="_Toc102494675"></a><a name="_Toc151732207"><span style='mso-bookmark:
9991 _Toc102494675'><span style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:
9992 _Toc101065206'>Installing BLAST for T-Coffee</span></span></span></a><span
9993 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
9994 style='mso-bookmark:_Toc101065206'></span></span></span></h2>
9995
9996 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
9997 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
9998 lang=AF>BLAST is a program that search sequence databases for homologues of a
9999 query sequence. It works for proteins and Nucleic Acids. In theory BLAST is
10000 just a package like any, but in practice things are a bit more complex. To run
10001 well, BLST requires up to date databases (that can be fairly large, like NR or
10002 UNIPROT) and a powerful computer.</span></span></span></span></p>
10003
10004 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10005 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10006 lang=AF>Fortunately, an increasing number of institutes or companies are now
10007 providing BLAST clients that run over the net. It means that all you need is a
10008 small program that send your query to the big server and gets the results back.
10009 This prevents you from the hassle of installing and maintaining BLAST, but of
10010 course it is less private and you rely on the network and the current load of
10011 these busy servers.</span></span></span></span></p>
10012
10013 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10014 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10015 lang=AF>Thanks to its interaction with BLAST, T-Coffee can gather structures
10016 and protein profiles and deliver an alignment significantly more accurate than
10017 the default you would get with T-Coffee or any similar method.</span></span></span></span></p>
10018
10019 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10020 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10021 lang=AF>Let us go through the various modes available for T-Coffee</span></span></span></span></p>
10022
10023 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10024 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10025 lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>
10026
10027 <h3><span style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
10028 style='mso-bookmark:_Toc101065206'><a name="_Toc151732208">Why Do I need BLAST
10029 with T-Coffee?</a></span></span></span></h3>
10030
10031 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10032 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10033 lang=AF>The most accurate modes of T-Coffe scan the databases for templates
10034 that they use to align the sequences. There are currently two types of templates
10035 for proteins:</span></span></span></span></p>
10036
10037 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10038 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10039 lang=AF>structures (PDB) that can be found by a blastp against the PDB database
10040 and profiles that can be constructed with eiether a blastp or a psiblast
10041 against nr or uniprot.</span></span></span></span></p>
10042
10043 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10044 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10045 lang=AF>These templates are automatically built if you use:</span></span></span></span></p>
10046
10047 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
10048 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
10049 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
10050 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
10051
10052 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
10053 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
10054 style='mso-bookmark:_Toc101065206'><span style='mso-tab-count:1'>&nbsp;&nbsp; </span>t_coffee
10055 &lt;yourseq&gt; -mode expresso</span></span></span></p>
10056
10057 </div>
10058
10059 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10060 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10061 lang=AF><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>that
10062 fetches aand uses pdb templates, or</span></span></span></span></p>
10063
10064 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
10065 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
10066 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
10067 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
10068
10069 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
10070 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
10071 style='mso-bookmark:_Toc101065206'><span style='mso-tab-count:1'>&nbsp;&nbsp; </span><span
10072 style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>t_coffee
10073 &lt;your seq&gt; -mode psicoffee</span></span></span></p>
10074
10075 </div>
10076
10077 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10078 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10079 lang=AF><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>that
10080 fetches and uses profile templates, or</span></span></span></span></p>
10081
10082 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
10083 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
10084 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
10085 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
10086
10087 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
10088 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
10089 style='mso-bookmark:_Toc101065206'><span style='mso-tab-count:1'>&nbsp;&nbsp; </span><span
10090 style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>t_coffee
10091 &lt;your seq&gt; -mode accurate</span></span></span></p>
10092
10093 </div>
10094
10095 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10096 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10097 lang=AF><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>that
10098 does everything and tries to use the best template. Now that you see why it is
10099 useful let's see how to get BLAST up and running, from the easy solution to
10100 tailor made ones.</span></span></span></span></p>
10101
10102 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10103 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10104 lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>
10105
10106 <h3><span style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
10107 style='mso-bookmark:_Toc101065206'><a name="_Toc151732209">Using the EBI BLAST
10108 Client</a></span></span></span></h3>
10109
10110 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10111 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10112 lang=AF>This is by far the easiest (and the default mode). The perl clients are
10113 already incorporated in T-Coffee and all you need is are the proper perl
10114 library. In theory, T-Coffee should have already installed these libraries during
10115 the standard installation. Yet, this requires having toot access. It really is
10116 worth the effort, since the EBI is providing one of the best webservice available
10117 around, and most notably, the only public psiblast via a web service.</span></span></span></span></p>
10118
10119 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10120 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10121 lang=AF>Whenever you use a T-Coffee mode requiring Blast access, it will ask
10122 you for an authentification E-mail. <b>Be Careful! </b>If you provide a fake
10123 E-mail, the EBI may suspend the service for all machines associated with your
10124 IP address (that could mean your entire lab, or entire institute, or even the
10125 entire country or, but I doubt it, the whole universe).</span></span></span></span></p>
10126
10127 <h3><span style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
10128 style='mso-bookmark:_Toc101065206'><a name="_Toc151732210">Using the NCBI BLAST
10129 Client</a></span></span></span></h3>
10130
10131 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10132 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10133 lang=AF>The NCBI is the next best alternative. In my hand it was always a bit
10134 slower and most of all, it does not incorporate PSI-BLAST (as a web sevice). A
10135 big miss. The NCBI web blast client is a small executable that you should
10136 install on your system following the instructions given on this link</span></span></span></span></p>
10137
10138 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
10139 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
10140 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
10141 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
10142
10143 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
10144 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
10145 style='mso-bookmark:_Toc101065206'>ftp://ftp.ncbi.nih.gov/blast/executables/LATEST</span></span></span></p>
10146
10147 </div>
10148
10149 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10150 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10151 lang=AF>Simply go for <b>netbl,</b> download the executable that corresponds to
10152 your architecture (cygwin users should go for the win executable). Despite all
10153 the files that come along the executable blastcl3 is a stand alone executable
10154 that you can safely move to your $BIN.</span></span></span></span></p>
10155
10156 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10157 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10158 lang=AF>All you will then need to do is to make sure that T-Coffee uses the
10159 right client, when you run it.</span></span></span></span></p>
10160
10161 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
10162 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
10163 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
10164 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
10165
10166 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
10167 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
10168 style='mso-bookmark:_Toc101065206'>-blast_server=NCBI</span></span></span></p>
10169
10170 </div>
10171
10172 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10173 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10174 lang=AF>No need for any E-mail here, but you don't get psiblast, and whenever
10175 T-Coffee wants to use it, blastp will be used instead.</span></span></span></span></p>
10176
10177 <h3><span style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
10178 style='mso-bookmark:_Toc101065206'><a name="_Toc151732211">Using another Client</a></span></span></span></h3>
10179
10180 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10181 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10182 lang=AF>You may have your own client (lucky you). If that is so, all you need
10183 is to make sure that this client is complient with the blast command line. If
10184 your client is named foo.pl, all you need to to is run T-Coffee with</span></span></span></span></p>
10185
10186 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
10187 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
10188 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
10189 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
10190
10191 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
10192 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
10193 style='mso-bookmark:_Toc101065206'>-blast_server=CLIENT_foo.pl</span></span></span></p>
10194
10195 </div>
10196
10197 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10198 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10199 lang=AF>Foo will be called as if it were blastpgp, and it is your
10200 responsability to make sure it can handle the following command line:</span></span></span></span></p>
10201
10202 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
10203 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
10204 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
10205 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
10206
10207 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
10208 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
10209 style='mso-bookmark:_Toc101065206'>foo.pl -p &lt;method&gt; -d &lt;db&gt; -i &lt;infile&gt;
10210 -o &lt;outfile&gt; -m 7</span></span></span></p>
10211
10212 </div>
10213
10214 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10215 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10216 lang=AF>method can either be blastp or psiblast.</span></span></span></span></p>
10217
10218 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10219 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10220 lang=AF>infile is a FASTA file</span></span></span></span></p>
10221
10222 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10223 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10224 lang=AF>-m7 triggers the XML output. T-Coffee is able to parse both the EBI XML
10225 output and the NCBI XML output.</span></span></span></span></p>
10226
10227 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10228 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10229 lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>
10230
10231 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10232 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10233 lang=AF>If foo.pl behaves differently, the easiest will probably be to write a
10234 wrapper around it so that wrapped_foo.pl behaves like blastpgp</span></span></span></span></p>
10235
10236 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10237 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10238 lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>
10239
10240 <h3><span style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
10241 style='mso-bookmark:_Toc101065206'><a name="_Toc151732212">Using a BLAST local
10242 version on UNIX</a></span></span></span></h3>
10243
10244 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10245 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10246 lang=AF>If you have blastpgp installed, you can run it instead of the remote
10247 clients by using:</span></span></span></span></p>
10248
10249 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
10250 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
10251 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
10252 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
10253
10254 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
10255 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
10256 style='mso-bookmark:_Toc101065206'>-blast_server=LOCAL</span></span></span></p>
10257
10258 </div>
10259
10260 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10261 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10262 lang=AF><span style="mso-spacerun: yes">&nbsp;</span>The documentation for
10263 blastpgp can be found on:</span></span></span></span></p>
10264
10265 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
10266 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
10267 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
10268 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
10269
10270 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
10271 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
10272 style='mso-bookmark:_Toc101065206'>www.ncbi.nlm.nih.gov/staff/tao/URLAPI/blastpgp.html</span></span></span></p>
10273
10274 </div>
10275
10276 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10277 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10278 lang=AF>and the package is part of the standard BLAST distribution</span></span></span></span></p>
10279
10280 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
10281 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
10282 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
10283 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
10284
10285 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
10286 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
10287 style='mso-bookmark:_Toc101065206'>ftp://ftp.ncbi.nih.gov/blast/executables/LATEST</span></span></span></p>
10288
10289 </div>
10290
10291 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10292 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10293 lang=AF>Depending on your system, your own skills, your requirements and on
10294 more parameters than I have fingers to count, installing a BLAST server suited
10295 for your needs can range from a 10 minutes job to an achivement spread over
10296 several generations. So at this point, you should roam the NCBI website for
10297 suitable information.</span></span></span></span></p>
10298
10299 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10300 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10301 lang=AF>If you want to have your own BLAST server to run your own databases,
10302 you should know that it is possible to control both the database and the
10303 program used by BLAST:</span></span></span></span></p>
10304
10305 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10306 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10307 lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>
10308
10309 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
10310 mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
10311 background:#E6E6E6'>
10312
10313 <p class=examplefileCxSpFirst><span style='mso-bookmark:_Toc102494675'><span
10314 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>-protein_db:
10315 will specify the database used by all the psi-blast modes</span></span></span></p>
10316
10317 <p class=examplefileCxSpLast><span style='mso-bookmark:_Toc102494675'><span
10318 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>-pdb_db:
10319 will specify the database used by the pdb modes</span></span></span></p>
10320
10321 </div>
10322
10323 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10324 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><b
10325 style='mso-bidi-font-weight:normal'><span lang=AF><o:p>&nbsp;</o:p></span></b></span></span></span></p>
10326
10327 <div style='mso-element:para-border-div;border:solid windowtext 1.5pt;
10328 padding:0cm 0cm 0cm 0cm;background:#F7CBB7'>
10329
10330 <p class=Warning><span style='mso-bookmark:_Toc102494675'><span
10331 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>Note
10332 that T-Coffee is compliant with BLAST+, the latest NCBI Blast.</span></span></span></p>
10333
10334 </div>
10335
10336 <h3><span style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
10337 style='mso-bookmark:_Toc101065206'><a name="_Toc151732213">Using a BLAST local
10338 version on Windows/cygwin</a></span></span></span></h3>
10339
10340 <h4><span style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
10341 style='mso-bookmark:_Toc101065206'><a name="_Toc151732214"><span lang=AF>BLAST+</span></a></span></span></span></h4>
10342
10343 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10344 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10345 lang=AF>Blast+ is tghe latest NCBI Blast. IT is easier to install. A default
10346 installation should be compliant with a default T-Coffee installation. </span></span></span></span></p>
10347
10348 <p class=MsoNormal><span style='mso-bookmark:_Toc102494675'><span
10349 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><o:p>&nbsp;</o:p></span></span></span></p>
10350
10351 <h4><span style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
10352 style='mso-bookmark:_Toc101065206'><a name="_Toc151732215"><span lang=AF>ORIGINAL
10353 NCBI BLAST</span></a></span></span></span></h4>
10354
10355 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10356 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10357 lang=AF>For those of you using cygwin, be careful. While cygwin behaves like a
10358 UNIX system, the BLAST executable required for cygwin (win32) is expecting
10359 WINDOWS path and not UNIX path. This has three important consequences:</span></span></span></span></p>
10360
10361 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10362 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10363 lang=AF>1- the ncbi file declaring the Data directory must be:</span></span></span></span></p>
10364
10365 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10366 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10367 lang=AF><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>C:WINDOWS//ncbi.init<span
10368 style="mso-spacerun: yes">&nbsp; </span>[at the root of your WINDOWS]</span></span></span></span></p>
10369
10370 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10371 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10372 lang=AF>2- the address mentionned with this file must be WINDOWS formated, for
10373 instance, on my system:</span></span></span></span></p>
10374
10375 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10376 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10377 lang=AF>Data=C:\cygwin\home\notredame\blast\data</span></span></span></span></p>
10378
10379 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10380 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10381 lang=AF>3- When you pass database addresses to BLAST, these must be in Windows format:</span></span></span></span></p>
10382
10383 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10384 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10385 lang=AF><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>-protein_db=&quot;c:/somewhere/somewhereelse/database&quot;</span></span></span></span></p>
10386
10387 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10388 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10389 lang=AF>(using the slash (/) or the andtislash (\) does not matter on new
10390 systems but I would reommand against incorporating white spaces.</span></span></span></span></p>
10391
10392 <h2><span style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
10393 style='mso-bookmark:_Toc101065206'><a name="_Toc151732216">Installing Other
10394 Companion Packages</a></span></span></span></h2>
10395
10396 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10397 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10398 lang=AF>T-Coffee is meant to interact with as many packages as possible, either
10399 for aligning or using predictions. If you type </span></span></span></span></p>
10400
10401 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
10402 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
10403 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
10404 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
10405
10406 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
10407 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
10408 style='mso-bookmark:_Toc101065206'><span style='mso-tab-count:1'>&nbsp;&nbsp; </span>t_coffee</span></span></span></p>
10409
10410 </div>
10411
10412 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10413 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10414 lang=AF>You will receive a list of supported packages that looks like the next
10415 table. In theory, most of these packages can be installed by T-Coffee <b
10416 style='mso-bidi-font-weight:normal'>and we welcome any reasonnable request.<o:p></o:p></b></span></span></span></span></p>
10417
10418 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10419 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10420 lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>
10421
10422 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
10423 mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
10424 background:#E6E6E6'>
10425
10426 <p class=examplefileCxSpFirst><span style='mso-bookmark:_Toc102494675'><span
10427 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>******
10428 Pairwise Sequence Alignment Methods:</span></span></span></p>
10429
10430 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10431 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>--------------------------------------------</span></span></span></p>
10432
10433 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10434 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>fast_pair<span
10435 style="mso-spacerun:
10436 yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>built_in</span></span></span></p>
10437
10438 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10439 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>exon3_pair<span
10440 style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
10441 </span>built_in</span></span></span></p>
10442
10443 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10444 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>exon2_pair<span
10445 style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
10446 </span>built_in</span></span></span></p>
10447
10448 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10449 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>exon_pair<span
10450 style="mso-spacerun:
10451 yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>built_in</span></span></span></p>
10452
10453 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10454 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>slow_pair<span
10455 style="mso-spacerun:
10456 yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>built_in</span></span></span></p>
10457
10458 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10459 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>proba_pair<span
10460 style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
10461 </span>built_in</span></span></span></p>
10462
10463 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10464 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>lalign_id_pair<span
10465 style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp; </span>built_in</span></span></span></p>
10466
10467 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10468 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>seq_pair<span
10469 style="mso-spacerun:
10470 yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
10471 </span>built_in</span></span></span></p>
10472
10473 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10474 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>externprofile_pair
10475 built_in</span></span></span></p>
10476
10477 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10478 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>hh_pair<span
10479 style="mso-spacerun:
10480 yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
10481 </span>built_in</span></span></span></p>
10482
10483 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10484 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>profile_pair<span
10485 style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>built_in</span></span></span></p>
10486
10487 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10488 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>cdna_fast_pair<span
10489 style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp; </span>built_in</span></span></span></p>
10490
10491 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10492 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>cdna_cfast_pair<span
10493 style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp; </span>built_in</span></span></span></p>
10494
10495 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10496 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>clustalw_pair<span
10497 style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>ftp://www.ebi.ac.uk/pub/clustalw</span></span></span></p>
10498
10499 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10500 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>mafft_pair<span
10501 style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
10502 </span>http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft/</span></span></span></p>
10503
10504 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10505 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>mafftjtt_pair<span
10506 style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
10507 </span>http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft/</span></span></span></p>
10508
10509 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10510 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>mafftgins_pair<span
10511 style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;
10512 </span>http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft/</span></span></span></p>
10513
10514 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10515 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>dialigntx_pair<span
10516 style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;
10517 </span>http://dialign-tx.gobics.de/</span></span></span></p>
10518
10519 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10520 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>dialignt_pair<span
10521 style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
10522 </span>http://dialign-t.gobics.de/</span></span></span></p>
10523
10524 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10525 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>poa_pair<span
10526 style="mso-spacerun:
10527 yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
10528 </span>http://www.bioinformatics.ucla.edu/poa/</span></span></span></p>
10529
10530 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10531 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>probcons_pair<span
10532 style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
10533 </span>http://probcons.stanford.edu/</span></span></span></p>
10534
10535 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10536 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>muscle_pair<span
10537 style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
10538 </span>http://www.drive5.com/muscle/</span></span></span></p>
10539
10540 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10541 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>t_coffee_pair<span
10542 style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
10543 </span>http://www.tcoffee.org</span></span></span></p>
10544
10545 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10546 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>pcma_pair<span
10547 style="mso-spacerun:
10548 yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
10549 </span>ftp://iole.swmed.edu/pub/PCMA/</span></span></span></p>
10550
10551 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10552 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>kalign_pair<span
10553 style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
10554 </span>http://msa.cgb.ki.se</span></span></span></p>
10555
10556 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10557 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>amap_pair<span
10558 style="mso-spacerun:
10559 yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
10560 </span>http://bio.math.berkeley.edu/amap/</span></span></span></p>
10561
10562 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10563 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>proda_pair<span
10564 style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
10565 </span>http://bio.math.berkeley.edu/proda/</span></span></span></p>
10566
10567 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10568 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>prank_pair<span
10569 style="mso-spacerun: yes">&nbsp;&nbsp; </span><span style="mso-spacerun:
10570 yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span>http://www.ebi.ac.uk/goldman-srv/prank/</span></span></span></p>
10571
10572 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10573 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>consan_pair<span
10574 style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
10575 </span>http://selab.janelia.org/software/consan/</span></span></span></p>
10576
10577 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10578 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><o:p>&nbsp;</o:p></span></span></span></p>
10579
10580 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10581 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>******
10582 Pairwise Structural Alignment Methods:</span></span></span></p>
10583
10584 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10585 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>--------------------------------------------</span></span></span></p>
10586
10587 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10588 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>align_pdbpair<span
10589 style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>built_in</span></span></span></p>
10590
10591 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10592 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>lalign_pdbpair<span
10593 style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp; </span>built_in</span></span></span></p>
10594
10595 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10596 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>extern_pdbpair<span
10597 style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp; </span>built_in</span></span></span></p>
10598
10599 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10600 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>thread_pair<span
10601 style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
10602 </span>built_in</span></span></span></p>
10603
10604 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10605 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>fugue_pair<span
10606 style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
10607 </span>http://www-cryst.bioc.cam.ac.uk/fugue/download.html</span></span></span></p>
10608
10609 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10610 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>pdb_pair<span
10611 style="mso-spacerun:
10612 yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
10613 </span>built_in</span></span></span></p>
10614
10615 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10616 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>sap_pair<span
10617 style="mso-spacerun:
10618 yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
10619 </span>http://www-cryst.bioc.cam.ac.uk/fugue/download.html</span></span></span></p>
10620
10621 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10622 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>mustang_pair<span
10623 style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
10624 </span>http://www.cs.mu.oz.au/~arun/mustang/</span></span></span></p>
10625
10626 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10627 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>tmalign_pair<span
10628 style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
10629 </span>http://zhang.bioinformatics.ku.edu/TM-align/</span></span></span></p>
10630
10631 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10632 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><o:p>&nbsp;</o:p></span></span></span></p>
10633
10634 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10635 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>******
10636 Multiple Sequence Alignment Methods:</span></span></span></p>
10637
10638 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10639 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>--------------------------------------------</span></span></span></p>
10640
10641 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10642 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>clustalw_msa<span
10643 style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
10644 </span>ftp://www.ebi.ac.uk/pub/clustalw</span></span></span></p>
10645
10646 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10647 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>mafft_msa<span
10648 style="mso-spacerun:
10649 yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft/</span></span></span></p>
10650
10651 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10652 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>mafftjtt_msa<span
10653 style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
10654 </span>http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft/</span></span></span></p>
10655
10656 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10657 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>mafftgins_msa<span
10658 style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
10659 </span>http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft/</span></span></span></p>
10660
10661 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10662 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>dialigntx_msa<span
10663 style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
10664 </span>http://dialign-tx.gobics.de/</span></span></span></p>
10665
10666 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10667 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>dialignt_msa<span
10668 style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
10669 </span>http://dialign-t.gobics.de/</span></span></span></p>
10670
10671 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10672 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>poa_msa<span
10673 style="mso-spacerun:
10674 yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
10675 </span>http://www.bioinformatics.ucla.edu/poa/</span></span></span></p>
10676
10677 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10678 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>probcons_msa<span
10679 style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
10680 </span>http://probcons.stanford.edu/</span></span></span></p>
10681
10682 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10683 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>muscle_msa<span
10684 style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
10685 </span>http://www.drive5.com/muscle/</span></span></span></p>
10686
10687 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10688 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>t_coffee_msa<span
10689 style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
10690 </span>http://www.tcoffee.org</span></span></span></p>
10691
10692 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10693 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>pcma_msa<span
10694 style="mso-spacerun:
10695 yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
10696 </span>ftp://iole.swmed.edu/pub/PCMA/</span></span></span></p>
10697
10698 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10699 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>kalign_msa<span
10700 style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
10701 </span>http://msa.cgb.ki.se</span></span></span></p>
10702
10703 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10704 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>amap_msa<span
10705 style="mso-spacerun:
10706 yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
10707 </span>http://bio.math.berkeley.edu/amap/</span></span></span></p>
10708
10709 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10710 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>proda_msa<span
10711 style="mso-spacerun:
10712 yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
10713 </span>http://bio.math.berkeley.edu/proda/</span></span></span></p>
10714
10715 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10716 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>prank_msa<span
10717 style="mso-spacerun:
10718 yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
10719 </span>http://www.ebi.ac.uk/goldman-srv/prank/</span></span></span></p>
10720
10721 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10722 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><o:p>&nbsp;</o:p></span></span></span></p>
10723
10724 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10725 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>#######<span
10726 style="mso-spacerun: yes">&nbsp;&nbsp; </span>Prediction Methods available to
10727 generate Templates</span></span></span></p>
10728
10729 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10730 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>-------------------------------------------------------------</span></span></span></p>
10731
10732 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10733 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>RNAplfold<span
10734 style="mso-spacerun:
10735 yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
10736 </span>http://www.tbi.univie.ac.at/~ivo/RNA/</span></span></span></p>
10737
10738 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10739 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>HMMtop<span
10740 style="mso-spacerun:
10741 yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
10742 </span>www.enzim.hu/hmmtop/</span></span></span></p>
10743
10744 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10745 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>GOR4<span
10746 style="mso-spacerun:
10747 yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
10748 </span>http://mig.jouy.inra.fr/logiciels/gorIV/</span></span></span></p>
10749
10750 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10751 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>wublast_client<span
10752 style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;
10753 </span>http://www.ebi.ac.uk/Tools/webservices/services/wublast</span></span></span></p>
10754
10755 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10756 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>blastpgp_client<span
10757 style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;
10758 </span>http://www.ebi.ac.uk/Tools/webservices/services/blastpgp<span
10759 style="mso-spacerun:
10760 yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span></span></p>
10761
10762 <p class=examplefileCxSpLast><span style='mso-bookmark:_Toc102494675'><span
10763 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>==========================================================</span></span></span></p>
10764
10765 </div>
10766
10767 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10768 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10769 lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>
10770
10771 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10772 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10773 lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>
10774
10775 <h2><span style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
10776 style='mso-bookmark:_Toc101065206'><a name="_Toc151732217">Installation of
10777 PSI-Coffee and Expresso</a></span></span></span></h2>
10778
10779 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10780 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10781 lang=AF>PSI-Coffee is a mode of T-Coffee that runs a a Psi-BLAST on each of
10782 your sequences and makes a multiple profile alignment. If you do not have any
10783 structural information, it is by far the most accurate mode of T-Coffee. To use
10784 it, you must have SOAP installed so that the EBI BLAST client can run on your
10785 system.</span></span></span></span></p>
10786
10787 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10788 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10789 lang=AF>It is a bit slow, but really worth it if your sequences are hard to
10790 align and if the accuracy of your alignment is important.<span
10791 style="mso-spacerun: yes">&nbsp; </span></span></span></span></span></p>
10792
10793 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10794 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10795 lang=AF>To use this mode, try:</span></span></span></span></p>
10796
10797 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
10798 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
10799 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
10800 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
10801
10802 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
10803 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
10804 style='mso-bookmark:_Toc101065206'><span style='mso-tab-count:1'>&nbsp;&nbsp; </span>t_coffee
10805 &lt;yoursequence&gt; -mode psicoffee</span></span></span></p>
10806
10807 </div>
10808
10809 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10810 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10811 lang=AF>Note that because PSI-BLAST is time consuming, T-Coffee stores the runs
10812 in its cache (./tcoffee/cache) so that it does not need to be re-run. It means
10813 that if you re-align your sequences (or add a few extra sequences), things will
10814 be considerably faster.</span></span></span></span></p>
10815
10816 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10817 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10818 lang=AF>If your installation procedure has managed to compile TMalign, and if
10819 T-Coffee has access to the EBI BLAST server (or any other server) you can also
10820 do the following:</span></span></span></span></p>
10821
10822 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
10823 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
10824 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
10825 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
10826
10827 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
10828 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
10829 style='mso-bookmark:_Toc101065206'><span style='mso-tab-count:1'>&nbsp;&nbsp; </span>t_coffee
10830 &lt;yoursequence&gt; -mode expresso</span></span></span></p>
10831
10832 </div>
10833
10834 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10835 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10836 lang=AF>That will look for structural templates. And if both these modes are
10837 running fine, then you are ready for the best, the &quot;crème de la
10838 crème&quot;:</span></span></span></span></p>
10839
10840 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
10841 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
10842 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
10843 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
10844
10845 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
10846 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
10847 style='mso-bookmark:_Toc101065206'><span style='mso-tab-count:1'>&nbsp;&nbsp; </span>t_coffee
10848 &lt;yoursequence&gt; -mode accurate</span></span></span></p>
10849
10850 </div>
10851
10852 <h2><span style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
10853 style='mso-bookmark:_Toc101065206'><a name="_Toc151732218">Installation of
10854 M-Coffee</a></span></span></span></h2>
10855
10856 <p class=MsoNormal><span style='mso-bookmark:_Toc102494675'><span
10857 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><o:p>&nbsp;</o:p></span></span></span></p>
10858
10859 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10860 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10861 lang=AF>M-Coffee is a special mode of T-Coffee that makes it possible to combine
10862 the output of many multiple sequence alignment packages. </span></span></span></span><span
10863 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
10864 style='mso-bookmark:_Toc101065206'><span style='mso-ansi-language:EN-US'><o:p></o:p></span></span></span></span></p>
10865
10866 <h3><span style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
10867 style='mso-bookmark:_Toc101065206'><a name="_Toc151732219">Automated
10868 Installation</a></span></span></span></h3>
10869
10870 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10871 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10872 lang=AF>In the T-Coffee distribution, type:</span></span></span></span></p>
10873
10874 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
10875 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
10876 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
10877 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
10878
10879 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
10880 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
10881 style='mso-bookmark:_Toc101065206'>./install mcoffee</span></span></span></p>
10882
10883 </div>
10884
10885 <p class=MsoNormal><span style='mso-bookmark:_Toc102494675'><span
10886 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><o:p>&nbsp;</o:p></span></span></span></p>
10887
10888 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10889 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10890 lang=AF>In theory, this command should download and install every required
10891 package. If, however, it fails, you should switch to the manual installation
10892 (see next).</span></span></span></span></p>
10893
10894 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10895 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10896 lang=AF>By default these packages will be in </span></span></span></span></p>
10897
10898 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
10899 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
10900 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
10901 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
10902
10903 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
10904 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
10905 style='mso-bookmark:_Toc101065206'>$HOME/.t_coffee/plugins</span></span></span></p>
10906
10907 </div>
10908
10909 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10910 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10911 lang=AF>If you want to have these companion packages in a different directory,
10912 you can either set the environement variable </span></span></span></span></p>
10913
10914 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
10915 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
10916 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
10917 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
10918
10919 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
10920 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
10921 style='mso-bookmark:_Toc101065206'>setenv PLUGINS_4_TCOFFEE=&lt;plugins dir&gt;</span></span></span></p>
10922
10923 </div>
10924
10925 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10926 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10927 lang=AF>Or use the command line flag -plugin (over-rides every other setting)</span></span></span></span></p>
10928
10929 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
10930 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
10931 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
10932 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
10933
10934 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
10935 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
10936 style='mso-bookmark:_Toc101065206'>t_coffee ... -plugins=&lt;plugins dir&gt;</span></span></span></p>
10937
10938 </div>
10939
10940 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10941 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10942 lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>
10943
10944 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10945 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10946 lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>
10947
10948 <h3><span style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
10949 style='mso-bookmark:_Toc101065206'><a name="_Toc151732220">Manual Installation</a></span></span></span></h3>
10950
10951 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10952 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10953 lang=AF>M-Coffee requires a standard T-Coffee installation (c.f. previous
10954 section) and the following packages to be installed on your system:</span></span></span></span></p>
10955
10956 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
10957 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10958 lang=AF><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span></span></span></p>
10959
10960 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
10961 mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
10962 background:#E6E6E6'>
10963
10964 <p class=examplefileCxSpFirst><span style='mso-bookmark:_Toc102494675'><span
10965 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>Package<span
10966 style='mso-tab-count:2'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Where
10967 From</span></span></span></p>
10968
10969 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10970 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>==========================================================</span></span></span></p>
10971
10972 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10973 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>ClustalW<span
10974 style='mso-tab-count:2'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>can
10975 interact with t_coffee</span></span></span></p>
10976
10977 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10978 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>----------------------------------------------------------</span></span></span></p>
10979
10980 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10981 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>Poa<span
10982 style='mso-tab-count:3'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>http://www.bioinformatics.ucla.edu/poa/</span></span></span></p>
10983
10984 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10985 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>----------------------------------------------------------</span></span></span></p>
10986
10987 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10988 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>Muscle<span
10989 style='mso-tab-count:2'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>http://www.drive5.com</span></span></span></p>
10990
10991 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10992 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
10993 style="mso-spacerun:
10994 yes">&nbsp;</span>----------------------------------------------------------</span></span></span></p>
10995
10996 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
10997 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>ProbCons<span
10998 style='mso-tab-count:2'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>http://probcons.stanford.edu/</span></span></span></p>
10999
11000 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
11001 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>ProbConsRNA<span
11002 style='mso-tab-count:2'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>http://probcons.stanford.edu/</span></span></span></p>
11003
11004 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
11005 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>----------------------------------------------------------</span></span></span></p>
11006
11007 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
11008 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>MAFFT<span
11009 style='mso-tab-count:1'> </span></span></span></span><a
11010 href="http://www.biophys.kyoto-/"><span style='mso-bookmark:_Toc102494675'><span
11011 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>http://www.biophys.kyoto-</span></span></span><span
11012 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
11013 style='mso-bookmark:_Toc101065206'></span></span></span></a><span
11014 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
11015 style='mso-bookmark:_Toc101065206'>u.ac.jp/~katoh/programs/align/mafft/</span></span></span></p>
11016
11017 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
11018 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>----------------------------------------------------------</span></span></span></p>
11019
11020 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
11021 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>Dialign-T<span
11022 style='mso-tab-count:2'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span></span><a
11023 href="http://dialign-t.gobics.de/"><span style='mso-bookmark:_Toc102494675'><span
11024 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>http://dialign-t.gobics.de/</span></span></span><span
11025 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
11026 style='mso-bookmark:_Toc101065206'></span></span></span></a><span
11027 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
11028 style='mso-bookmark:_Toc101065206'></span></span></span></p>
11029
11030 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
11031 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>Dialign-TX<span
11032 style='mso-tab-count:2'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span></span><a
11033 href="http://dialign-t.gobics.de/"><span style='mso-bookmark:_Toc102494675'><span
11034 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>http://dialign-tx.gobics.de/</span></span></span><span
11035 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
11036 style='mso-bookmark:_Toc101065206'></span></span></span></a><span
11037 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
11038 style='mso-bookmark:_Toc101065206'></span></span></span></p>
11039
11040 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
11041 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>----------------------------------------------------------</span></span></span></p>
11042
11043 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
11044 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>PCMA<span
11045 style='mso-tab-count:3'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span></span><a
11046 href="file://localhost/pub/PCMA"><span style='mso-bookmark:_Toc102494675'><span
11047 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>ftp://iole.swmed.edu/pub/PCMA/</span></span></span><span
11048 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
11049 style='mso-bookmark:_Toc101065206'></span></span></span></a><span
11050 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
11051 style='mso-bookmark:_Toc101065206'></span></span></span></p>
11052
11053 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
11054 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>----------------------------------------------------------</span></span></span></p>
11055
11056 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
11057 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>kalign<span
11058 style="mso-spacerun:
11059 yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
11060 </span>http://msa.cgb.ki.se</span></span></span></p>
11061
11062 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
11063 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>----------------------------------------------------------</span></span></span></p>
11064
11065 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
11066 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>amap<span
11067 style="mso-spacerun:
11068 yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
11069 </span>http://bio.math.berkeley.edu/amap/</span></span></span></p>
11070
11071 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
11072 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>-----------------------------------------------------------</span></span></span></p>
11073
11074 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
11075 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>proda_msa<span
11076 style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
11077 </span>http://bio.math.berkeley.edu/proda/</span></span></span></p>
11078
11079 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
11080 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>-----------------------------------------------------------</span></span></span></p>
11081
11082 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
11083 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>prank_msa<span
11084 style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
11085 </span>http://www.ebi.ac.uk/goldman-srv/prank/</span></span></span></p>
11086
11087 <p class=examplefileCxSpLast><span style='mso-bookmark:_Toc102494675'><span
11088 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><o:p>&nbsp;</o:p></span></span></span></p>
11089
11090 </div>
11091
11092 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
11093 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
11094 lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>
11095
11096 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
11097 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
11098 lang=AF>In our hands all these packages where very straightforward to compile
11099 and install on a standard cygwin or Linux configuration. Just make sure you
11100 have gcc, the C compiler, properly installed.</span></span></span></span></p>
11101
11102 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
11103 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
11104 lang=AF>Once the package is compiled and ready to use, make sure that the
11105 executable is on your path, so that t_coffee can find it automatically. Our
11106 favorite procedure is to create a bin directory in the home. If you do so, make
11107 sure this bin is in your path and fill it with all your executables (this is a
11108 standard Unix practice).</span></span></span></span></p>
11109
11110 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
11111 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
11112 lang=AF>If for some reason, you do not want this directory to be on your path,
11113 or you want to specify a precise directory containing the executables, you can
11114 use:</span></span></span></span></p>
11115
11116 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
11117 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
11118 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
11119 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
11120
11121 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
11122 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
11123 style='mso-bookmark:_Toc101065206'><span style='mso-tab-count:1'>&nbsp;&nbsp; </span>export
11124 PLUGINS_4_TCOFFEE=&lt;dir&gt;</span></span></span></p>
11125
11126 </div>
11127
11128 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
11129 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
11130 lang=AF>By default this directory is set to $HOME/.t_coffee/plugins/$OS, but
11131 you can over-ride it with the environement variable or using the flag:</span></span></span></span></p>
11132
11133 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
11134 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
11135 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
11136 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
11137
11138 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
11139 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
11140 style='mso-bookmark:_Toc101065206'><span style='mso-tab-count:1'>&nbsp;&nbsp; </span>t_coffee
11141 ...-plugins=&lt;dir&gt;</span></span></span></p>
11142
11143 </div>
11144
11145 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
11146 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
11147 lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>
11148
11149 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
11150 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
11151 lang=AF>If you cannot, or do not want to use a single bin directory, you can
11152 set the following environment variables to the absolute path values of the
11153 executable you want to use. Whenever they are set, these variables will
11154 supersede any other declaration. This is a convenient way to experiment with
11155 multiple package versions.</span></span></span></span></p>
11156
11157 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
11158 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
11159 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
11160 background:#FFFFCC;margin-left:70.2pt;margin-right:0cm'>
11161
11162 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
11163 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
11164 style='mso-bookmark:_Toc101065206'>POA_4_TCOOFFEE<br>
11165 CLUSTALW_4_TCOFFEE<br>
11166 POA_4_TCOFFEE<br>
11167 TCOFFEE_4_TCOFFEE<br>
11168 MAFFT_4_TCOFFEE<br>
11169 MUSCLE_4_TCOFFEE<br>
11170 DIALIGNT_4_TCOFFEE<br>
11171 PRANK_4_TCOFFEE<br>
11172 DIALIGNTX_4_TCOFFEE<br>
11173 <span style="mso-spacerun: yes">&nbsp;</span></span></span></span></p>
11174
11175 </div>
11176
11177 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
11178 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
11179 lang=AF>For three of these packages, you will need to copy some of the files in
11180 a special T-Coffee directory.</span></span></span></span></p>
11181
11182 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
11183 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
11184 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
11185 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
11186
11187 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
11188 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
11189 style='mso-bookmark:_Toc101065206'><span style='mso-tab-count:1'>&nbsp;&nbsp; </span>cp
11190 POA_DIR/* ~/.t_coffee/mcoffee/</span></span></span></p>
11191
11192 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
11193 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
11194 style='mso-bookmark:_Toc101065206'><span style='mso-tab-count:1'>&nbsp;&nbsp; </span>cp
11195 DIALIGN-T/conf/*<span style="mso-spacerun: yes">&nbsp;
11196 </span>~/.t_coffee/mcoffee</span></span></span></p>
11197
11198 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
11199 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
11200 style='mso-bookmark:_Toc101065206'><span style='mso-tab-count:1'>&nbsp;&nbsp; </span>cp
11201 DIALIGN-TX/conf/*<span style="mso-spacerun: yes">&nbsp;
11202 </span>~/.t_coffee/mcoffee</span></span></span></p>
11203
11204 </div>
11205
11206 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
11207 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
11208 lang=AF>Note that the following files are enough for default usage:</span></span></span></span></p>
11209
11210 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
11211 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
11212 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
11213 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
11214
11215 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
11216 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
11217 style='mso-bookmark:_Toc101065206'>BLOSUM.diag_prob_t10<span
11218 style="mso-spacerun: yes">&nbsp;&nbsp; </span>BLOSUM75.scr<span
11219 style="mso-spacerun: yes">&nbsp; </span>blosum80_trunc.mat<span
11220 style="mso-spacerun:
11221 yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span></span></p>
11222
11223 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
11224 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
11225 style='mso-bookmark:_Toc101065206'>dna_diag_prob_100_exp_330000<span
11226 style="mso-spacerun: yes">&nbsp; </span>dna_diag_prob_200_exp_110000</span></span></span></p>
11227
11228 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
11229 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
11230 style='mso-bookmark:_Toc101065206'>BLOSUM.scr<span style="mso-spacerun:
11231 yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
11232 </span>BLOSUM90.scr<span style="mso-spacerun: yes">&nbsp;
11233 </span>dna_diag_prob_100_exp_110000</span></span></span></p>
11234
11235 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
11236 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
11237 style='mso-bookmark:_Toc101065206'>dna_diag_prob_100_exp_550000<span
11238 style="mso-spacerun: yes">&nbsp; </span>dna_diag_prob_250_exp_110000</span></span></span></p>
11239
11240 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
11241 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
11242 style='mso-bookmark:_Toc101065206'>BLOSUM75.diag_prob_t2<span
11243 style="mso-spacerun: yes">&nbsp; </span>blosum80.mat<span style="mso-spacerun:
11244 yes">&nbsp; </span>dna_diag_prob_100_exp_220000<span style="mso-spacerun:
11245 yes">&nbsp; </span></span></span></span></p>
11246
11247 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
11248 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
11249 style='mso-bookmark:_Toc101065206'>dna_diag_prob_150_exp_110000<span
11250 style="mso-spacerun: yes">&nbsp; </span>dna_matrix.scr</span></span></span></p>
11251
11252 </div>
11253
11254 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
11255 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
11256 lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>
11257
11258 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
11259 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
11260 lang=AF>If you would rather have the mcoffee directory in some other location,
11261 set the MCOFFEE_4_TCOFFEE environement variable to the propoer directory:</span></span></span></span></p>
11262
11263 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
11264 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
11265 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
11266 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
11267
11268 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
11269 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
11270 style='mso-bookmark:_Toc101065206'><span style='mso-tab-count:1'>&nbsp;&nbsp; </span>setenv
11271 MCOFFEE_4_TCOFFEE &lt;directory containing mcoffee files&gt;</span></span></span></p>
11272
11273 </div>
11274
11275 <h2><span style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
11276 style='mso-bookmark:_Toc101065206'><a name="_Toc151732221">Installation of APDB
11277 and iRMSD</a></span></span></span></h2>
11278
11279 <p class=MsoBodyText><span style='mso-bookmark:_Toc102494675'><span
11280 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>APDB
11281 and iRMSD are incorporated in T-Coffee. Once t_coffee is installed, you can
11282 invoque these programs by typing:</span></span></span></p>
11283
11284 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
11285 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
11286 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
11287 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
11288
11289 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
11290 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
11291 style='mso-bookmark:_Toc101065206'><span style='mso-tab-count:1'>&nbsp;&nbsp; </span>t_coffee
11292 &#8211;other_pg apdb<br>
11293 <span style='mso-tab-count:1'>&nbsp;&nbsp; </span>t_coffee &#8211;other_pg
11294 irmsd</span></span></span></p>
11295
11296 </div>
11297
11298 <h2><span style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
11299 style='mso-bookmark:_Toc101065206'><a name="_Toc151732222">Installation of tRMSD</a></span></span></span></h2>
11300
11301 <p class=MsoBodyText><span style='mso-bookmark:_Toc102494675'><span
11302 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>tRMSD
11303 comes along with t_coffee but it also requires the package phylip in order to
11304 be functional. Phylip can be obtained from:</span></span></span></p>
11305
11306 <p class=MyNormal><span style='mso-bookmark:_Toc102494675'><span
11307 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
11308 lang=AF><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span></span></span></p>
11309
11310 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
11311 mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
11312 background:#E6E6E6'>
11313
11314 <p class=examplefileCxSpFirst><span style='mso-bookmark:_Toc102494675'><span
11315 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>Package<span
11316 style='mso-tab-count:2'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Function</span></span></span></p>
11317
11318 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
11319 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>===================================================</span></span></span></p>
11320
11321 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
11322 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>---------------------------------------------------</span></span></span></p>
11323
11324 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
11325 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>Phylip<span
11326 style='mso-tab-count:2'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Phylogenetic
11327 tree computation</span></span></span></p>
11328
11329 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494675'><span
11330 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><span
11331 style='mso-tab-count:3'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>evolution.genetics.washington.edu/phylip.html</span></span></span></p>
11332
11333 <p class=examplefileCxSpLast><span style='mso-bookmark:_Toc102494675'><span
11334 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>---------------------------------------------------</span></span></span></p>
11335
11336 </div>
11337
11338 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
11339 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
11340 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
11341 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
11342
11343 <p class=MyExample style='margin-left:0cm;text-indent:14.1pt;background:#FFFFCC'><span
11344 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
11345 style='mso-bookmark:_Toc101065206'>t_coffee &#8211;other_pg trmsd</span></span></span></p>
11346
11347 </div>
11348
11349 <h2><span style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
11350 style='mso-bookmark:_Toc101065206'><o:p>&nbsp;</o:p></span></span></span></h2>
11351
11352 <h2><span style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
11353 style='mso-bookmark:_Toc101065206'><a name="_Toc151732223">Installation of
11354 seq_reformat</a></span></span></span></h2>
11355
11356 <p class=MsoBodyText><span style='mso-bookmark:_Toc102494675'><span
11357 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>Seq_reformat
11358 is a reformatting package that is part of t_coffee. To use it (and see the
11359 available options), type:</span></span></span></p>
11360
11361 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
11362 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
11363 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
11364 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
11365
11366 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
11367 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
11368 style='mso-bookmark:_Toc101065206'><span style='mso-tab-count:1'>&nbsp;&nbsp; </span>t_coffee
11369 &#8211;other_pg seq_reformat</span></span></span></p>
11370
11371 </div>
11372
11373 <h2><span style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
11374 style='mso-bookmark:_Toc101065206'><a name="_Toc151732224">Installation of
11375 extract_from_pdb</a></span></span></span></h2>
11376
11377 <p class=MsoBodyText><span style='mso-bookmark:_Toc102494675'><span
11378 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>Extract_from_pdb
11379 is a PDB reformatting package that is part of t_coffee. To use it (and see the
11380 available options), type.</span></span></span></p>
11381
11382 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
11383 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
11384 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
11385 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
11386
11387 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
11388 style='mso-bookmark:_Toc102494675'><span style='mso-bookmark:_Toc102494295'><span
11389 style='mso-bookmark:_Toc101065206'><span style='mso-tab-count:1'>&nbsp;&nbsp; </span>t_coffee
11390 &#8211;other_pg extract_from_pdb &#8211;h</span></span></span></p>
11391
11392 </div>
11393
11394 <p class=MsoBodyText><span style='mso-bookmark:_Toc102494675'><span
11395 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'>Extract_from_pdb
11396 requires wget in order to automatically fetch PDB structures.</span></span></span></p>
11397
11398 <p class=MsoBodyText><span style='mso-bookmark:_Toc102494675'><span
11399 style='mso-bookmark:_Toc102494295'><span style='mso-bookmark:_Toc101065206'><o:p>&nbsp;</o:p></span></span></span></p>
11400
11401 <span style='mso-bookmark:_Toc101065206'></span><span style='mso-bookmark:_Toc102494295'></span><span
11402 style='mso-bookmark:_Toc102494675'></span>
11403
11404 <h2><a name="_Toc151732225">Installation of 3D-Coffee/Expresso</a></h2>
11405
11406 <p class=MyNormal><span lang=AF>3D-Coffee/Expresso is a special mode of
11407 T-Coffee that makes it possible to combine sequences and structures. The main
11408 difference between Expresso and 3D-Coffee is that Expresso fetches the
11409 structures itself. </span><span style='mso-ansi-language:EN-US'><o:p></o:p></span></p>
11410
11411 <h3><a name="_Toc151732226">Automated Installation</a></h3>
11412
11413 <p class=MyNormal><span lang=AF>In the T-Coffee distribution, type:</span></p>
11414
11415 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
11416 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
11417 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
11418 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
11419
11420 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>./install
11421 expresso</p>
11422
11423 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>OR</p>
11424
11425 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>./install
11426 3dcoffee</p>
11427
11428 </div>
11429
11430 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
11431
11432 <p class=MyNormal><span lang=AF>In theory, this command should download and
11433 install every required package (<b>except fugue</b>). If, however, it fails,
11434 you should switch to the manual installation (see next).</span></p>
11435
11436 <h3><a name="_Toc151732227">Manual Installation</a></h3>
11437
11438 <p class=MyNormal><span lang=AF>In order to make the most out of T-Coffee, you
11439 will need to install the following packages (make sure the executable is named
11440 as indicated below):</span></p>
11441
11442 <p class=MyNormal><span lang=AF><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></p>
11443
11444 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
11445 mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
11446 background:#E6E6E6'>
11447
11448 <p class=examplefileCxSpFirst>Package<span style='mso-tab-count:2'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Function</p>
11449
11450 <p class=examplefileCxSpMiddle>===================================================</p>
11451
11452 <p class=examplefileCxSpMiddle>---------------------------------------------------</p>
11453
11454 <p class=examplefileCxSpMiddle>wget<span style='mso-tab-count:3'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>3DCoffee
11455 </p>
11456
11457 <p class=examplefileCxSpMiddle><span style='mso-tab-count:3'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Automatic
11458 Downloading of Structures</p>
11459
11460 <p class=examplefileCxSpMiddle>---------------------------------------------------</p>
11461
11462 <p class=examplefileCxSpMiddle>sap<span style='mso-tab-count:3'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>structure/structure
11463 comparisons </p>
11464
11465 <p class=examplefileCxSpMiddle>(obtain it from W. Taylor, NIMR-MRC).</p>
11466
11467 <p class=examplefileCxSpMiddle>---------------------------------------------------</p>
11468
11469 <p class=examplefileCxSpMiddle>TMalign<span style='mso-tab-count:2'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>zhang.bioinformatics.ku.edu/TM-align/</p>
11470
11471 <p class=examplefileCxSpMiddle>---------------------------------------------------</p>
11472
11473 <p class=examplefileCxSpMiddle>mustang<span style='mso-tab-count:2'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>www.cs.mu.oz.au/~arun/mustang/</p>
11474
11475 <p class=examplefileCxSpMiddle>---------------------------------------------------</p>
11476
11477 <p class=examplefileCxSpMiddle>wublastclient<span style="mso-spacerun:
11478 yes">&nbsp;&nbsp;&nbsp;&nbsp;
11479 </span>www.ebi.ac.uk/Tools/webservices/clients/wublast</p>
11480
11481 <p class=examplefileCxSpMiddle>---------------------------------------------------</p>
11482
11483 <p class=examplefileCxSpMiddle>Blast<span style='mso-tab-count:3'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><a
11484 href="http://www.ncbi.nih.nlm.gov/">www.ncbi.nih.nlm.gov</a></p>
11485
11486 <p class=examplefileCxSpMiddle>---------------------------------------------------</p>
11487
11488 <p class=examplefileCxSpMiddle>Fugue*<span style='mso-tab-count:2'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>protein
11489 to structure alignment program</p>
11490
11491 <p class=examplefileCxSpMiddle><span style='mso-tab-count:3'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>http://www-cryst.bioc.cam.ac.uk/fugue/download.html</p>
11492
11493 <p class=examplefileCxSpLast><span style='mso-tab-count:3'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>***NOT
11494 COMPULSORY***</p>
11495
11496 </div>
11497
11498 <p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>
11499
11500 <p class=MyNormal><span lang=AF>Once the package is installed, make sure make
11501 sure that the executable is on your path, so that t_coffee can find it
11502 automatically.</span></p>
11503
11504 <p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>
11505
11506 <p class=MyNormal><span lang=AF>The wublast client makes it possible to run
11507 BLAST at the EBI without having to install any database locally. It is an ideal
11508 solution if you are only using expresso occasionally.</span></p>
11509
11510 <p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>
11511
11512 <h3><a name="_Toc151732228">Installing Fugue for T-Coffee</a></h3>
11513
11514 <p class=MyNormal><span lang=AF>Uses a standard fugue installation. You only
11515 need to install the following packages:</span></p>
11516
11517 <p class=MyNormal><span lang=AF><span style="mso-spacerun:
11518 yes">&nbsp;</span>joy, melody, fugueali, sstruc, hbond</span></p>
11519
11520 <p class=MyNormal><span lang=AF>If you have root privileges, you can install
11521 the common data in: </span></p>
11522
11523 <p class=MyNormal><span lang=AF>cp fugue/classdef.dat<span style='mso-tab-count:
11524 1'> </span>/data/fugue/SUBST/classdef.dat</span></p>
11525
11526 <p class=MyNormal><span lang=AF>otherwise</span></p>
11527
11528 <p class=MyNormal><span lang=AF>Setenv MELODY_CLASSDEF=&lt;location&gt;</span></p>
11529
11530 <p class=MyNormal><span lang=AF>Setenv MELODY_SUBST=fugue/allmat.dat</span></p>
11531
11532 <p class=MyNormal><span lang=AF><span style="mso-spacerun: yes">&nbsp;</span></span></p>
11533
11534 <p class=MyNormal><span lang=AF>All the other configuration files must be in
11535 the right location. </span></p>
11536
11537 <h2><a name="_Toc151732229">Installation of R-Coffee</a></h2>
11538
11539 <p class=MyNormal><span lang=AF>R-Coffee is a special mode able to align RNA
11540 sequences while taking into account their secondary structure.</span><span
11541 style='mso-ansi-language:EN-US'><o:p></o:p></span></p>
11542
11543 <h3><a name="_Toc151732230">Automated Installation</a></h3>
11544
11545 <p class=MyNormal><span lang=AF>In the T-Coffee distribution, type:</span></p>
11546
11547 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
11548 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
11549 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
11550 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
11551
11552 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>./install rcoffee</p>
11553
11554 </div>
11555
11556 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
11557
11558 <p class=MyNormal><span lang=AF>In theory, this command should download and
11559 install every required package (except <b>consan</b>). If, however, it fails,
11560 you should switch to the manual installation (see next).</span></p>
11561
11562 <h3><a name="_Toc151732231">Manual Installation</a></h3>
11563
11564 <p class=MyNormal><span lang=AF>R-Coffee only requires the package Vienna to be
11565 installed, in order to compute multiple sequence alignments. To make the best
11566 out of it, you should also have all the packages required by M-Coffee</span></p>
11567
11568 <p class=MyNormal><span lang=AF><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></p>
11569
11570 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
11571 mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
11572 background:#E6E6E6'>
11573
11574 <p class=examplefileCxSpFirst>Package<span style='mso-tab-count:2'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Function</p>
11575
11576 <p class=examplefileCxSpMiddle>===================================================</p>
11577
11578 <p class=examplefileCxSpMiddle>---------------------------------------------------</p>
11579
11580 <p class=examplefileCxSpMiddle>consan<span style='mso-tab-count:2'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>R-Coffee
11581 </p>
11582
11583 <p class=examplefileCxSpMiddle><span style='mso-tab-count:3'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Computes
11584 highly accurate pairwise Alignments</p>
11585
11586 <p class=examplefileCxSpMiddle><span style='mso-tab-count:3'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>***NOT
11587 COMPULSORY***</p>
11588
11589 <p class=examplefileCxSpMiddle><span style='mso-tab-count:3'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>selab.janelia.org/software/consan/</p>
11590
11591 <p class=examplefileCxSpMiddle>---------------------------------------------------</p>
11592
11593 <p class=examplefileCxSpMiddle>RNAplfold<span style='mso-tab-count:2'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Computes
11594 RNA secondary Structures </p>
11595
11596 <p class=examplefileCxSpMiddle><span style='mso-tab-count:3'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>www.tbi.univie.ac.at/~ivo/RNA/</p>
11597
11598 <p class=examplefileCxSpMiddle>---------------------------------------------------</p>
11599
11600 <p class=examplefileCxSpMiddle>probconsRNA<span style='mso-tab-count:2'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>probcons.stanford.edu/</p>
11601
11602 <p class=examplefileCxSpMiddle><span style="mso-spacerun:
11603 yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></p>
11604
11605 <p class=examplefileCxSpMiddle>---------------------------------------------------</p>
11606
11607 <p class=examplefileCxSpMiddle>M-Coffee<span style='mso-tab-count:2'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>T-Coffee
11608 and the most common MSA Packages</p>
11609
11610 <p class=examplefileCxSpLast><span style='mso-tab-count:3'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>(cf
11611 M-Coffee in this installation guide)</p>
11612
11613 </div>
11614
11615 <h3><a name="_Toc151732232">Installing ProbbonsRNA for R-Coffee</a></h3>
11616
11617 <p class=MyNormal><span lang=AF>Follow the installation procedure, but make
11618 sure you rename the probcons executable into probconsRNA.</span></p>
11619
11620 <h3><a name="_Toc151732233">Installing Consan for R-Coffee</a></h3>
11621
11622 <p class=MyNormal><span lang=AF>In order to insure a proper interface beween
11623 consan and R-Coffee, you must make sure that the file mix80.mod is in the
11624 directory ~/.t_coffee/mcoffee or in the mcoffee directory otherwise declared.</span></p>
11625
11626 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
11627
11628 <div style='mso-element:para-border-div;border:solid windowtext 3.0pt;
11629 padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#CCCCCC;margin-left:0cm;margin-right:
11630 4.25pt'>
11631
11632 <p class=ChapterTitle><a name="_Toc101065207"></a><a name="_Toc102494676"><span
11633 style='mso-bookmark:_Toc101065207'>Q</span></a>uick Start</p>
11634
11635 </div>
11636
11637 <p class=MsoBodyText>We only give you the very basics here. Please use the
11638 Tutorial for more detailed information on how to use our tools.</p>
11639
11640 <div style='mso-element:para-border-div;border:solid windowtext 1.5pt;
11641 padding:0cm 0cm 0cm 0cm;background:#F7CBB7'>
11642
11643 <p class=Warning><a name="_Toc101065208"></a><a name="_Toc102494296"></a><a
11644 name="_Toc102494677"><span style='mso-bookmark:_Toc102494296'><span
11645 style='mso-bookmark:_Toc101065208'>IMPORTANT: All the files mentionned here
11646 (sampe_seq...) can be found in the example directory of the distribution.</span></span></a></p>
11647
11648 </div>
11649
11650 <h2><span style='mso-bookmark:_Toc102494677'><span style='mso-bookmark:_Toc102494296'><span
11651 style='mso-bookmark:_Toc101065208'><a name="_Toc151732234">T-COFFEE</a></span></span></span></h2>
11652
11653 <p class=MyNormal><span lang=AF>Write your sequences in the same file
11654 (Swiss-prot, Fasta or Pir) and type. </span></p>
11655
11656 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
11657 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
11658 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
11659 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
11660
11661 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
11662 sample_seq1.fasta<span style="mso-spacerun: yes">&nbsp; </span></p>
11663
11664 </div>
11665
11666 <p class=MyNormal><span lang=AF>This will output two files:</span></p>
11667
11668 <p class=example2CxSpFirst>sample_seq1.aln: your Multiple Sequence Alignment</p>
11669
11670 <p class=example2CxSpLast>sample_seq1.dnd: The Guide tree (newick Format)</p>
11671
11672 <div style='mso-element:para-border-div;border:solid windowtext 1.5pt;
11673 padding:0cm 0cm 0cm 0cm;background:#F7CBB7'>
11674
11675 <p class=Warning>IMPORTANT: </p>
11676
11677 <p class=Warning>In theory nucleic acids should be automatically detected and
11678 the default methods should be adapted appropriately. However, sometimes this
11679 may fail, either because the sequences are too short or contain too many
11680 ambiguity codes. </p>
11681
11682 <p class=Warning>When this happens, you are advised to explicitly set the type
11683 of your sequences</p>
11684
11685 <p class=Warning>NOTE: the &#8211;mode=dna is not needed or supported anymore</p>
11686
11687 </div>
11688
11689 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
11690 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
11691 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
11692 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
11693
11694 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
11695 sample_dnaseq1.fasta &#8211;type=dna</p>
11696
11697 </div>
11698
11699 <h2><a name="_Toc101065209"></a><a name="_Toc102494297"></a><a
11700 name="_Toc102494678"></a><a name="_Toc151732235"><span style='mso-bookmark:
11701 _Toc102494678'><span style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:
11702 _Toc101065209'>M-Coffee</span></span></span></a><span style='mso-bookmark:_Toc102494678'><span
11703 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'></span></span></span></h2>
11704
11705 <p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
11706 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
11707 lang=AF>M-Coffee is a Meta version of T-Coffee that makes it possible to
11708 combine the output of at least eight packages (Muscle, probcons, poa, dialignT,
11709 mafft, clustalw, PCMA and T-Coffee).</span></span></span></span></p>
11710
11711 <p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
11712 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
11713 lang=AF>If all these packages are already installed on your machine. You must:</span></span></span></span></p>
11714
11715 <p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
11716 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
11717 lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>
11718
11719 <p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
11720 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
11721 lang=AF>1-set the following environment variables</span></span></span></span></p>
11722
11723 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
11724 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
11725 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
11726 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
11727
11728 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
11729 style='mso-bookmark:_Toc102494678'><span style='mso-bookmark:_Toc102494297'><span
11730 style='mso-bookmark:_Toc101065209'><span style='mso-tab-count:1'>&nbsp;&nbsp; </span>export
11731 POA_DIR=[absolute path of the POA installation dir]</span></span></span></p>
11732
11733 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
11734 style='mso-bookmark:_Toc102494678'><span style='mso-bookmark:_Toc102494297'><span
11735 style='mso-bookmark:_Toc101065209'><span style='mso-tab-count:1'>&nbsp;&nbsp; </span>export
11736 DIALIGNT_DIR=[Absolute path of the DIALIGN-T/conf</span></span></span></p>
11737
11738 </div>
11739
11740 <p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
11741 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
11742 lang=AF>Once this is done, write your sequences in a file and run: same file
11743 (Swiss-prot, Fasta or Pir) and type. </span></span></span></span></p>
11744
11745 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
11746 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
11747 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
11748 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
11749
11750 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
11751 style='mso-bookmark:_Toc102494678'><span style='mso-bookmark:_Toc102494297'><span
11752 style='mso-bookmark:_Toc101065209'>PROMPT: t_coffee sample_seq1.fasta &#8211;mode
11753 mcoffee </span></span></span></p>
11754
11755 </div>
11756
11757 <p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
11758 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
11759 lang=AF>If the program starts complaining one package or the other is missing,
11760 this means you will have to go the hard way and install all these packages
11761 yourself... Proceed to the M-Coffee section for more detailed instructions.</span></span></span></span></p>
11762
11763 <h2><span style='mso-bookmark:_Toc102494678'><span style='mso-bookmark:_Toc102494297'><span
11764 style='mso-bookmark:_Toc101065209'><a name="_Toc151732236">Expresso</a></span></span></span></h2>
11765
11766 <p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
11767 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
11768 lang=AF>If you have installed the EBI wublast.pl client, Expresso will BLAST
11769 your sequences against PDB, identify the best targets and use these to align
11770 your proteins.</span></span></span></span></p>
11771
11772 <p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
11773 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
11774 lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>
11775
11776 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
11777 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
11778 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
11779 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
11780
11781 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
11782 style='mso-bookmark:_Toc102494678'><span style='mso-bookmark:_Toc102494297'><span
11783 style='mso-bookmark:_Toc101065209'>PROMPT: t_coffee sample_seq1.fasta &#8211;mode
11784 expresso</span></span></span></p>
11785
11786 </div>
11787
11788 <p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
11789 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
11790 lang=AF>If you did not manage to install all the required structural packages
11791 for Expresso, like Fugue or Sap, you can still run expresso by selecting
11792 yourself the structural packages you want to use. For instance, if you'd rather
11793 use TM-Align than sap, try: </span></span></span></span></p>
11794
11795 <p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
11796 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
11797 lang=AF><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span></span></span></p>
11798
11799 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
11800 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
11801 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
11802 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
11803
11804 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
11805 style='mso-bookmark:_Toc102494678'><span style='mso-bookmark:_Toc102494297'><span
11806 style='mso-bookmark:_Toc101065209'>PROMPT: t_coffee sample_seq1.fasta
11807 &#8211;template_file EXPRESSO -method TMalign_pair</span></span></span></p>
11808
11809 </div>
11810
11811 <p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
11812 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
11813 lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>
11814
11815 <h2><span style='mso-bookmark:_Toc102494678'><span style='mso-bookmark:_Toc102494297'><span
11816 style='mso-bookmark:_Toc101065209'><a name="_Toc151732237">R-Coffee</a></span></span></span></h2>
11817
11818 <p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
11819 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
11820 lang=AF>R-Coffee can be used to align RNA sequences, using their RNApfold
11821 predicted secondary structures. The best results are obtained by using the
11822 consan pairwise method. If you have consan installed:</span></span></span></span></p>
11823
11824 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
11825 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
11826 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
11827 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
11828
11829 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
11830 style='mso-bookmark:_Toc102494678'><span style='mso-bookmark:_Toc102494297'><span
11831 style='mso-bookmark:_Toc101065209'>t_coffee sample_rnaseq1.fasta
11832 &#8211;special_mode rcoffee_consan </span></span></span></p>
11833
11834 </div>
11835
11836 <p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
11837 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
11838 lang=AF>This will only work if your sequences are short enough (less than 200
11839 nucleotides). A good alternative is the rmcoffee mode that will run Muscle,
11840 Probcons4RNA and MAfft and then use the secondary structures predicted by
11841 RNApfold. </span></span></span></span></p>
11842
11843 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
11844 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
11845 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
11846 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
11847
11848 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
11849 style='mso-bookmark:_Toc102494678'><span style='mso-bookmark:_Toc102494297'><span
11850 style='mso-bookmark:_Toc101065209'>PROMPT: t_coffee sample_rnaseq1.fasta
11851 &#8211;mode mrcoffee </span></span></span></p>
11852
11853 </div>
11854
11855 <p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
11856 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
11857 lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>
11858
11859 <p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
11860 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
11861 lang=AF>If you want to decide yourself which methods should be combined by
11862 R-Coffee, run:</span></span></span></span></p>
11863
11864 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
11865 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
11866 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
11867 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
11868
11869 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
11870 style='mso-bookmark:_Toc102494678'><span style='mso-bookmark:_Toc102494297'><span
11871 style='mso-bookmark:_Toc101065209'>PROMPT: t_coffee sample_rnaseq1.fasta
11872 &#8211;mode rcoffee -method lalign_id_pair slow_pair </span></span></span></p>
11873
11874 </div>
11875
11876 <p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
11877 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
11878 lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>
11879
11880 <p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
11881 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
11882 lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>
11883
11884 <h2><span style='mso-bookmark:_Toc102494678'><span style='mso-bookmark:_Toc102494297'><span
11885 style='mso-bookmark:_Toc101065209'><br>
11886 <a name="_Toc151732238">iRMSD and APDB</a></span></span></span></h2>
11887
11888 <p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
11889 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
11890 lang=AF>All you need is a file containing the alignment of sequences with a
11891 known structure. These sequences must be named according to their PDB ID,
11892 followed by the chain index ( 1aabA for instance). All the sequences do not
11893 need to have a known structure, but at least two need to have it.</span></span></span></span></p>
11894
11895 <p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
11896 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
11897 lang=AF>Given the alignment:</span></span></span></span></p>
11898
11899 <p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
11900 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
11901 lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>
11902
11903 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
11904 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
11905 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
11906 background:#FFFFCC;margin-left:42.55pt;margin-right:0cm'>
11907
11908 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
11909 style='mso-bookmark:_Toc102494678'><span style='mso-bookmark:_Toc102494297'><span
11910 style='mso-bookmark:_Toc101065209'>PROMPT: t_coffee &#8211;other_pg irmsd -aln
11911 3d_sample4.aln </span></span></span></p>
11912
11913 </div>
11914
11915 <h2><span style='mso-bookmark:_Toc102494678'><span style='mso-bookmark:_Toc102494297'><span
11916 style='mso-bookmark:_Toc101065209'><a name="_Toc151732239">tRMSD</a></span></span></span></h2>
11917
11918 <p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
11919 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
11920 lang=AF>tRMSD is a structure based clustering method using the iRMSD to drive
11921 the clustering. The T-RMSD supports all the parameters supported by iRMSD or
11922 APDB.</span></span></span></span></p>
11923
11924 <p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
11925 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
11926 lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>
11927
11928 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
11929 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
11930 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
11931 background:#FFFFCC;margin-left:42.55pt;margin-right:0cm'>
11932
11933 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
11934 style='mso-bookmark:_Toc102494678'><span style='mso-bookmark:_Toc102494297'><span
11935 style='mso-bookmark:_Toc101065209'>PROMPT: t_coffee &#8211;other_pg trmsd -aln
11936 3d_sample5.aln -template_file 3d_sample5.template_list </span></span></span></p>
11937
11938 </div>
11939
11940 <p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
11941 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
11942 style='mso-ansi-language:EN-US'>3d_sample5.aln is a multiple alignment in which
11943 each sequence has a known structure. The file </span><span lang=AF>3d_sample5.template_list
11944 is a fasta like file declaring the structure associated with each sequence, in
11945 the form: </span></span></span></span></p>
11946
11947 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
11948 mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
11949 background:#E6E6E6;margin-left:0cm;margin-right:1.0cm'>
11950
11951 <p class=examplefilesmall><span style='mso-bookmark:_Toc102494678'><span
11952 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'>&gt;
11953 &lt;seq_name&gt; _P_ &lt;PDB structure file or name&gt; </span></span></span></p>
11954
11955 </div>
11956
11957 <p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
11958 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
11959 lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>
11960
11961 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
11962 mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
11963 background:#E6E6E6'>
11964
11965 <p class=examplefileCxSpFirst><span style='mso-bookmark:_Toc102494678'><span
11966 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'>*******
11967 3d_sample5.template_list ********<span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span></span></p>
11968
11969 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494678'><span
11970 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'>&gt;2UWI-3A
11971 _P_ 2UWI-3.pdb</span></span></span></p>
11972
11973 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494678'><span
11974 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'>&gt;2UWI-2A
11975 _P_ 2UWI-2.pdb</span></span></span></p>
11976
11977 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494678'><span
11978 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'>&gt;2UWI-1A
11979 _P_ 2UWI-1.pdb</span></span></span></p>
11980
11981 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494678'><span
11982 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'>&gt;2HEY-4R
11983 _P_ 2HEY-4.pdb</span></span></span></p>
11984
11985 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494678'><span
11986 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'>...</span></span></span></p>
11987
11988 <p class=examplefileCxSpLast><span style='mso-bookmark:_Toc102494678'><span
11989 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'>**************************************</span></span></span></p>
11990
11991 </div>
11992
11993 <p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
11994 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
11995 lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>
11996
11997 <p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
11998 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
11999 lang=AF>The program then outputs a series of files</span></span></span></span></p>
12000
12001 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
12002 mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
12003 background:#E6E6E6'>
12004
12005 <p class=examplefileCxSpFirst><span style='mso-bookmark:_Toc102494678'><span
12006 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
12007 style='font-size:8.0pt'>Template Type: [3d_sample5.template_list] Mode Or File:
12008 [3d_sample5.template_list] [Start]<o:p></o:p></span></span></span></span></p>
12009
12010 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494678'><span
12011 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
12012 style='font-size:8.0pt'><span style="mso-spacerun:
12013 yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>[Sample
12014 Columns][TOT=<span style="mso-spacerun: yes">&nbsp;&nbsp; </span>51][100
12015 %][ELAPSED TIME:<span style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp; </span>0
12016 sec.]<o:p></o:p></span></span></span></span></p>
12017
12018 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494678'><span
12019 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
12020 style='font-size:8.0pt'><span style="mso-spacerun:
12021 yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>[Tree
12022 Cmp][TOT=<span style="mso-spacerun: yes">&nbsp;&nbsp; </span>13][ 92 %][ELAPSED
12023 TIME:<span style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp; </span>0 sec.]<o:p></o:p></span></span></span></span></p>
12024
12025 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494678'><span
12026 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
12027 style='font-size:8.0pt'><span style="mso-spacerun: yes">&nbsp;</span>#### File
12028 Type=<span style="mso-spacerun: yes">&nbsp;&nbsp; </span>TreeList Format=<span
12029 style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp; </span>newick Name=
12030 3d_sample5.tot_pos_list<o:p></o:p></span></span></span></span></p>
12031
12032 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494678'><span
12033 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
12034 style='font-size:8.0pt'><span style="mso-spacerun: yes">&nbsp;</span>#### File
12035 Type=<span style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
12036 </span>Tree Format=<span style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;
12037 </span>newick Name= 3d_sample5.struc_tree10<o:p></o:p></span></span></span></span></p>
12038
12039 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494678'><span
12040 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
12041 style='font-size:8.0pt'><span style="mso-spacerun: yes">&nbsp;</span>#### File
12042 Type=<span style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
12043 </span>Tree Format=<span style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;
12044 </span>newick Name= 3d_sample5.struc_tree50<o:p></o:p></span></span></span></span></p>
12045
12046 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494678'><span
12047 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
12048 style='font-size:8.0pt'><span style="mso-spacerun: yes">&nbsp;</span>#### File
12049 Type=<span style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
12050 </span>Tree Format=<span style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;
12051 </span>newick Name= 3d_sample5.struc_tree100<o:p></o:p></span></span></span></span></p>
12052
12053 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494678'><span
12054 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
12055 style='font-size:8.0pt'><span style="mso-spacerun: yes">&nbsp;</span>#### File
12056 Type= Colored MSA Format= score_html Name= 3d_sample5.struc_tree.html<o:p></o:p></span></span></span></span></p>
12057
12058 <p class=examplefileCxSpLast><span style='mso-bookmark:_Toc102494678'><span
12059 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><o:p>&nbsp;</o:p></span></span></span></p>
12060
12061 </div>
12062
12063 <p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
12064 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
12065 lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>
12066
12067 <p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
12068 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
12069 lang=AF>3d_sample5.tot_pos_list <span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp; </span>is
12070 a list of the tRMSD tree associated with every position. </span></span></span></span></p>
12071
12072 <p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
12073 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
12074 lang=AF>3d_sample5.struc_tree100<span style='mso-tab-count:1'>&nbsp;&nbsp; </span>is
12075 a consensus tree (phylip/consense) of the trees contained in the previous file.
12076 <b>This file is the default output<o:p></o:p></b></span></span></span></span></p>
12077
12078 <p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
12079 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
12080 lang=AF>3d_sample5.struc_tree10<span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp; </span>is
12081 a consensus tree (phylip/consense) of the 10% trees having the higest average
12082 agreement with the rest</span></span></span></span></p>
12083
12084 <p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
12085 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
12086 lang=AF>3d_sample5.struc_tree10<span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp; </span>is
12087 a consensus tree (phylip/consense) of the 50% trees having the higest average
12088 agreement with the rest</span></span></span></span></p>
12089
12090 <p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
12091 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
12092 lang=AF>3d_sample5.html<span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>is
12093 a colored version of the output showing in red the positions that give the
12094 highest support to 3d_sample5.struc_tree100</span></span></span></span></p>
12095
12096 <p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
12097 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
12098 lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>
12099
12100 <p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
12101 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
12102 lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>
12103
12104 <p class=MyNormal><span style='mso-bookmark:_Toc102494678'><span
12105 style='mso-bookmark:_Toc102494297'><span style='mso-bookmark:_Toc101065209'><span
12106 lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>
12107
12108 <h2><span style='mso-bookmark:_Toc102494678'><span style='mso-bookmark:_Toc102494297'><span
12109 style='mso-bookmark:_Toc101065209'><a name="_Toc151732240">MOCCA</a></span></span></span></h2>
12110
12111 <p class=MyNormal><span lang=AF>Write your sequences in the same file
12112 (Swiss-prot, Fasta or Pir) and type. </span></p>
12113
12114 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
12115 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
12116 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
12117 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
12118
12119 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
12120 &#8211;other_pg mocca sample_seq1.fasta </p>
12121
12122 </div>
12123
12124 <p class=MyNormal><span lang=AF>This command output one files (&lt;your
12125 sequences&gt;.mocca_lib) and starts an interactive menu. </span></p>
12126
12127 <div style='mso-element:para-border-div;border:solid windowtext 3.0pt;
12128 padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#CCCCCC;margin-left:0cm;margin-right:
12129 4.25pt'>
12130
12131 <p class=ChapterTitle><a name="_Toc101065210"></a><a name="_Toc102494679"><span
12132 style='mso-bookmark:_Toc101065210'>Recent M</span></a>odifications</p>
12133
12134 </div>
12135
12136 <p class=MyNormal><span lang=AF>Warning: This log of recent modifications is
12137 not as thorough and accurate as it should be.</span></p>
12138
12139 <p class=MyNormal><span lang=AF>-9.86 New data structure for the primary
12140 library that results in highly improved running times for mcoffee and
12141 significantly decreased memory usage.</span></p>
12142
12143 <p class=MyNormal><span lang=AF>-5.80 Novel assembly algorithm
12144 (linked_pair_wise) and the primary library is now made of probcons style
12145 pairwise alignments (proba_pair)</span></p>
12146
12147 <p class=MyNormal><span lang=AF>-4.30 and upward: the FAQ has moved into a new
12148 tutorial document</span></p>
12149
12150 <p class=MyNormal><span lang=AF>-4.30 and upward: -in has will be deprecated
12151 and replaced by the flags: -profile,-method,-aln,-seq,-pdb</span></p>
12152
12153 <p class=MyNormal><span lang=AF>-4.02: -mode=dna is still available but not any
12154 more needed or supported. Use type=protein or dna if you need to force things</span></p>
12155
12156 <p class=MyNormal><b style='mso-bidi-font-weight:normal'><span lang=AF>-</span></b><span
12157 lang=AF>3.28: corrected a bug that prevents short sequences from being
12158 correctly aligned</span></p>
12159
12160 <p class=MyNormal><span lang=AF>-Use of @ as a separator when specifying
12161 methods parameters</span></p>
12162
12163 <p class=MyNormal><span lang=AF>-The most notable modifications have to do with
12164 the structure of the input. From version 2.20, all files must be tagged to
12165 indicate their nature (A: alignment, S: Sequence, L: Library\85). We are becoming
12166 stricter, but that\92s for your own good\85 </span></p>
12167
12168 <p class=MyNormal><span lang=AF>Another important modification has to do with
12169 the flag -matrix: it now controls the matrix being used for the computation </span></p>
12170
12171 <span lang=AF style='font-size:11.0pt;font-family:"Times New Roman";mso-fareast-font-family:
12172 "Times New Roman";mso-bidi-font-family:"Courier New";mso-ansi-language:AF;
12173 mso-fareast-language:EN-US'><br clear=ALL style='page-break-before:always'>
12174 </span>
12175
12176 <div style='mso-element:para-border-div;border:solid windowtext 3.0pt;
12177 padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#CCCCCC;margin-left:0cm;margin-right:
12178 4.25pt'>
12179
12180 <p class=ChapterTitle>Reference Manual</p>
12181
12182 </div>
12183
12184 <p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>
12185
12186 <p class=MyNormal><span lang=AF>This reference manual gives a list of all the
12187 flags that can be used to modify the behavior of T-Coffee. For your
12188 convenience, we have grouped them according to their nature. To display a list
12189 of all the flags used in the version of T-Coffee you are using (along with
12190 their default value), type:</span></p>
12191
12192 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
12193 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
12194 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
12195 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
12196
12197 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee </p>
12198
12199 </div>
12200
12201 <p class=MyNormal><span lang=AF>Or</span></p>
12202
12203 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
12204 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
12205 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
12206 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
12207
12208 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
12209 &#8211;help </p>
12210
12211 </div>
12212
12213 <p class=MyNormal><span lang=AF>Or</span></p>
12214
12215 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
12216 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
12217 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
12218 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
12219
12220 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
12221 &#8211;help &#8211;in<span class=MyNormalChar><span style='font-size:11.0pt;
12222 mso-ansi-language:EN-US'><o:p></o:p></span></span></p>
12223
12224 </div>
12225
12226 <p class=MyNormal><span lang=AF>Or any other parameter</span></p>
12227
12228 <h2><a name="_Toc101065212"></a><a name="_Toc102494358"></a><a
12229 name="_Toc102494743"><span style='mso-bookmark:_Toc102494358'><span
12230 style='mso-bookmark:_Toc101065212'><o:p>&nbsp;</o:p></span></span></a></h2>
12231
12232 <h2><span style='mso-bookmark:_Toc102494743'><span style='mso-bookmark:_Toc102494358'><span
12233 style='mso-bookmark:_Toc101065212'><a name="_Toc151732241">Environment
12234 Variables</a></span></span></span></h2>
12235
12236 <p class=MsoBodyText><span style='mso-bookmark:_Toc102494743'><span
12237 style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc101065212'>It
12238 is possible to modify T-Coffee\92s behavior by setting any of the following
12239 environment variables. On the bash shell, use export VAR=\94value\94. On the
12240 cshell, use set $VAR=\94xxx\94</span></span></span></p>
12241
12242 <h3><span style='mso-bookmark:_Toc102494743'><span style='mso-bookmark:_Toc102494358'><span
12243 style='mso-bookmark:_Toc101065212'><o:p>&nbsp;</o:p></span></span></span></h3>
12244
12245 <h3><span style='mso-bookmark:_Toc102494743'><span style='mso-bookmark:_Toc102494358'><span
12246 style='mso-bookmark:_Toc101065212'><a name="_Toc151732242">http_proxy_4_TCOFFEE</a></span></span></span></h3>
12247
12248 <p class=MyNormal><span style='mso-bookmark:_Toc102494743'><span
12249 style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc101065212'><span
12250 lang=AF>Sets the http_proxy and HTTP_proxy values used by T-Coffee. </span></span></span></span></p>
12251
12252 <p class=MyNormal><span style='mso-bookmark:_Toc102494743'><span
12253 style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc101065212'><span
12254 lang=AF>These values get supersede http_proxy and HTTP_proxy.
12255 http_proxy_4_TCOFFEE gets superseded by the command line values (-proxy and
12256 -email)</span></span></span></span></p>
12257
12258 <p class=MyNormal><span style='mso-bookmark:_Toc102494743'><span
12259 style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc101065212'><span
12260 lang=AF>If you have no proxy, just set this value to an empty string.</span></span></span></span></p>
12261
12262 <h3><span style='mso-bookmark:_Toc102494743'><span style='mso-bookmark:_Toc102494358'><span
12263 style='mso-bookmark:_Toc101065212'><a name="_Toc151732243">email_4_TCOFFEE</a></span></span></span></h3>
12264
12265 <p class=MyNormal><span style='mso-bookmark:_Toc102494743'><span
12266 style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc101065212'><span
12267 lang=AF>Set the E-mail values provided to web services called upon by T-Coffee.
12268 Can be over-riden by the flag <i>-email.<o:p></o:p></i></span></span></span></span></p>
12269
12270 <h3><span style='mso-bookmark:_Toc102494743'><span style='mso-bookmark:_Toc102494358'><span
12271 style='mso-bookmark:_Toc101065212'><a name="_Toc151732244">DIR_4_TCOFFEE</a></span></span></span></h3>
12272
12273 <p class=MyNormal><span style='mso-bookmark:_Toc102494743'><span
12274 style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc101065212'><span
12275 lang=AF>By default this variable is set to $HOME/.t_coffee. This is where
12276 T-Coffee expects to find its cache, tmp dir and possibly any temporary data
12277 stored by the program.</span></span></span></span></p>
12278
12279 <h3><span style='mso-bookmark:_Toc102494743'><span style='mso-bookmark:_Toc102494358'><span
12280 style='mso-bookmark:_Toc101065212'><a name="_Toc151732245">TMP_4_TCOFFEE</a></span></span></span></h3>
12281
12282 <p class=MyNormal><span style='mso-bookmark:_Toc102494743'><span
12283 style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc101065212'><span
12284 lang=AF>By default this variable is set to $HOME/.t_coffee/tmp. This is where
12285 T-Coffee stores temporary files.</span></span></span></span></p>
12286
12287 <h3><span style='mso-bookmark:_Toc102494743'><span style='mso-bookmark:_Toc102494358'><span
12288 style='mso-bookmark:_Toc101065212'><a name="_Toc151732246">CACHE_4_TCOFFEE</a></span></span></span></h3>
12289
12290 <p class=MyNormal><span style='mso-bookmark:_Toc102494743'><span
12291 style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc101065212'><span
12292 lang=AF>By default this variable is set to $HOME/.t_coffee/cache. This is where
12293 T-Coffee stores any data expensive to obtain: pdb files, sap alignments....</span></span></span></span></p>
12294
12295 <h3><span style='mso-bookmark:_Toc102494743'><span style='mso-bookmark:_Toc102494358'><span
12296 style='mso-bookmark:_Toc101065212'><a name="_Toc151732247">PLUGINS_4_TCOFFEE</a></span></span></span></h3>
12297
12298 <p class=MyNormal><span style='mso-bookmark:_Toc102494743'><span
12299 style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc101065212'><span
12300 lang=AF>By default all the companion packages are searched in the directory
12301 DIR_4_TCOFFEE/plugins/&lt;OS&gt;. This variable overrides the default. This
12302 variable can also be overriden by the <i>-plugins</i> T-Coffee flag</span></span></span></span></p>
12303
12304 <h3><span style='mso-bookmark:_Toc102494743'><span style='mso-bookmark:_Toc102494358'><span
12305 style='mso-bookmark:_Toc101065212'><a name="_Toc151732248">NO_ERROR_REPORT_4_TCOFFEE</a></span></span></span></h3>
12306
12307 <p class=MyNormal><span style='mso-bookmark:_Toc102494743'><span
12308 style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc101065212'><span
12309 lang=AF>By default this variable is no set. Set it if you do not want the
12310 program to generate a verbose error output file (useful for running a server).</span></span></span></span></p>
12311
12312 <h3><span style='mso-bookmark:_Toc102494743'><span style='mso-bookmark:_Toc102494358'><span
12313 style='mso-bookmark:_Toc101065212'><a name="_Toc151732249">PDB_DIR</a></span></span></span></h3>
12314
12315 <p class=MyNormal><span style='mso-bookmark:_Toc102494743'><span
12316 style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc101065212'><span
12317 lang=AF>Indicate the location of your local PDB installation.</span></span></span></span></p>
12318
12319 <h3><span style='mso-bookmark:_Toc102494743'><span style='mso-bookmark:_Toc102494358'><span
12320 style='mso-bookmark:_Toc101065212'><a name="_Toc151732250">NO_WARNING_4_TCOFFEE</a></span></span></span></h3>
12321
12322 <p class=MyNormal><span style='mso-bookmark:_Toc102494743'><span
12323 style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc101065212'><span
12324 lang=AF>Suppresses all the warnings.</span></span></span></span></p>
12325
12326 <h3><span style='mso-bookmark:_Toc102494743'><span style='mso-bookmark:_Toc102494358'><span
12327 style='mso-bookmark:_Toc101065212'><a name="_Toc151732251">UNIQUE_DIR_4_TCOFFEE</a></span></span></span></h3>
12328
12329 <p class=MyNormal><span style='mso-bookmark:_Toc102494743'><span
12330 style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc101065212'><span
12331 lang=AF>Sets:</span></span></span></span></p>
12332
12333 <p class=MyNormal><span style='mso-bookmark:_Toc102494743'><span
12334 style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc101065212'><span
12335 lang=AF><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>DIR_4_TCOFFEE</span></span></span></span></p>
12336
12337 <p class=MyNormal><span style='mso-bookmark:_Toc102494743'><span
12338 style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc101065212'><span
12339 lang=AF><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>CACHE_4_TCOFFEE</span></span></span></span></p>
12340
12341 <p class=MyNormal><span style='mso-bookmark:_Toc102494743'><span
12342 style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc101065212'><span
12343 lang=AF><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>TMP_4_TCOFFEE</span></span></span></span></p>
12344
12345 <p class=MyNormal><span style='mso-bookmark:_Toc102494743'><span
12346 style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc101065212'><span
12347 lang=AF><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>PLUGINS_4_TCOFFEE</span></span></span></span></p>
12348
12349 <p class=MyNormal><span style='mso-bookmark:_Toc102494743'><span
12350 style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc101065212'><span
12351 lang=AF>To the same unique value. The string MUST be a valid directory<span
12352 style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp; </span></span></span></span></span></p>
12353
12354 <h2><span style='mso-bookmark:_Toc102494743'><span style='mso-bookmark:_Toc102494358'><span
12355 style='mso-bookmark:_Toc101065212'><a name="_Toc151732252">Setting up the
12356 T-Coffee environment variables</a></span></span></span></h2>
12357
12358 <p class=MsoBodyText><span style='mso-bookmark:_Toc102494743'><span
12359 style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc101065212'>T-Coffee
12360 can have its own environment file. This environment is kept in a file named
12361 $HOME/.t_coffee/t_coffee_env and can be edited. The value of any legal variable
12362 can be modified through that file. For instance, here is an example of a
12363 configuration file when not requiring a proxy.</span></span></span></p>
12364
12365 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
12366 mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
12367 background:#E6E6E6'>
12368
12369 <p class=examplefileCxSpFirst><span style='mso-bookmark:_Toc102494743'><span
12370 style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc101065212'>http_proxy_4_TCOFFEE=</span></span></span></p>
12371
12372 <p class=examplefileCxSpLast><span style='mso-bookmark:_Toc102494743'><span
12373 style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc101065212'>EMAIL_4_TCOFFEE=cedric.notredame@europe.com</span></span></span></p>
12374
12375 </div>
12376
12377 <p class=MsoBodyText><span style='mso-bookmark:_Toc102494743'><span
12378 style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc101065212'>If
12379 you want to use a specific configuration file:</span></span></span></p>
12380
12381 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
12382 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
12383 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
12384 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
12385
12386 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
12387 style='mso-bookmark:_Toc102494743'><span style='mso-bookmark:_Toc102494358'><span
12388 style='mso-bookmark:_Toc101065212'>t_coffee \85 -setenv
12389 ENV_4_TCOFFEE=&lt;location&gt;</span></span></span></p>
12390
12391 </div>
12392
12393 <p class=MsoBodyText><span style='mso-bookmark:_Toc102494743'><span
12394 style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc101065212'>In
12395 general, you can set any environment variable using the &#8211;setenv flag. You
12396 can also simply do an export:</span></span></span></p>
12397
12398 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
12399 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
12400 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
12401 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
12402
12403 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
12404 style='mso-bookmark:_Toc102494743'><span style='mso-bookmark:_Toc102494358'><span
12405 style='mso-bookmark:_Toc101065212'>export ENV_4_TCOFFEE=&lt;location&gt;</span></span></span></p>
12406
12407 </div>
12408
12409 <div style='mso-element:para-border-div;border:solid windowtext 1.5pt;
12410 padding:0cm 0cm 0cm 0cm;background:#F7CBB7'>
12411
12412 <p class=Warning><span style='mso-bookmark:_Toc102494743'><span
12413 style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc101065212'>IMPORTANT:
12414 </span></span></span></p>
12415
12416 <p class=Warning style='text-align:justify;text-indent:35.4pt;background:#F7CBB7'><span
12417 style='mso-bookmark:_Toc102494743'><span style='mso-bookmark:_Toc102494358'><span
12418 style='mso-bookmark:_Toc101065212'>export &gt; &#8211;setenv &gt; -proxy,
12419 -email &gt; t_coffee_env &gt; default<span style="mso-spacerun: yes">&nbsp;
12420 </span>environment</span></span></span></p>
12421
12422 <p class=Warning style='text-align:justify;background:#F7CBB7'><span
12423 style='mso-bookmark:_Toc102494743'><span style='mso-bookmark:_Toc102494358'><span
12424 style='mso-bookmark:_Toc101065212'><o:p>&nbsp;</o:p></span></span></span></p>
12425
12426 </div>
12427
12428 <p class=MsoBodyText><span style='mso-bookmark:_Toc102494743'><span
12429 style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc101065212'>Note
12430 that when you use &#8211;setenv for <b style='mso-bidi-font-weight:normal'>PATH,</b>
12431 the value you provide is concatenated <b style='mso-bidi-font-weight:normal'>TO
12432 THE BEGINNING </b>of the current PATH value. This way you can force T-Coffee to
12433 use a specific version of an aligner.</span></span></span></p>
12434
12435 <p class=MsoBodyText><span style='mso-bookmark:_Toc102494743'><span
12436 style='mso-bookmark:_Toc102494358'><span style='mso-bookmark:_Toc101065212'><o:p>&nbsp;</o:p></span></span></span></p>
12437
12438 <h2><span style='mso-bookmark:_Toc102494743'><span style='mso-bookmark:_Toc102494358'><span
12439 style='mso-bookmark:_Toc101065212'><a name="_Toc151732253">Well Behaved
12440 Parameters</a></span></span></span></h2>
12441
12442 <h3><a name="_Toc101065213"></a><a name="_Toc102494359"></a><a
12443 name="_Toc102494744"></a><a name="_Toc151732254"><span style='mso-bookmark:
12444 _Toc102494744'><span style='mso-bookmark:_Toc102494359'><span style='mso-bookmark:
12445 _Toc101065213'>Separation</span></span></span></a></h3>
12446
12447 <p class=MyNormal><span lang=AF>You can use any kind of separator you want
12448 (i.e. ,; &lt;space&gt;=). The syntax used in this document is meant to be
12449 consistent with that of ClustalW. However, in order to take advantage of the
12450 automatic filename compleation provided by many shells, you can replace \93=\94 and
12451 \93,\94 with a space.</span></p>
12452
12453 <h3><a name="_Toc101065214"></a><a name="_Toc102494360"></a><a
12454 name="_Toc102494745"></a><a name="_Toc151732255"><span style='mso-bookmark:
12455 _Toc102494745'><span style='mso-bookmark:_Toc102494360'><span style='mso-bookmark:
12456 _Toc101065214'>Posix</span></span></span></a></h3>
12457
12458 <p class=MyNormal><span lang=AF>T-Coffee is not POSIX compliant (sorry </span><span
12459 lang=AF style='font-family:Wingdings;mso-ascii-font-family:"Times New Roman";
12460 mso-hansi-font-family:"Times New Roman";mso-char-type:symbol;mso-symbol-font-family:
12461 Wingdings'><span style='mso-char-type:symbol;mso-symbol-font-family:Wingdings'>L</span></span><span
12462 lang=AF>).</span></p>
12463
12464 <h3><a name="_Toc101065215"></a><a name="_Toc102494361"></a><a
12465 name="_Toc102494746"></a><a name="_Toc151732256"><span style='mso-bookmark:
12466 _Toc102494746'><span style='mso-bookmark:_Toc102494361'><span style='mso-bookmark:
12467 _Toc101065215'>Entering the right parameters</span></span></span></a></h3>
12468
12469 <p class=MyNormal><span lang=AF>There are many ways to enter parameters in T-Coffee,
12470 see the -parameter flag in </span></p>
12471
12472 <p class=Noteboxtitle><o:p>&nbsp;</o:p></p>
12473
12474 <div style='mso-element:para-border-div;border:solid windowtext 1.5pt;
12475 padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#FFFF89'>
12476
12477 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut align=center
12478 style='text-align:center;background:#FFFF89'><span style='font-size:20.0pt;
12479 mso-bidi-font-size:10.0pt'>Parameters Priority<o:p></o:p></span></p>
12480
12481 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><o:p>&nbsp;</o:p></p>
12482
12483 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut>In general you will
12484 not need to use these complicated parameters. Yet, if you find yourself typing
12485 long command lines on a regular basis, it may be worth reading this section.</p>
12486
12487 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><o:p>&nbsp;</o:p></p>
12488
12489 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut>One may easily feel
12490 confused with the various manners in which the parameters can be passed to
12491 t_coffee. The reason for these many mechanisms is that they allow several
12492 levels of intervention. For instance, you may install t_coffee for all the
12493 users and decide that the defaults we provide are not the proper ones\85 In this
12494 case, you will need to make your own t_coffee_default file.</p>
12495
12496 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><o:p>&nbsp;</o:p></p>
12497
12498 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut>Later on, a user
12499 may find that he/she needs to keep re-using a specific set of parameters,
12500 different from those in t_coffee_default, hence the possibility to write an
12501 extra parameter file: parameters. In summary:</p>
12502
12503 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><o:p>&nbsp;</o:p></p>
12504
12505 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut>-parameters &gt;
12506 prompt parameters &gt; -t_coffee_defaults &gt; -mode</p>
12507
12508 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><o:p>&nbsp;</o:p></p>
12509
12510 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut>This means that -<i>parameters</i>
12511 supersede all the others, while parameters provided via -<i>special mode</i>
12512 are the weakest.</p>
12513
12514 </div>
12515
12516 <p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>
12517
12518 <p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>
12519
12520 <h2><a name="_Toc101065216"></a><a name="_Toc102494362"></a><a
12521 name="_Toc102494747"></a><a name="_Toc151732257"><span style='mso-bookmark:
12522 _Toc102494747'><span style='mso-bookmark:_Toc102494362'><span style='mso-bookmark:
12523 _Toc101065216'>Parameters Syntax</span></span></span></a></h2>
12524
12525 <p class=flag><a name="_Toc101065218"></a><a name="_Toc102494748"></a><a
12526 name="_Toc151732258"><span style='mso-bookmark:_Toc102494748'><span
12527 style='mso-bookmark:_Toc101065218'><span lang=AF>No Flag</span></span></span></a></p>
12528
12529 <p class=flagdescription>If no flag is used<b style='mso-bidi-font-weight:normal'>
12530 </b><i style='mso-bidi-font-style:normal'>&lt;your sequence&gt; </i>must be the
12531 first argument. See format for further information.</p>
12532
12533 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
12534 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
12535 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
12536 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
12537
12538 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
12539 sample_seq1.fasta </p>
12540
12541 </div>
12542
12543 <p class=flagdescription>Which is equivalent to</p>
12544
12545 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
12546 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
12547 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
12548 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
12549
12550 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
12551 Ssample_seq1.fasta </p>
12552
12553 </div>
12554
12555 <p class=flagdescription>When you do so, <b style='mso-bidi-font-weight:normal'>sample_seq1</b>
12556 is used as a name prefix for every file the program outputs.</p>
12557
12558 <p class=flag><a name="_Toc101065219"></a><a name="_Toc102494749"></a><a
12559 name="_Toc151732259"><span style='mso-bookmark:_Toc102494749'><span
12560 style='mso-bookmark:_Toc101065219'><span lang=AF>-parameters</span></span></span></a><span
12561 lang=AF style='background:gray;mso-highlight:gray'><o:p></o:p></span></p>
12562
12563 <p class=flagusage><span lang=FR>Usage: -parameters=parameters_file</span></p>
12564
12565 <p class=instruction>Default: no parameters file</p>
12566
12567 <p class=flagdescription>Indicates a file containing extra parameters.
12568 Parameters read this way behave as if they had been added on the right end of
12569 the command line that they either supersede(one value parameter) or complete
12570 (list of values). For instance, the following file (parameter.file) could be
12571 used </p>
12572
12573 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
12574 mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
12575 background:#E6E6E6'>
12576
12577 <p class=examplefileCxSpFirst>*******sample_param_file.param********<span
12578 style='mso-tab-count:1'>&nbsp;&nbsp; </span></p>
12579
12580 <p class=examplefileCxSpMiddle><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>-in=Ssample_seq1.fasta,Mfast_pair</p>
12581
12582 <p class=examplefileCxSpMiddle><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>-output=msf_aln</p>
12583
12584 <p class=examplefileCxSpLast>**************************************</p>
12585
12586 </div>
12587
12588 <p class=Note><span style='mso-ansi-language:EN-US'>Note: This is one of the
12589 exceptions (with &#8211;infile) where the identifier tag (S,A,L,M\85) can be
12590 omitted. Any dataset provided this way will be assumed to be a sequence (S).
12591 These exceptions have been designed to keep the program compatible with
12592 ClustalW.<o:p></o:p></span></p>
12593
12594 <p class=Note><span style='mso-ansi-language:EN-US'>Note: This parameter file
12595 can ONLY contain valid parameters. Comments are not allowed. Parameters passed
12596 this way will be checked like normal parameters.<o:p></o:p></span></p>
12597
12598 <p class=flagdescription>Used with:</p>
12599
12600 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
12601 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
12602 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
12603 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
12604
12605 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
12606 -parameters=sample_param_file.param</p>
12607
12608 </div>
12609
12610 <p class=flagdescription>Will cause t_coffee to apply the fast_pair method onto
12611 to the sequences contained in sample_seq.fasta. If you wish, you can also pipe
12612 these arguments into t_coffee, by naming the parameter file &quot;stdin&quot;
12613 (as a rule, any file named stdin is expected to receive its content via the
12614 stdin)</p>
12615
12616 <p class=example2>cat sample_param_file.param<span style="mso-spacerun:
12617 yes">&nbsp; </span>| t_coffee -parameters=stdin <a name="_Toc101065220"></a></p>
12618
12619 <p class=flag><span style='mso-bookmark:_Toc101065220'><a name="_Toc102494750"></a><a
12620 name="_Toc151732260"><span style='mso-bookmark:_Toc102494750'><span lang=AF>-t_coffee_defaults</span></span></a></span></p>
12621
12622 <p class=flagusage><span lang=FR>Usage: -t_coffee_defaults=&lt;file_name&gt;</span></p>
12623
12624 <p class=instruction>Default: not used.</p>
12625
12626 <p class=flagdescription>This flag tells the program to use some default
12627 parameter file for t_coffee. The format of that file is the same as the one
12628 used with -parameters. The file used is either:</p>
12629
12630 <p class=flagdescription><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>1.
12631 &lt;file name&gt; if a name has been specified</p>
12632
12633 <p class=flagdescription><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>2.<span
12634 style="mso-spacerun: yes">&nbsp; </span><b>~/.t_coffee_defaults </b>if no file
12635 was specified</p>
12636
12637 <p class=flagdescription><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>3.
12638 The file indicated by the environment variable <b>TCOFFEE_DEFAULTS</b></p>
12639
12640 <p class=flag><a name="_Toc151732261"><span lang=AF>-mode</span></a></p>
12641
12642 <p class=flagusage><span lang=FR>Usage: -mode= hard coded mode</span></p>
12643
12644 <p class=instruction>Default: not used.</p>
12645
12646 <p class=flagdescription>It indicates that t_coffee will use some hard coded
12647 parameters. These include:</p>
12648
12649 <p class=flagdescription><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><b
12650 style='mso-bidi-font-weight:normal'>quickaln</b>: very fast approximate
12651 alignment</p>
12652
12653 <p class=flagdescription><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><b
12654 style='mso-bidi-font-weight:normal'>dali</b>: a mode used to combine dali
12655 pairwise alignments</p>
12656
12657 <p class=flagdescription><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><b
12658 style='mso-bidi-font-weight:normal'>evaluate</b>: defaults for evaluating an
12659 alignment</p>
12660
12661 <p class=flagdescription><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><b
12662 style='mso-bidi-font-weight:normal'>3dcoffee</b>: runs t_coffee with the
12663 3dcoffee parameterization</p>
12664
12665 <p class=flagdescription><o:p>&nbsp;</o:p></p>
12666
12667 <p class=flagdescription>Other modes exist that are not yet fully supported<span
12668 style='mso-tab-count:1'> </span></p>
12669
12670 <p class=flag><a name="_Toc101065222"></a><a name="_Toc102494752"></a><a
12671 name="_Toc151732262"><span style='mso-bookmark:_Toc102494752'><span
12672 style='mso-bookmark:_Toc101065222'><span lang=AF>-score</span></span><span
12673 lang=AF> [Deprecated]</span></span></a></p>
12674
12675 <p class=flagusage><span lang=FR>Usage: -score</span></p>
12676
12677 <p class=instruction>Default: not used</p>
12678
12679 <p class=flagdescription>Toggles on the evaluate mode and causes t_coffee to
12680 evaluates a precomputed alignment provided via <b>-infile=&lt;alignment&gt;</b>.
12681 The flag <b>-output</b> must be set to an appropriate format (i.e.
12682 -output=score_ascii, score_html or score_pdf). A better default
12683 parameterization is obtained when using the flag <b>-mode=evaluate.</b></p>
12684
12685 <p class=flag><a name="_Toc102494753"></a><a name="_Toc151732263"><span
12686 style='mso-bookmark:_Toc102494753'><span lang=AF>-evaluate</span></span></a></p>
12687
12688 <p class=flagusage><span lang=FR>Usage: -evaluate</span></p>
12689
12690 <p class=instruction>Default: not used</p>
12691
12692 <p class=flagdescription>Replaces &#8211;score. This flag toggles on the
12693 evaluate mode and causes t_coffee to evaluates a pre-computed alignment
12694 provided via <b>-infile=&lt;alignment&gt;</b>. The flag <b>-output</b> must be
12695 set to an appropriate format (i.e. -output=score_ascii, score_html or
12696 score_pdf). </p>
12697
12698 <p class=flagdescription><o:p>&nbsp;</o:p></p>
12699
12700 <p class=flagdescription>The main purpose of &#8211;evaluate is to let you
12701 control every aspect of the evaluation. Yet it is advisable to use pre-defined
12702 parameterization: <b>mode=evaluate.</b></p>
12703
12704 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
12705 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
12706 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
12707 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
12708
12709 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
12710 &#8211;infile=sample_aln1.aln -mode=evaluate </p>
12711
12712 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
12713 &#8211;infile=sample_seq1.aln &#8211;in<span style="mso-spacerun: yes">&nbsp;
12714 </span>Lsample_lib1.tc_lib &#8211;mode=evaluate </p>
12715
12716 </div>
12717
12718 <p class=flag><a name="_Toc101065223"></a><a name="_Toc102494754"></a><a
12719 name="_Toc151732264"><span style='mso-bookmark:_Toc102494754'><span
12720 style='mso-bookmark:_Toc101065223'><span lang=AF>-convert [cw]</span></span></span></a></p>
12721
12722 <p class=flagusage><span lang=FR>Usage: -convert</span></p>
12723
12724 <p class=instruction>Default: turned off</p>
12725
12726 <p class=flagdescription>Toggles on the conversion mode and causes T-Coffee to
12727 convert the sequences, alignments, libraries or structures provided via the <b>-infile</b>
12728 and <b>-in</b> flags. The output format must be set via the <b>-output</b>
12729 flag. This flag can also be used if you simply want to compute a library (i.e.
12730 you have an alignment and you want to turn it into a library).</p>
12731
12732 <p class=flagdescription>This flag is ClustalW compliant.</p>
12733
12734 <p class=flag><a name="_Toc101065224"></a><a name="_Toc102494755"></a><a
12735 name="_Toc151732265"><span style='mso-bookmark:_Toc102494755'><span
12736 style='mso-bookmark:_Toc101065224'><span lang=AF>-do_align [cw]</span></span></span></a></p>
12737
12738 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
12739 </span>-do_align</span></p>
12740
12741 <p class=instruction>Default: turned on</p>
12742
12743 <h2><a name="_Toc101065225"></a><a name="_Toc102494363"></a><a
12744 name="_Toc102494756"></a><a name="_Toc151732266"><span style='mso-bookmark:
12745 _Toc102494756'><span style='mso-bookmark:_Toc102494363'><span style='mso-bookmark:
12746 _Toc101065225'>Special Parameters</span></span></span></a></h2>
12747
12748 <p class=flag><a name="_Toc101065226"></a><a name="_Toc102494757"></a><a
12749 name="_Toc151732267"><span style='mso-bookmark:_Toc102494757'><span
12750 style='mso-bookmark:_Toc101065226'><span lang=AF>-version</span></span></span></a></p>
12751
12752 <p class=flagusage><span lang=FR>Usage: -version</span></p>
12753
12754 <p class=instruction>Default: not used</p>
12755
12756 <p class=flagdescription>Returns the current version number</p>
12757
12758 <p class=flag><a name="_Toc101065227"></a><a name="_Toc102494758"></a><a
12759 name="_Toc151732268"><span style='mso-bookmark:_Toc102494758'><span
12760 style='mso-bookmark:_Toc101065227'><span lang=AF>-proxy</span></span></span></a><span
12761 style='mso-bookmark:_Toc102494758'><span style='mso-bookmark:_Toc101065227'></span></span></p>
12762
12763 <p class=flagusage><span style='mso-bookmark:_Toc102494758'><span
12764 style='mso-bookmark:_Toc101065227'><span lang=FR>Usage: -proxy=&lt;proxy&gt;</span></span></span></p>
12765
12766 <p class=instruction><span style='mso-bookmark:_Toc102494758'><span
12767 style='mso-bookmark:_Toc101065227'>Default: not used</span></span></p>
12768
12769 <p class=flagdescription><span style='mso-bookmark:_Toc102494758'><span
12770 style='mso-bookmark:_Toc101065227'>Sets the proxy used by HTTP_proxy AND
12771 http_proxy. Setting with the propmpt supersedes ANY other setting.</span></span></p>
12772
12773 <p class=flagdescription><span style='mso-bookmark:_Toc102494758'><span
12774 style='mso-bookmark:_Toc101065227'>Note that if you use no proxy, you should
12775 set</span></span></p>
12776
12777 <p class=flagdescription><span style='mso-bookmark:_Toc102494758'><span
12778 style='mso-bookmark:_Toc101065227'><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>-proxy</span></span></p>
12779
12780 <p class=flag><span style='mso-bookmark:_Toc102494758'><span style='mso-bookmark:
12781 _Toc101065227'><a name="_Toc151732269"><span lang=AF>-email</span></a></span></span></p>
12782
12783 <p class=flagusage><span style='mso-bookmark:_Toc102494758'><span
12784 style='mso-bookmark:_Toc101065227'><span lang=FR>Usage: -email=&lt;email&gt;</span></span></span></p>
12785
12786 <p class=instruction><span style='mso-bookmark:_Toc102494758'><span
12787 style='mso-bookmark:_Toc101065227'>Default: not used</span></span></p>
12788
12789 <p class=flagdescription><span style='mso-bookmark:_Toc102494758'><span
12790 style='mso-bookmark:_Toc101065227'>Sets your email value as provided to web
12791 services</span></span></p>
12792
12793 <p class=flag><span style='mso-bookmark:_Toc102494758'><span style='mso-bookmark:
12794 _Toc101065227'><a name="_Toc151732270"><span lang=AF>-check_configuration</span></a></span></span></p>
12795
12796 <p class=flagusage><span lang=FR>Usage: -check_configuration</span></p>
12797
12798 <p class=instruction>Default: not used</p>
12799
12800 <p class=flagdescription>Checks your system to determine whether all the
12801 programs T-Coffee can interact with are installed.</p>
12802
12803 <p class=flag><a name="_Toc101065228"></a><a name="_Toc102494759"></a><a
12804 name="_Toc151732271"><span style='mso-bookmark:_Toc102494759'><span
12805 style='mso-bookmark:_Toc101065228'><span lang=AF>-cache</span></span></span></a></p>
12806
12807 <p class=flagusage><span lang=FR>Usage: -cache=&lt;use, update, ignore,
12808 &lt;filename&gt;&gt;</span></p>
12809
12810 <p class=instruction>Default: -cache=use</p>
12811
12812 <p class=flagdescription>By default, t_coffee stores in a cache directory, the
12813 results of computationally expensive (structural alignment) or network
12814 intensive (BLAST search) operations.<a name="_Toc101065229"></a></p>
12815
12816 <p class=flag><span style='mso-bookmark:_Toc101065229'><a name="_Toc102494760"></a><a
12817 name="_Toc151732272"><span style='mso-bookmark:_Toc102494760'><span lang=AF>-update</span></span></a></span></p>
12818
12819 <p class=flagusage><span lang=FR>Usage: -update</span></p>
12820
12821 <p class=instruction>Default: turned off</p>
12822
12823 <p class=flagdescription>Causes a <span
12824 class=StyleflagdescriptionBoldItalicChar>wget</span> access that checks whether
12825 the t_coffee version you are using needs updating.<a name="_Toc101065230"></a></p>
12826
12827 <p class=flag><span style='mso-bookmark:_Toc101065230'><a name="_Toc102494761"></a><a
12828 name="_Toc151732273"><span style='mso-bookmark:_Toc102494761'><span lang=AF>-full_log</span></span></a></span></p>
12829
12830 <p class=flagusage><span lang=FR>Usage: -full_log=&lt;filename&gt;</span></p>
12831
12832 <p class=instruction>Default: turned off</p>
12833
12834 <p class=flagdescription>Causes t_coffee to output a full log file that
12835 contains all the input/output files.<a name="_Toc101065231"></a></p>
12836
12837 <p class=flag><span style='mso-bookmark:_Toc101065231'><a name="_Toc102494762"></a><a
12838 name="_Toc151732274"><span style='mso-bookmark:_Toc102494762'><span lang=AF>-plugins</span></span></a><span
12839 style='mso-bookmark:_Toc102494762'></span></span></p>
12840
12841 <p class=flagusage><span style='mso-bookmark:_Toc101065231'><span
12842 style='mso-bookmark:_Toc102494762'><span lang=FR>Usage: -plugins=&lt;dir&gt;</span></span></span></p>
12843
12844 <p class=instruction><span style='mso-bookmark:_Toc101065231'><span
12845 style='mso-bookmark:_Toc102494762'>Default: default</span></span></p>
12846
12847 <p class=flagdescription><span style='mso-bookmark:_Toc101065231'><span
12848 style='mso-bookmark:_Toc102494762'>Specifies the directory in which the
12849 companion packages (other multiple aligners used by M-Coffee, structural
12850 aligners, etc\85) are kept as an alternative, you can also set the environment
12851 variable PLUGINS_4_TCOFFEE</span></span></p>
12852
12853 <p class=flagdescription><span style='mso-bookmark:_Toc101065231'><span
12854 style='mso-bookmark:_Toc102494762'>The default is ~/.t_coffee/plugins/</span></span></p>
12855
12856 <p class=flag><span style='mso-bookmark:_Toc101065231'><span style='mso-bookmark:
12857 _Toc102494762'><a name="_Toc151732275"><span lang=AF>-other_pg</span></a></span></span></p>
12858
12859 <p class=flagusage><span lang=FR>Usage: -other_pg=&lt;filename&gt;</span></p>
12860
12861 <p class=instruction>Default: turned off</p>
12862
12863 <p class=flagdescription>Some rumours claim that Tetris is embedded within
12864 T-Coffee and could be ran using some special set of commands. We wish to deny
12865 these rumours, although we may admit that several interesting reformatting
12866 programs are now embedded in t_coffee and can be ran through the
12867 &#8211;other_pg flag.</p>
12868
12869 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
12870 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
12871 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
12872 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
12873
12874 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
12875 &#8211;other_pg=seq_reformat </p>
12876
12877 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
12878 &#8211;other_pg=unpack_all </p>
12879
12880 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
12881 &#8211;other_pg=unpack_extract_from_pdb </p>
12882
12883 </div>
12884
12885 <h2><a name="_Toc101065232"></a><a name="_Toc102494364"></a><a
12886 name="_Toc102494763"></a><a name="_Toc151732276"><span style='mso-bookmark:
12887 _Toc102494763'><span style='mso-bookmark:_Toc102494364'><span style='mso-bookmark:
12888 _Toc101065232'>Input</span></span></span></a> </h2>
12889
12890 <h3><a name="_Toc101065233"></a><a name="_Toc102494365"></a><a
12891 name="_Toc102494764"></a><a name="_Toc151732277"><span style='mso-bookmark:
12892 _Toc102494764'><span style='mso-bookmark:_Toc102494365'><span style='mso-bookmark:
12893 _Toc101065233'>Sequence Input</span></span></span></a></h3>
12894
12895 <p class=flag><a name="_Toc101065234"></a><a name="_Toc102494765"></a><a
12896 name="_Toc151732278"><span style='mso-bookmark:_Toc102494765'><span
12897 style='mso-bookmark:_Toc101065234'><span lang=AF>-infile [cw]</span></span></span></a></p>
12898
12899 <p class=flagdescription>To remain compatible with ClustalW, it is possible to
12900 indicate the sequences with this flag</p>
12901
12902 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
12903 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
12904 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
12905 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
12906
12907 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
12908 -infile=sample_seq1.fasta </p>
12909
12910 </div>
12911
12912 <p class=Note><span style='mso-ansi-language:EN-US'>Note: Common multiple sequence
12913 alignments format constitute a valid input format.<o:p></o:p></span></p>
12914
12915 <p class=Note><span style='mso-ansi-language:EN-US'>Note: T-Coffee
12916 automatically removes the gaps </span><i><span style='mso-ansi-language:EN-US;
12917 mso-bidi-font-weight:bold'>before</span></i><span style='mso-ansi-language:
12918 EN-US'> doing the alignment. This behaviour is different from that of ClustalW
12919 where the gaps are kept.<o:p></o:p></span></p>
12920
12921 <p class=flag><a name="_Toc101065235"></a><a name="_Toc102494766"></a><a
12922 name="_Toc151732279"><span style='mso-bookmark:_Toc102494766'><span
12923 style='mso-bookmark:_Toc101065235'><span lang=AF>-in</span></span><span
12924 lang=AF> (Cf &#8211;in from the Method and Library Input section)</span></span></a></p>
12925
12926 <p class=flag><a name="_Toc101065236"></a><a name="_Toc102494767"></a><a
12927 name="_Toc151732280"><span style='mso-bookmark:_Toc102494767'><span
12928 style='mso-bookmark:_Toc101065236'><span lang=AF>-get_type</span></span></span></a></p>
12929
12930 <p class=flagusage><span lang=FR>Usage: -get_type</span></p>
12931
12932 <p class=instruction>Default: turned off</p>
12933
12934 <p class=flagdescription>Forces t_coffee to identify the sequences type
12935 (PROTEIN, DNA).</p>
12936
12937 <p class=flag><a name="_Toc101065237"></a><a name="_Toc102494768"></a><a
12938 name="_Toc151732281"><span style='mso-bookmark:_Toc102494768'><span
12939 style='mso-bookmark:_Toc101065237'><span lang=AF>-type [cw]</span></span></span></a></p>
12940
12941 <p class=flagusage><span lang=FR>Usage: -type=DNA ¦ PROTEIN¦ DNA_PROTEIN</span></p>
12942
12943 <p class=instruction>Default: -type=&lt;automatically set&gt;</p>
12944
12945 <p class=flagdescription>This flag sets the type of the sequences. If omitted,
12946 the type is guessed automatically. This flag is compatible with ClustalW.</p>
12947
12948 <div style='mso-element:para-border-div;border:solid windowtext 1.5pt;
12949 padding:0cm 0cm 0cm 0cm;background:#F7CBB7'>
12950
12951 <p class=Warning>Warning:<span style="mso-spacerun: yes">&nbsp; </span>In case
12952 of low complexity or short sequences, it is recommended to set the type
12953 manually.<a name="_Toc101065238"></a></p>
12954
12955 </div>
12956
12957 <p class=flag><span style='mso-bookmark:_Toc101065238'><a name="_Toc102494769"></a><a
12958 name="_Toc151732282"><span style='mso-bookmark:_Toc102494769'><span lang=AF>-seq</span></span></a></span></p>
12959
12960 <p class=flagusage><span lang=FR>Usage: -seq=[&lt;P,S&gt;&lt;name&gt;,]</span></p>
12961
12962 <p class=instruction>Default: none</p>
12963
12964 <p class=MyNormal><span lang=AF>-seq is now the recommended flag to provide
12965 your sequences. It behaves mostly like the -in flag.</span></p>
12966
12967 <p class=flag><a name="_Toc101065239"></a><a name="_Toc102494770"></a><a
12968 name="_Toc151732283"><span style='mso-bookmark:_Toc102494770'><span
12969 style='mso-bookmark:_Toc101065239'><span lang=AF>-seq_source</span></span></span></a></p>
12970
12971 <p class=flagusage><span lang=FR>Usage: -seq_source=&lt;ANY or<span
12972 style="mso-spacerun: yes">&nbsp; </span>_LS or LS &gt;</span></p>
12973
12974 <p class=instruction>Default: ANY.</p>
12975
12976 <p class=flagdescription>You may not want to combine all the provided sequences
12977 into a single sequence list. You can do by specifying that you do not want to
12978 treat all the &#8211;in files as potential sequence sources.</p>
12979
12980 <p class=flagdescription>-seq_source=_LA indicates that neither sequences
12981 provided via the A (Alignment) flag or via the L (Library flag) should be added
12982 to the sequence list.</p>
12983
12984 <p class=flagdescription>-seq_source=S means that only sequences provided via
12985 the S tag will be considered. All the other sequences will be ignored.</p>
12986
12987 <p class=Note><span style='mso-ansi-language:EN-US'>Note:<span
12988 style="mso-spacerun: yes">&nbsp; </span>This flag is mostly designed for
12989 interactions between T-Coffee and T-CoffeeDPA (the large scale version of
12990 T-Coffee).</span><span style='mso-ansi-language:EN-US;mso-bidi-font-weight:
12991 bold'><o:p></o:p></span></p>
12992
12993 <h3><a name="_Toc101065241"></a><a name="_Toc102494366"></a><a
12994 name="_Toc102494771"></a><a name="_Toc151732284"><span style='mso-bookmark:
12995 _Toc102494771'><span style='mso-bookmark:_Toc102494366'><span style='mso-bookmark:
12996 _Toc101065241'>Structure Input</span></span></span></a></h3>
12997
12998 <p class=flag><a name="_Toc101065242"></a><a name="_Toc102494772"></a><a
12999 name="_Toc151732285"><span style='mso-bookmark:_Toc102494772'><span
13000 style='mso-bookmark:_Toc101065242'><span lang=AF>-pdb</span></span></span></a></p>
13001
13002 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
13003 </span>-pdb=&lt;pdbid1&gt;,&lt;pdbid2&gt;\85[Max 200]</span></p>
13004
13005 <p class=instruction>Default: None</p>
13006
13007 <p class=flagdescription>Reads or fetch a pdb file. It is possible to specify a
13008 chain or even a sub-chain:</p>
13009
13010 <p class=example2>PDBID(PDB_CHAIN)[opt] (FIRST,LAST)[opt]<a name="_Toc101065243"></a></p>
13011
13012 <p class=flagdescription><span style='mso-bookmark:_Toc101065243'>It is also
13013 possible to input structures via the &#8211;in flag. In that case, you will
13014 need to use the TAG identifier:</span></p>
13015
13016 <p class=example2><span style='mso-bookmark:_Toc101065243'>-in Ppdb1 Ppdb2\85 </span></p>
13017
13018 <h3><span style='mso-bookmark:_Toc101065243'><a name="_Toc102494367"></a><a
13019 name="_Toc102494773"></a><a name="_Toc151732286"><span style='mso-bookmark:
13020 _Toc102494773'><span style='mso-bookmark:_Toc102494367'>Tree Input</span></span></a></span></h3>
13021
13022 <p class=flag><a name="_Toc101065244"></a><a name="_Toc102494774"></a><a
13023 name="_Toc151732287"><span style='mso-bookmark:_Toc102494774'><span
13024 style='mso-bookmark:_Toc101065244'><span lang=AF>-usetree</span></span></span></a></p>
13025
13026 <p class=flagusage><span lang=FR>Usage: -usetree=&lt;tree file&gt;</span></p>
13027
13028 <p class=instruction>Default: No file specified</p>
13029
13030 <p class=instruction>Format: newick tree format (ClustalW Style)</p>
13031
13032 <p class=flagdescription>This flag indicates that rather than computing a new
13033 dendrogram, t_coffee must use a pre-computed one. The tree files are in phylips
13034 format and compatible with ClustalW. In most cases, using a pre-computed tree
13035 will halve the computation time required by t_coffee. It is also possible to
13036 use trees output by ClustalW, Phylips and any other program.</p>
13037
13038 <h3><a name="_Toc101065245"></a><a name="_Toc102494368"></a><a
13039 name="_Toc102494775"></a><a name="_Toc151732288"><span style='mso-bookmark:
13040 _Toc102494775'><span style='mso-bookmark:_Toc102494368'><span style='mso-bookmark:
13041 _Toc101065245'>Structures, Sequences Methods and Library Input</span></span></span>
13042 via the </a><span style='mso-bookmark:_Toc151732288'><span style='font-family:
13043 Symbol;mso-ascii-font-family:"Arial Black"'>-</span>in Flag</span></h3>
13044
13045 <div style='mso-element:para-border-div;border:solid windowtext 1.5pt;
13046 padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#FFFF89'>
13047
13048 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut align=center
13049 style='text-align:center;background:#FFFF89'><a name="_Toc101065246"><span
13050 style='font-size:20.0pt;mso-bidi-font-size:10.0pt'>The -in Flag and its
13051 Identifier TAGS<o:p></o:p></span></a></p>
13052
13053 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span
13054 style='mso-bookmark:_Toc101065246'><o:p>&nbsp;</o:p></span></p>
13055
13056 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span
13057 style='mso-bookmark:_Toc101065246'>&lt;-in&gt; is the real grinder of T-Coffee.
13058 Sequences, methods and alignments all pass through so that T-Coffee can turn it
13059 all into a single list of constraints (the library). Everything is done
13060 automatically with T-Coffee going through each file to extract the sequences it
13061 contains. The methods are then applied to the sequences. Pre-compiled
13062 constraint list can also be provided. Each file provided via this flag must be
13063 preceded with a symbol (Identifier TAG) that indicates its nature to T-Coffee.
13064 The TAGs currently supported are the following:</span></p>
13065
13066 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span
13067 style='mso-bookmark:_Toc101065246'><o:p>&nbsp;</o:p></span></p>
13068
13069 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span
13070 style='mso-bookmark:_Toc101065246'>P<span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>PDB
13071 structure</span></p>
13072
13073 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span
13074 style='mso-bookmark:_Toc101065246'>S <span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>for
13075 sequences (use it as well to treat an MSA as unaligned sequences)</span></p>
13076
13077 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span
13078 style='mso-bookmark:_Toc101065246'><o:p>&nbsp;</o:p></span></p>
13079
13080 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span
13081 style='mso-bookmark:_Toc101065246'>M <span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Methods
13082 used to build the library</span></p>
13083
13084 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span
13085 style='mso-bookmark:_Toc101065246'>L <span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Pre-computed
13086 T-Coffee library</span></p>
13087
13088 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span
13089 style='mso-bookmark:_Toc101065246'>A <span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Multiple
13090 Alignments that must be turned into a Library</span></p>
13091
13092 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span
13093 style='mso-bookmark:_Toc101065246'><o:p>&nbsp;</o:p></span></p>
13094
13095 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><span
13096 style='mso-bookmark:_Toc101065246'>X <span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Substitution
13097 matrices.</span></p>
13098
13099 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut style='margin-left:
13100 35.25pt;text-indent:-35.25pt;background:#FFFF89'><span style='mso-bookmark:
13101 _Toc101065246'>R <span style='mso-tab-count:2'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Profiles.
13102 This is a legal multiple alignments that will be treated as single sequences
13103 (the sequences it contains will not be realigned). </span></p>
13104
13105 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut style='margin-left:
13106 35.25pt;text-indent:-35.25pt;background:#FFFF89'><span style='mso-bookmark:
13107 _Toc101065246'><o:p>&nbsp;</o:p></span></p>
13108
13109 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut style='margin-left:
13110 35.25pt;text-indent:-35.25pt;background:#FFFF89'><span style='mso-bookmark:
13111 _Toc101065246'>If you do not want to use the TAGS, you will need to use the
13112 following flags in replacement of -in. Do not use the TAGS when using these
13113 flags:</span></p>
13114
13115 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut style='margin-left:
13116 35.25pt;text-indent:-35.25pt;background:#FFFF89'><span style='mso-bookmark:
13117 _Toc101065246'><o:p>&nbsp;</o:p></span></p>
13118
13119 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut style='margin-left:
13120 35.25pt;text-indent:-35.25pt;background:#FFFF89'><span style='mso-bookmark:
13121 _Toc101065246'>-aln <span style='mso-tab-count:3'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Alignments
13122 <span style='mso-tab-count:1'>&nbsp; </span>(A)</span></p>
13123
13124 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut style='margin-left:
13125 35.25pt;text-indent:-35.25pt;background:#FFFF89'><span style='mso-bookmark:
13126 _Toc101065246'>-profile<span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Profiles
13127 <span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>(R)</span></p>
13128
13129 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut style='margin-left:
13130 35.25pt;text-indent:-35.25pt;background:#FFFF89'><span style='mso-bookmark:
13131 _Toc101065246'>-method<span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Method
13132 <span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>(M)</span></p>
13133
13134 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut style='margin-left:
13135 35.25pt;text-indent:-35.25pt;background:#FFFF89'><span style='mso-bookmark:
13136 _Toc101065246'>-seq<span style='mso-tab-count:3'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Sequences
13137 <span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp; </span>(S)</span></p>
13138
13139 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut style='margin-left:
13140 35.25pt;text-indent:-35.25pt;background:#FFFF89'><span style='mso-bookmark:
13141 _Toc101065246'>-lib<span style='mso-tab-count:3'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Libraries<span
13142 style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>(L)<a
13143 name="_Toc102494776"></a></span></p>
13144
13145 </div>
13146
13147 <p class=flag><span style='mso-bookmark:_Toc101065246'><span style='mso-bookmark:
13148 _Toc102494776'><a name="_Toc151732289"><span lang=AF>-in</span></a></span></span></p>
13149
13150 <p class=flagusage><span lang=FR>Usage: -in=[&lt;P,S,A,L,M,X&gt;&lt;name&gt;,]</span></p>
13151
13152 <p class=instruction>Default: -in=Mlalign_id_pair,Mclustalw_pair</p>
13153
13154 <div style='mso-element:para-border-div;border:solid windowtext 1.5pt;
13155 padding:0cm 0cm 0cm 0cm;background:#F7CBB7'>
13156
13157 <p class=Warning>Note: -in can be replaced with the combined usage of -aln,
13158 iprofile, .pdb, .lib, -method.</p>
13159
13160 </div>
13161
13162 <p class=flagdescription>See the box for an explanation of the -in flag. The
13163 following argument passed via -in</p>
13164
13165 <p class=flagdescription><o:p>&nbsp;</o:p></p>
13166
13167 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
13168 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
13169 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
13170 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
13171
13172 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
13173 -in=Ssample_seq1.fasta,Asample_aln1.aln,Asample_aln2.msf,Mlalign_id_pair,Lsample_lib1.tc_lib
13174 &#8211;outfile=outaln</p>
13175
13176 </div>
13177
13178 <p class=flagdescription><o:p>&nbsp;</o:p></p>
13179
13180 <p class=flagdescription>This command will trigger the following chain of
13181 events:</p>
13182
13183 <p class=flagdescription><o:p>&nbsp;</o:p></p>
13184
13185 <p class=flagdescription>1-Gather all the sequences</p>
13186
13187 <p class=flagdescription>Sequences within all the provided files are pooled
13188 together. Format recognition is automatic. Duplicates are removed (if they have
13189 the same name). Duplicates in a single file are only tolerated in FASTA format
13190 file, although they will cause sequences to be renamed.</p>
13191
13192 <p class=flagdescription>In the above case, the total set of sequences will be
13193 made of sequences contained in sequences1.seq, alignment1.aln, alignment2.msf
13194 and library.lib, plus the sequences initially gathered<span
13195 style="mso-spacerun: yes">&nbsp; </span>by -infile.</p>
13196
13197 <p class=flagdescription>2-Turn alignments into libraries</p>
13198
13199 <p class=flagdescription>alignment1.aln and alignment2.msf will be read and
13200 turned into libraries. Another library will be produced by applying the method
13201 lalign_id_pair to the set of sequences previously obtained (1). The final
13202 library used for the alignment will be the combination of all this information.
13203 </p>
13204
13205 <p class=flagdescription>Note as well the following rules: </p>
13206
13207 <p class=flagdescription><o:p>&nbsp;</o:p></p>
13208
13209 <p class=flagdescription><b style='mso-bidi-font-weight:normal'>1-Order</b><span
13210 style='mso-bidi-font-weight:bold'>:</span> The order in which sequences,
13211 methods, alignments and libraries are fed in is irrelevant.</p>
13212
13213 <p class=flagdescription><b style='mso-bidi-font-weight:normal'>2-Heterogeneity</b><span
13214 style='mso-bidi-font-weight:bold'>:</span> There is no need for each element
13215 (A, S, L) to contain the same sequences.</p>
13216
13217 <p class=flagdescription><b style='mso-bidi-font-weight:normal'>3-No Duplicate</b><span
13218 style='mso-bidi-font-weight:bold'>:</span> Each file should contain only one
13219 copy of each sequence. Duplicates are only allowed in FASTA files but will
13220 cause the sequences to be renamed.</p>
13221
13222 <p class=flagdescription><b style='mso-bidi-font-weight:normal'>4-Reconciliation</b><span
13223 style='mso-bidi-font-weight:bold'>:</span> If two files (for instance two
13224 alignments) contain different versions of the same sequence due to an indel, a
13225 new sequence will be reconstructed and used instead:</p>
13226
13227 <p class=example2CxSpFirst>aln 1:hgab1 <span style='mso-tab-count:1'>&nbsp; </span>AAAAABAAAAA</p>
13228
13229 <p class=example2CxSpLast>aln 2:hgab1<span style='mso-tab-count:1'>&nbsp;&nbsp; </span>AAAAAAAAAACCC</p>
13230
13231 <p class=flagdescription>will cause the program to reconstruct and use the
13232 following sequence </p>
13233
13234 <p class=example2>hgab1<span style='mso-tab-count:1'>&nbsp;&nbsp; </span>AAAAABAAAAACCC
13235 </p>
13236
13237 <p class=flagdescription>This can be useful if you are trying to combine
13238 several runs of blast, or structural information where residues may have been
13239 deleted. However substitutions are forbidden. If two sequences with the same
13240 name cannot be merged, they will cause the program to exit with an information
13241 message.</p>
13242
13243 <p class=flagdescription><b style='mso-bidi-font-weight:normal'>5-Methods</b><span
13244 style='mso-bidi-font-weight:bold'>:</span> The method describer can either be
13245 built in (See ### for a list of all the available methods) or be a file
13246 describing the method to be used. The exact syntax is provided in part 4 of
13247 this manual.</p>
13248
13249 <p class=flagdescription><b style='mso-bidi-font-weight:normal'>6-Substitution
13250 Matrices</b><span style='mso-bidi-font-weight:bold'>: </span>If the method is a
13251 substitution matrix (X) then no other type of information should be provided.
13252 For instance:</p>
13253
13254 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
13255 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
13256 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
13257 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
13258
13259 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
13260 sample_seq1.fasta -in=Xpam250mt<span style="mso-spacerun: yes">&nbsp;
13261 </span>-gapopen=-10<span style="mso-spacerun: yes">&nbsp; </span>-gapext=-1 </p>
13262
13263 </div>
13264
13265 <p class=flagdescription>This command results in a progressive alignment
13266 carried out on the sequences in seqfile. The procedure does not use any more
13267 the T-Coffee concistency based algorithm, but switches to a standard
13268 progressive alignment algorithm (like ClustalW or Pileup) much less accurate.
13269 In this context, appropriate gap penalties should be provided. The matrices are
13270 in the file source/matrices.h. Add-Hoc matrices can also be provided by the
13271 user (see the matrices format section at the end of this manual).</p>
13272
13273 <div style='mso-element:para-border-div;border:solid windowtext 1.5pt;
13274 padding:0cm 0cm 0cm 0cm;background:#F7CBB7'>
13275
13276 <p class=Warning>Warning: Xmatrix does not have the same effect as using the
13277 -matrix flag.<span style="mso-spacerun: yes">&nbsp; </span>The -matrix defines
13278 the matrix that will be used while compiling the library while the Xmatrix
13279 defines the matrix used when assembling the final alignment.</p>
13280
13281 </div>
13282
13283 <h3><a name="_Toc101065247"></a><a name="_Toc102494369"></a><a
13284 name="_Toc102494777"></a><a name="_Toc151732290"><span style='mso-bookmark:
13285 _Toc102494777'><span style='mso-bookmark:_Toc102494369'><span style='mso-bookmark:
13286 _Toc101065247'>Profile Input</span></span></span></a></h3>
13287
13288 <p class=flag><a name="_Toc101065248"></a><a name="_Toc102494778"></a><a
13289 name="_Toc151732291"><span style='mso-bookmark:_Toc102494778'><span
13290 style='mso-bookmark:_Toc101065248'><span lang=AF>-profile</span></span></span></a></p>
13291
13292 <p class=flagusage><span lang=FR>Usage: -profile=[&lt;name&gt;,] maximum of 200
13293 profiles.</span></p>
13294
13295 <p class=instruction>Default: no default</p>
13296
13297 <p class=flagdescription>This flag causes T-Coffee to treat multiple alignments
13298 as a single sequences, thus making it possible to make multiple profile alignments.
13299 The profile-profile alignment is controlled by <span style='mso-bidi-font-weight:
13300 bold'>-profile_mode</span> and <span style='mso-bidi-font-weight:bold'>-profile_comparison</span>.
13301 When provided with the <b style='mso-bidi-font-weight:normal'>-in</b> flag,
13302 profiles must be preceded with the letter R.</p>
13303
13304 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
13305 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
13306 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
13307 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
13308
13309 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
13310 &#8211;profile sample_aln1.aln,sample_aln2.aln &#8211;outfile=profile_aln</p>
13311
13312 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
13313 &#8211;in Rsample_aln1.aln,Rsample_aln2.aln,Mslow_pair,Mlalign_id_pair
13314 &#8211;outfile=profile_aln</p>
13315
13316 </div>
13317
13318 <p class=flagdescription>Note that when using &#8211;template_file, the program
13319 will also look for the templates associated with the profiles, even if the
13320 profiles have been provided as templates themselves (however it will not look
13321 for the template of the profile templates of the profile templates\85)</p>
13322
13323 <p class=flag><a name="_Toc101065249"></a><a name="_Toc102494779"></a><a
13324 name="_Toc151732292"><span style='mso-bookmark:_Toc102494779'><span
13325 style='mso-bookmark:_Toc101065249'><span lang=AF>-profile1 [cw]</span></span></span></a></p>
13326
13327 <p class=flagusage><span lang=FR>Usage: -profile1=[&lt;name&gt;], one name only</span></p>
13328
13329 <p class=instruction>Default: no default</p>
13330
13331 <p class=flagdescription>Similar to the previous one and was provided for
13332 compatibility with ClustalW.</p>
13333
13334 <p class=flag><a name="_Toc101065250"></a><a name="_Toc102494780"></a><a
13335 name="_Toc151732293"><span style='mso-bookmark:_Toc102494780'><span
13336 style='mso-bookmark:_Toc101065250'><span lang=AF>-profile2 [cw]</span></span></span></a></p>
13337
13338 <p class=flagusage><span lang=FR>Usage: -profile1=[&lt;name&gt;], one name only</span></p>
13339
13340 <p class=instruction>Default: no default</p>
13341
13342 <p class=flagdescription>Similar to the previous one and was provided for
13343 compatibility with ClustalW.</p>
13344
13345 <h2><a name="_Toc101065251"></a><a name="_Toc102494370"></a><a
13346 name="_Toc102494781"></a><a name="_Toc151732294"><span style='mso-bookmark:
13347 _Toc102494781'><span style='mso-bookmark:_Toc102494370'><span style='mso-bookmark:
13348 _Toc101065251'>Alignment Computation</span></span></span></a></h2>
13349
13350 <h3><a name="_Toc101065252"></a><a name="_Toc102494371"></a><a
13351 name="_Toc102494782"></a><a name="_Toc151732295"><span style='mso-bookmark:
13352 _Toc102494782'><span style='mso-bookmark:_Toc102494371'><span style='mso-bookmark:
13353 _Toc101065252'>Library Computation: Methods</span></span></span></a></h3>
13354
13355 <p class=flag><a name="_Toc102494783"></a><a name="_Toc151732296"><span
13356 style='mso-bookmark:_Toc102494783'><span lang=AF>-lalign_n_top</span></span></a></p>
13357
13358 <p class=flagusage><span lang=FR>Usage: -lalign_n_top=&lt;Integer&gt;</span></p>
13359
13360 <p class=instruction>Default: -lalign_n_top=10</p>
13361
13362 <p class=flagdescription>Number of alignment reported by the local method
13363 (lalign).</p>
13364
13365 <p class=flag><a name="_Toc102494784"></a><a name="_Toc151732297"><span
13366 style='mso-bookmark:_Toc102494784'><span lang=AF>-align_pdb_param_file</span></span></a></p>
13367
13368 <p class=flagdescription>Unsuported</p>
13369
13370 <p class=flag><a name="_Toc102494785"></a><a name="_Toc151732298"><span
13371 style='mso-bookmark:_Toc102494785'><span lang=AF>-align_pdb_hasch_mode</span></span></a></p>
13372
13373 <p class=flagdescription>Unsuported<a name="_Toc101065253"></a></p>
13374
13375 <h3><span style='mso-bookmark:_Toc101065253'><a name="_Toc102494372"></a><a
13376 name="_Toc102494786"></a><a name="_Toc151732299"><span style='mso-bookmark:
13377 _Toc102494786'><span style='mso-bookmark:_Toc102494372'>Library Computation:
13378 Extension</span></span></a></span></h3>
13379
13380 <p class=flag><a name="_Toc101065255"></a><a name="_Toc101065254"></a><a
13381 name="_Toc102494787"></a><a name="_Toc151732300"><span style='mso-bookmark:
13382 _Toc102494787'><span style='mso-bookmark:_Toc101065254'><span style='mso-bookmark:
13383 _Toc101065255'><span lang=AF>-</span></span></span><span style='mso-bookmark:
13384 _Toc101065255'><span lang=AF>lib_list [Unsupported]</span></span></span></a><span
13385 style='mso-bookmark:_Toc101065255'></span></p>
13386
13387 <p class=flagusage><span style='mso-bookmark:_Toc101065255'><span lang=FR>Usage:<span
13388 style="mso-spacerun: yes">&nbsp; </span>-lib_list=&lt;filename&gt; </span></span></p>
13389
13390 <p class=instruction><span style='mso-bookmark:_Toc101065255'>Default:unset</span></p>
13391
13392 <p class=flagdescription><span style='mso-bookmark:_Toc101065255'>Use this flag
13393 if you do not want the library computation to take into account all the
13394 possible pairs in your dataset. For instance</span></p>
13395
13396 <p class=flagdescription><span style='mso-bookmark:_Toc101065255'>Format:</span></p>
13397
13398 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
13399 mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
13400 background:#E6E6E6'>
13401
13402 <p class=examplefileCxSpFirst><span style='mso-bookmark:_Toc101065255'><span
13403 style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>2 Name1 name2 </span></p>
13404
13405 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065255'><span
13406 style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>2 Name1 name4</span></p>
13407
13408 <p class=examplefileCxSpLast><span style='mso-bookmark:_Toc101065255'><span
13409 style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>3 Name1 Name2
13410 Name3\85</span></p>
13411
13412 </div>
13413
13414 <p class=flagdescription><span style='mso-bookmark:_Toc101065255'><span
13415 style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>(the
13416 line 3 would be used by a multiple alignment method).</span></p>
13417
13418 <p class=flag><span style='mso-bookmark:_Toc101065255'><a name="_Toc102494788"></a><a
13419 name="_Toc151732301"><span style='mso-bookmark:_Toc102494788'><span lang=AF>-do_normalise</span></span></a></span></p>
13420
13421 <p class=flagusage><span style='mso-bookmark:_Toc101065255'><span lang=FR>Usage:<span
13422 style="mso-spacerun: yes">&nbsp; </span>-do_normalise=&lt;0 or a positive
13423 value&gt; </span></span></p>
13424
13425 <p class=instruction><span style='mso-bookmark:_Toc101065255'>Default:-do_normalise=1000</span></p>
13426
13427 <p class=instruction><span style='mso-bookmark:_Toc101065255'>Development Only</span></p>
13428
13429 <p class=flagdescription><span style='mso-bookmark:_Toc101065255'>When using a
13430 value different from 0, this flag sets the score of the highest scoring pair to
13431 1000. </span></p>
13432
13433 <p class=flag><span style='mso-bookmark:_Toc101065255'><a name="_Toc102494789"></a><a
13434 name="_Toc151732302"><span style='mso-bookmark:_Toc102494789'><span lang=AF>-extend</span></span></a></span></p>
13435
13436 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
13437 </span>-extend=&lt;0,1 or a positive value&gt; </span></p>
13438
13439 <p class=instruction>Default:-extend=1</p>
13440
13441 <p class=instruction>Development Only</p>
13442
13443 <p class=flagdescription>When turned on, this flag indicates that the library
13444 extension should be carried out when performing the multiple alignment. If <b>-extend
13445 =0</b>, the extension is not made, if it is set to 1, the extension is made on
13446 all the pairs in the library. If the extension is set to another positive
13447 value, the extension is only carried out on pairs having a weight value
13448 superior to the specified limit.<a name="_Toc101065256"></a></p>
13449
13450 <p class=flag><span style='mso-bookmark:_Toc101065256'><a name="_Toc102494790"></a><a
13451 name="_Toc151732303"><span style='mso-bookmark:_Toc102494790'><span lang=AF>-extend_mode</span></span></a></span></p>
13452
13453 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
13454 </span>-extend=&lt;string&gt;</span></p>
13455
13456 <p class=instruction>Default:-extend=very_fast_triplet</p>
13457
13458 <p class=instruction>Warning: Development Only</p>
13459
13460 <p class=flagdescription>Controls the algorithm for matrix extension. Available
13461 modes include:</p>
13462
13463 <p class=flagdescription>relative_triplet<span style='mso-tab-count:2'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Unsupported</p>
13464
13465 <p class=flagdescription>g_coffee<span style='mso-tab-count:3'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Unsupported</p>
13466
13467 <p class=flagdescription>g_coffee_quadruplets<span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp; </span>Unsupported</p>
13468
13469 <p class=flagdescription>fast_triplet<span style='mso-tab-count:2'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Fast
13470 triplet extension</p>
13471
13472 <p class=flagdescription>very_fast_triplet<span style='mso-tab-count:2'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>slow
13473 triplet extension, limited to the <b>-max_n_pair</b> best sequence pairs when
13474 aligning two profiles</p>
13475
13476 <p class=flagdescription>slow_triplet<span style='mso-tab-count:2'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Exhaustive
13477 use of all the triplets</p>
13478
13479 <p class=flagdescription>mixt<span style='mso-tab-count:3'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Unsupported</p>
13480
13481 <p class=flagdescription>quadruplet<span style='mso-tab-count:2'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Unsupported</p>
13482
13483 <p class=flagdescription>test<span style='mso-tab-count:3'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Unsupported</p>
13484
13485 <p class=flagdescription>matrix<span style='mso-tab-count:3'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Use
13486 of the matrix <b>-matrix<o:p></o:p></b></p>
13487
13488 <p class=flagdescription>fast_matrix<span style='mso-tab-count:2'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Use
13489 of the matrix <b>-matrix</b>. Profiles are turned into consensus</p>
13490
13491 <p class=flag><a name="_Toc101065257"></a><a name="_Toc102494791"></a><a
13492 name="_Toc151732304"><span style='mso-bookmark:_Toc102494791'><span
13493 style='mso-bookmark:_Toc101065257'><span lang=AF>-max_n_pair</span></span></span></a></p>
13494
13495 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
13496 </span>-max_n_pair=&lt;integer&gt;</span></p>
13497
13498 <p class=instruction>Default:-extend=10</p>
13499
13500 <p class=instruction>Development Only</p>
13501
13502 <p class=flagdescription>Controls the number of pairs considered by the <b>-extend_mode</b>=very_fast_triplet.
13503 Setting it to 0 forces all the pairs to be considered (equivalent to <b>-extend_mode</b>=slow_triplet).</p>
13504
13505 <p class=flag><a name="_Toc101065258"></a><a name="_Toc102494792"></a><a
13506 name="_Toc151732305"><span style='mso-bookmark:_Toc102494792'><span
13507 style='mso-bookmark:_Toc101065258'><span lang=AF>-seq_name_for_quadruplet</span></span></span></a></p>
13508
13509 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
13510 </span>Unsupported</span></p>
13511
13512 <p class=flag><a name="_Toc101065259"></a><a name="_Toc102494793"></a><a
13513 name="_Toc151732306"><span style='mso-bookmark:_Toc102494793'><span
13514 style='mso-bookmark:_Toc101065259'><span lang=AF>-compact</span></span></span></a></p>
13515
13516 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
13517 </span>Unsupported</span></p>
13518
13519 <p class=flag><a name="_Toc101065260"></a><a name="_Toc102494794"></a><a
13520 name="_Toc151732307"><span style='mso-bookmark:_Toc102494794'><span
13521 style='mso-bookmark:_Toc101065260'><span lang=AF>-clean</span></span></span></a></p>
13522
13523 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
13524 </span>Unsupported</span></p>
13525
13526 <p class=flag><a name="_Toc101065261"></a><a name="_Toc102494795"></a><a
13527 name="_Toc151732308"><span style='mso-bookmark:_Toc102494795'><span
13528 style='mso-bookmark:_Toc101065261'><span lang=AF>-maximise</span></span></span></a></p>
13529
13530 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
13531 </span>Unsupported</span></p>
13532
13533 <p class=flag><a name="_Toc101065262"></a><a name="_Toc102494796"></a><a
13534 name="_Toc151732309"><span style='mso-bookmark:_Toc102494796'><span
13535 style='mso-bookmark:_Toc101065262'><span lang=AF>-do_self</span></span></span></a></p>
13536
13537 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
13538 </span>Flag -do_self</span></p>
13539
13540 <p class=flagusage><span lang=FR>Default: No</span></p>
13541
13542 <p class=flagdescription>This flag causes the extension to carried out within
13543 the sequences (as opposed to between sequences). This is necessary when looking
13544 for internal repeats with Mocca.</p>
13545
13546 <p class=flag><a name="_Toc101065263"></a><a name="_Toc102494797"></a><a
13547 name="_Toc151732310"><span style='mso-bookmark:_Toc102494797'><span
13548 style='mso-bookmark:_Toc101065263'><span lang=AF>-seq_name_for_quadruplet</span></span></span></a></p>
13549
13550 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
13551 </span>Unsupported</span></p>
13552
13553 <p class=flag><a name="_Toc101065264"></a><a name="_Toc102494798"></a><a
13554 name="_Toc151732311"><span style='mso-bookmark:_Toc102494798'><span
13555 style='mso-bookmark:_Toc101065264'><span lang=AF>-weight</span></span></span></a></p>
13556
13557 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
13558 </span>-weight=&lt;winsimN, sim or sim_&lt;matrix_name or matrix_file&gt; or
13559 &lt;integer value&gt;</span></p>
13560
13561 <p class=instruction>Default: -weight=sim</p>
13562
13563 <p class=flagdescription>Weight defines the way alignments are weighted when
13564 turned into a library.<span style="mso-spacerun: yes">&nbsp;
13565 </span>Overweighting can be obtained with the OW&lt;X&gt; weight mode.</p>
13566
13567 <p class=flagdescription><span class=StyleflagdescriptionBoldItalicChar><o:p>&nbsp;</o:p></span></p>
13568
13569 <p class=flagdescription><span class=StyleflagdescriptionBoldItalicChar>winsimN
13570 </span>indicates that the weight assigned to a given pair will be equal to the
13571 percent identity within a window of 2N+1 length centered on that pair. For
13572 instance winsim10 defines a window of 10 residues around the pair being
13573 considered. This gives its own weight to each residue in the output library. In
13574 our hands, this type of weighting scheme has not provided any significant
13575 improvement over the standard sim value.</p>
13576
13577 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
13578 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
13579 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
13580 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
13581
13582 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
13583 sample_seq1.fasta -weight=winsim10 &#8211;out_lib=test.tc_lib </p>
13584
13585 </div>
13586
13587 <p class=flagdescription><span class=StyleflagdescriptionBoldItalicChar>sim</span>
13588 indicates that the weight equals the average identity within the sequences
13589 containing the matched residues.</p>
13590
13591 <p class=flagdescription><span class=StyleflagdescriptionBoldItalicChar>OW&lt;X&gt;</span><span
13592 class=StyleflagdescriptionBoldItalicChar><span style='font-style:normal;
13593 mso-bidi-font-style:italic'> </span></span><span
13594 class=StyleflagdescriptionBoldItalicChar><span style='font-weight:normal;
13595 mso-bidi-font-weight:bold;font-style:normal;mso-bidi-font-style:italic'>Will
13596 cause the sim weight to be multiplied by X<o:p></o:p></span></span></p>
13597
13598 <p class=flagdescription><span class=StyleflagdescriptionBoldItalicChar>sim_matrix_name</span>
13599 indicates the average identity with two residues regarded as identical when
13600 their substitution value is positive. The valid matrices names are in <i
13601 style='mso-bidi-font-style:normal'>matrices.h (pam250mt) .</i>Matrices not
13602 found in this header are considered to be filenames. See the format section for
13603 matrices. For instance, <i style='mso-bidi-font-style:normal'>-weight=sim_pam250mt</i>
13604 indicates that the grouping used for similarity will be the set of classes with
13605 positive substitutions. </p>
13606
13607 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
13608 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
13609 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
13610 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
13611
13612 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
13613 sample_seq1.fasta -weight=winsim10 &#8211;out_lib=test.tc_lib </p>
13614
13615 </div>
13616
13617 <p class=flagdescription>Other groups include </p>
13618
13619 <p class=flagdescription><span class=StyleflagdescriptionBoldItalicChar>sim_clustalw_col</span><i
13620 style='mso-bidi-font-style:normal'> </i>( categories of clustalw marked with :)</p>
13621
13622 <p class=flagdescription><span class=StyleflagdescriptionBoldItalicChar>sim_clustalw_dot</span>
13623 ( categories of clustalw marked with .)</p>
13624
13625 <p class=flagdescription><span class=StyleflagdescriptionBoldItalicChar>Value</span><i
13626 style='mso-bidi-font-style:normal'> </i>indicates that all the pairs found in
13627 the alignments must be given the same weight equal to value. This is useful
13628 when the alignment one wishes to turn into a library must be given a
13629 pre-specified score (for instance if they come from a structure
13630 super-imposition program). Value is an integer:</p>
13631
13632 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
13633 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
13634 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
13635 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
13636
13637 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
13638 sample_seq1.fasta -weight=1000 &#8211;out_lib=test.tc_lib </p>
13639
13640 </div>
13641
13642 <h3><a name="_Toc101065265"></a><a name="_Toc102494373"></a><a
13643 name="_Toc102494799"></a><a name="_Toc151732312"><span style='mso-bookmark:
13644 _Toc102494799'><span style='mso-bookmark:_Toc102494373'><span style='mso-bookmark:
13645 _Toc101065265'>Tree Computation</span></span></span></a></h3>
13646
13647 <p class=flag><a name="_Toc101065266"></a><a name="_Toc102494800"></a><a
13648 name="_Toc151732313"><span style='mso-bookmark:_Toc102494800'><span
13649 style='mso-bookmark:_Toc101065266'><span lang=AF>-</span></span></span><span
13650 lang=AF>distance_matrix_mode</span></a></p>
13651
13652 <p class=flagusage><span lang=FR>Usage: -distance_matrix_mode=&lt;slow, fast,
13653 very_fast&gt;</span></p>
13654
13655 <p class=instruction>Default: very_fast</p>
13656
13657 <p class=flagdescription>This flag indicates the method used for computing the
13658 distance matrix (distance between every pair of sequences) required for the
13659 computation of the dendrogram. </p>
13660
13661 <p class=flagdescription><b style='mso-bidi-font-weight:normal'>Slow</b> <span
13662 style='mso-tab-count:1'> </span>The chosen dp_mode using the extended library, </p>
13663
13664 <p class=flagdescription><b style='mso-bidi-font-weight:normal'>fast</b>:<span
13665 style="mso-spacerun: yes">&nbsp;&nbsp; </span><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>The
13666 fasta dp_mode using the extended library.</p>
13667
13668 <p class=flagdescription><b style='mso-bidi-font-weight:normal'>very_fast</b><span
13669 style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>The
13670 fasta dp_mode using blosum62mt.</p>
13671
13672 <p class=flagdescription><b style='mso-bidi-font-weight:normal'>ktup<span
13673 style='mso-tab-count:1'>&nbsp; </span></b>Ktup matching (Muscle kind) </p>
13674
13675 <p class=flagdescription><b style='mso-bidi-font-weight:normal'>aln<span
13676 style='mso-tab-count:2'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></b>Read
13677 the distances on a precomputed MSA</p>
13678
13679 <p class=flag><a name="_Toc101065267"></a><a name="_Toc102494801"></a><a
13680 name="_Toc151732314"><span style='mso-bookmark:_Toc102494801'><span
13681 style='mso-bookmark:_Toc101065267'><span lang=AF>-quicktree [CW]</span></span></span></a></p>
13682
13683 <p class=flagusage><span lang=FR>Usage: -quicktree</span></p>
13684
13685 <p class=instruction>Description: Causes T-Coffee to compute a fast approximate
13686 guide tree</p>
13687
13688 <p class=MyNormal><span lang=AF>This flag is kept for compatibility with
13689 ClustalW. It indicates that:</span></p>
13690
13691 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
13692 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
13693 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
13694 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
13695
13696 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
13697 sample_seq1.fasta &#8211;distance_matrix_mode=very_fast </p>
13698
13699 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
13700 sample_seq1.fasta &#8211;quicktree </p>
13701
13702 </div>
13703
13704 <h3><a name="_Toc101065268"></a><a name="_Toc102494374"></a><a
13705 name="_Toc102494802"></a><a name="_Toc151732315"><span style='mso-bookmark:
13706 _Toc102494802'><span style='mso-bookmark:_Toc102494374'><span style='mso-bookmark:
13707 _Toc101065268'>Pair-wise Alignment Computation</span></span></span></a></h3>
13708
13709 <p class=Noteboxtitle><o:p>&nbsp;</o:p></p>
13710
13711 <div style='mso-element:para-border-div;border:solid windowtext 1.5pt;
13712 padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#FFFF89'>
13713
13714 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut align=center
13715 style='text-align:center;background:#FFFF89'><span style='font-size:20.0pt'>Controlling
13716 Alignment Computation<o:p></o:p></span></p>
13717
13718 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut><o:p>&nbsp;</o:p></p>
13719
13720 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut>Most parameters in
13721 this section refer to the alignment mode fasta_pair_wise and cfatsa_pair_wise.
13722 When using these alignment modes, things proceed as follow:</p>
13723
13724 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut>1-Sequences are
13725 recoded using a degenerated alphabet provided with &lt;-sim_matrix&gt; </p>
13726
13727 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut>2-Recoded sequences
13728 are then hashed into ktuples of size <u>&lt;-ktup&gt;</u></p>
13729
13730 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut>3-Dynamic
13731 programming runs on the <u>&lt;-ndiag&gt;</u> best diagonals whose score is
13732 higher than <u>&lt;-diag_threshold&gt;</u>, the way diagonals are scored is
13733 controlled via <u>&lt;-diag_mode&gt;</u> .</p>
13734
13735 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut>4-The Dynamic
13736 computation is made to optimize either the library scoring scheme (as defined
13737 by the <u>-in</u> flag) or a substitution matrix as provided via the <u>-matrix</u>
13738 flag. The penalty scheme is defined by <u>-gapopen</u> and <u>-gapext</u>. If <u>-gapopen</u>
13739 is undefined, the value defined in <u>-cosmetic_penalty</u> is used instead.</p>
13740
13741 <p class=StylenoteboxbodyBoldNotItalicBoxSinglesolidlineAut>5-Terminal gaps are
13742 scored according to <u>-tg_mode</u></p>
13743
13744 </div>
13745
13746 <p class=noteboxbody><o:p>&nbsp;</o:p></p>
13747
13748 <p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>
13749
13750 <p class=flag><a name="_Toc101065269"></a><a name="_Toc102494803"></a><a
13751 name="_Toc151732316"><span style='mso-bookmark:_Toc102494803'><span
13752 style='mso-bookmark:_Toc101065269'><span lang=AF>-dp_mode</span></span></span></a></p>
13753
13754 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
13755 </span>-dp_mode=&lt;string&gt;</span></p>
13756
13757 <p class=instruction>Default: -dp_mode=cfasta_fair_wise</p>
13758
13759 <p class=flagdescription>This flag indicates the type of dynamic programming
13760 used by the program:</p>
13761
13762 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
13763 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
13764 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
13765 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
13766
13767 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
13768 sample_seq1.fasta &#8211;dp_mode myers_miller_pair_wise </p>
13769
13770 </div>
13771
13772 <p class=flagdescription><span class=StyleflagdescriptionBoldItalicChar>gotoh_pair_wise</span>:
13773 implementation of the gotoh algorithm (quadratic in memory and time)</p>
13774
13775 <p class=flagdescription><span class=StyleflagdescriptionBoldItalicChar>myers_miller_pair_wise</span>:
13776 implementation of the Myers and Miller dynamic programming algorithm (
13777 quadratic in time and linear in space). This algorithm is recommended for very
13778 long sequences. It is about 2 times slower than gotoh and only accepts <i
13779 style='mso-bidi-font-style:normal'>tg_mode=1or 2 (i.e. gaps penalized for
13780 opening).<o:p></o:p></i></p>
13781
13782 <p class=flagdescription><span class=StyleflagdescriptionBoldItalicChar>fasta_pair_wise</span><i
13783 style='mso-bidi-font-style:normal'>: </i>implementation of the fasta algorithm.
13784 The sequence is hashed, looking for <i style='mso-bidi-font-style:normal'>ktuples</i>
13785 words. Dynamic programming is only carried out on the <i style='mso-bidi-font-style:
13786 normal'>ndiag</i> best scoring diagonals. This is much faster but less accurate
13787 than the two previous. This mode is controlled by the parameters <b>-ktuple,
13788 -diag_mode and -ndiag<o:p></o:p></b></p>
13789
13790 <p class=flagdescription><span class=StyleflagdescriptionBoldItalicChar>cfasta_pair_wise</span>:
13791 c stands for checked. It is the same algorithm. The dynamic programming is made
13792 on the <i style='mso-bidi-font-style:normal'>ndiag</i> best diagonals, and then
13793 on the 2*ndiags, and so on until the scores converge. Complexity will depend on
13794 the level of divergence of the sequences, but will usually be L*log(L), with an
13795 accuracy comparable to the two first mode ( this was checked on BaliBase). This
13796 mode is controlled by the parameters <b>-ktuple, -diag_mode and &#8211;ndiag<o:p></o:p></b></p>
13797
13798 <p class=Note><span style='mso-ansi-language:EN-US'>Note: Users may find by
13799 looking into the code that other modes with fancy names exists
13800 (viterby_pair_wise\85) Unless mentioned in this documentation, these modes are
13801 not supported.<o:p></o:p></span></p>
13802
13803 <p class=flag><a name="_Toc101065270"></a><a name="_Toc102494804"></a><a
13804 name="_Toc151732317"><span style='mso-bookmark:_Toc102494804'><span
13805 style='mso-bookmark:_Toc101065270'><span lang=AF>-ktuple</span></span></span></a></p>
13806
13807 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
13808 </span>-ktuple=&lt;value&gt;</span></p>
13809
13810 <p class=instruction>Default: -ktuple=1 or 2</p>
13811
13812 <p class=flagdescription>Indicates the ktuple size for cfasta_pair_wise dp_mode
13813 and fasta_pair_wise. It is set to 1 for proteins, and 2 for DNA. The alphabet
13814 used for protein can be a degenerated version, set with <b><u>-sim_matrix.</u></b>.
13815 </p>
13816
13817 <p class=flag><a name="_Toc101065271"></a><a name="_Toc102494805"></a><a
13818 name="_Toc151732318"><span style='mso-bookmark:_Toc102494805'><span
13819 style='mso-bookmark:_Toc101065271'><span lang=AF>-ndiag</span></span></span></a></p>
13820
13821 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
13822 </span>-ndiag=&lt;value&gt;</span></p>
13823
13824 <p class=instruction>Default: -ndiag=0</p>
13825
13826 <p class=flagdescription>Indicates the number of diagonals used by the <i>fasta_pair_wise</i>
13827 algorithm (cf <b>-dp_mode</b>). When<span style="mso-spacerun: yes">&nbsp;
13828 </span><b>-ndiag=0</b>, n_diag=Log (length of the smallest sequence)+1. </p>
13829
13830 <p class=Note><span style='mso-ansi-language:EN-US'>When &#8211;ndiag and
13831 &#8211;diag_threshold are set, diagonals are selected if and only if they
13832 fulfill both conditions.<o:p></o:p></span></p>
13833
13834 <p class=flag><a name="_Toc101065272"></a><a name="_Toc102494806"></a><a
13835 name="_Toc151732319"><span style='mso-bookmark:_Toc102494806'><span
13836 style='mso-bookmark:_Toc101065272'><span lang=AF>-diag_mode</span></span></span></a></p>
13837
13838 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
13839 </span>-diag_mode=&lt;value&gt;</span></p>
13840
13841 <p class=instruction>Default: -diag_mode=0</p>
13842
13843 <p class=flagdescription>Indicates the manner in which diagonals are scored
13844 during the fasta hashing. </p>
13845
13846 <p class=flagdescription>0: indicates that the score of a diagonal is equal to
13847 the sum of the scores of the exact matches it contains. </p>
13848
13849 <p class=flagdescription>1 indicates that this score is set equal to the score
13850 of the best uninterrupted segment (useful when dealing with fragments of
13851 sequences).</p>
13852
13853 <p class=flag><a name="_Toc101065273"></a><a name="_Toc102494807"></a><a
13854 name="_Toc151732320"><span style='mso-bookmark:_Toc102494807'><span
13855 style='mso-bookmark:_Toc101065273'><span lang=AF>-diag_threshold</span></span></span></a></p>
13856
13857 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
13858 </span>-diag_threshold=&lt;value&gt;</span></p>
13859
13860 <p class=instruction>Default: -diag_threshold=0</p>
13861
13862 <p class=flagdescription>Sets the value of the threshold when selecting
13863 diagonals. </p>
13864
13865 <p class=flagdescription>0: indicates that &#8211;ndiag should be used to
13866 select the diagonals (cf &#8211;ndiag section).</p>
13867
13868 <p class=flag><a name="_Toc101065274"></a><a name="_Toc102494808"></a><a
13869 name="_Toc151732321"><span style='mso-bookmark:_Toc102494808'><span
13870 style='mso-bookmark:_Toc101065274'><span lang=AF>-sim_matrix</span></span></span></a></p>
13871
13872 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
13873 </span>-sim_matrix=&lt;string&gt;</span></p>
13874
13875 <p class=instruction>Default: -sim_matrix=vasiliky</p>
13876
13877 <p class=flagdescription>Indicates the manner in which the amino acid alphabet
13878 is degenerated when hashing in the fasta_pairwise dynamic programming. Standard
13879 ClustalW matrices are all valid. They are used to define groups of amino acids
13880 having positive substitution values. In T-Coffee, the default is a 13 letter
13881 grouping named Vasiliky, with residues grouped as follows:</p>
13882
13883 <p class=example2>rk, de, qh, vilm, fy (other residues kept alone).</p>
13884
13885 <p class=flagdescription>This alphabet is set with the flag <b>-sim_matrix=vasiliky</b>.
13886 In order to keep the alphabet non degenerated, <b>-sim_matrix=idmat </b>can be
13887 used to retain the standard alphabet.</p>
13888
13889 <p class=flag><a name="_Toc101065275"></a><a name="_Toc102494809"></a><a
13890 name="_Toc151732322"><span style='mso-bookmark:_Toc102494809'><span
13891 style='mso-bookmark:_Toc101065275'><span lang=AF>-matrix [CW]</span></span></span></a></p>
13892
13893 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
13894 </span>-matrix=&lt;blosum62mt&gt;</span></p>
13895
13896 <p class=instruction>Default: -matrix=blosum62mt</p>
13897
13898 <p class=flagdescription>The usage of this flag has been modified from previous
13899 versions, due to frequent mistakes in its usage. This flag sets the matrix that
13900 will be used by alignment methods within t_coffee (slow_pair, lalign_id_pair).
13901 It does not affect external methods (like clustal_pair, clustal_aln\85). </p>
13902
13903 <p class=flagdescription>Users can also provide their own matrices, using the
13904 matrix format described in the appendix.</p>
13905
13906 <p class=flag><a name="_Toc101065276"></a><a name="_Toc102494810"></a><a
13907 name="_Toc151732323"><span style='mso-bookmark:_Toc102494810'><span
13908 style='mso-bookmark:_Toc101065276'><span lang=AF>-nomatch</span></span></span></a></p>
13909
13910 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
13911 </span>-nomatch=&lt;positive value&gt;</span></p>
13912
13913 <p class=instruction>Default: -nomatch=0</p>
13914
13915 <p class=flagdescription>Indicates the penalty to associate with a match. When
13916 using a library, all matches are positive or equal to 0. Matches equal to 0 are
13917 unsupported by the library but non-penalized. Setting nomatch to a non-negative
13918 value makes it possible to penalize these null matches and prevent unrelated
13919 sequences from being aligned (this can be useful when the alignments are meant
13920 to be used for structural modeling).</p>
13921
13922 <p class=flag><a name="_Toc101065277"></a><a name="_Toc102494811"></a><a
13923 name="_Toc151732324"><span style='mso-bookmark:_Toc102494811'><span
13924 style='mso-bookmark:_Toc101065277'><span lang=AF>-gapopen</span></span></span></a></p>
13925
13926 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
13927 </span>-gapopen=&lt;negative value&gt;</span></p>
13928
13929 <p class=instruction>Default: -gapopen=0</p>
13930
13931 <p class=flagdescription>Indicates the penalty applied for opening a gap. The
13932 penalty must be negative. If no value is provided when using a substitution
13933 matrix, a value will be automatically computed.</p>
13934
13935 <p class=flagdescription>Here are some guidelines regarding the tuning of
13936 gapopen and gapext. In T-Coffee matches get a score between 0 (match) and 1000
13937 (match perfectly consistent with the library). The default cosmetic penalty is
13938 set to -50 (5% of a perfect match). If you want to tune -gapoen and see a
13939 strong effect, you should therefore consider values between 0 and -1000. </p>
13940
13941 <p class=flag><a name="_Toc101065278"></a><a name="_Toc102494812"></a><a
13942 name="_Toc151732325"><span style='mso-bookmark:_Toc102494812'><span
13943 style='mso-bookmark:_Toc101065278'><span lang=AF>-gapext</span></span></span></a></p>
13944
13945 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
13946 </span>-gapext=&lt;negative value&gt;</span></p>
13947
13948 <p class=instruction>Default: -gapext=0</p>
13949
13950 <p class=flagdescription>Indicates the penalty applied for extending a gap (cf <b><u>-gapopen</u></b>)</p>
13951
13952 <p class=flag><a name="_Toc101065279"></a><a name="_Toc102494813"></a><a
13953 name="_Toc151732326"><span style='mso-bookmark:_Toc102494813'><span
13954 style='mso-bookmark:_Toc101065279'><span lang=AF>-fgapopen</span></span></span></a></p>
13955
13956 <p class=flagusage><span lang=FR>Unsupported</span></p>
13957
13958 <p class=flag><a name="_Toc101065280"></a><a name="_Toc102494814"></a><a
13959 name="_Toc151732327"><span style='mso-bookmark:_Toc102494814'><span
13960 style='mso-bookmark:_Toc101065280'><span lang=AF>-fgapext</span></span></span></a></p>
13961
13962 <p class=flagusage><span lang=FR>Unsupported</span></p>
13963
13964 <p class=flag><a name="_Toc101065281"></a><a name="_Toc102494815"></a><a
13965 name="_Toc151732328"><span style='mso-bookmark:_Toc102494815'><span
13966 style='mso-bookmark:_Toc101065281'><span lang=AF>-cosmetic_penalty</span></span></span></a></p>
13967
13968 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
13969 </span>-cosmetic_penalty=&lt;negative value&gt;</span></p>
13970
13971 <p class=instruction>Default: -cosmetic_penalty=-50</p>
13972
13973 <p class=flagdescription>Indicates the penalty applied for opening a gap. This
13974 penalty is set to a very low value. It will only have an influence on the
13975 portions of the alignment that are unalignable. It will not make them more
13976 correct, but only more pleasing to the eye ( i.e. Avoid stretches of lonely
13977 residues).</p>
13978
13979 <p class=flagdescription>The cosmetic penalty is automatically turned off if a
13980 substitution matrix is used rather than a library.</p>
13981
13982 <p class=flag><a name="_Toc101065282"></a><a name="_Toc102494816"></a><a
13983 name="_Toc151732329"><span style='mso-bookmark:_Toc102494816'><span
13984 style='mso-bookmark:_Toc101065282'><span lang=AF>-tg_mode</span></span></span></a></p>
13985
13986 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
13987 </span>-tg_mode=&lt;0, 1, or 2&gt;</span></p>
13988
13989 <p class=instruction>Default: -tg_mode=1</p>
13990
13991 <p class=flagdescription>0: terminal gaps penalized with <span
13992 class=StyleflagdescriptionBoldItalicChar>-gapopen + -gapext*len<o:p></o:p></span></p>
13993
13994 <p class=flagdescription>1: terminal gaps penalized with a <span
13995 class=StyleflagdescriptionBoldItalicChar>-gapext*len<o:p></o:p></span></p>
13996
13997 <p class=flagdescription>2: terminal gaps unpenalized.</p>
13998
13999 <p class=flagdescription><o:p>&nbsp;</o:p></p>
14000
14001 <h3><a name="_Toc101065283"></a><a name="_Toc102494375"></a><a
14002 name="_Toc102494817"></a><a name="_Toc151732330"><span style='mso-bookmark:
14003 _Toc102494817'><span style='mso-bookmark:_Toc102494375'><span style='mso-bookmark:
14004 _Toc101065283'>Weighting Schemes</span></span></span></a></h3>
14005
14006 <p class=flag><a name="_Toc101065284"></a><a name="_Toc102494818"></a><a
14007 name="_Toc151732331"><span style='mso-bookmark:_Toc102494818'><span
14008 style='mso-bookmark:_Toc101065284'><span lang=AF>-seq_weight</span></span></span></a></p>
14009
14010 <p class=flagusage><span lang=FR>Usage: -seq_weight=&lt;t_coffee or
14011 &lt;file_name&gt;&gt;</span></p>
14012
14013 <p class=instruction>Default: -seq_weight=t_coffee</p>
14014
14015 <p class=flagdescription>These are the individual weights assigned to each
14016 sequence. The t_coffee weights try to compensate the bias in consistency caused
14017 by redundancy in the sequences.</p>
14018
14019 <p class=Formula><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>sim(A,B)=%similarity
14020 between A and B, between 0 and 1. </p>
14021
14022 <p class=Formula><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>weight(A)=1/sum(sim(A,X)^3)</p>
14023
14024 <p class=flagdescription>Weights are normalized so that their sum equals the
14025 number of sequences. They are applied onto the primary library in the following
14026 manner:</p>
14027
14028 <p class=Formula><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>res_score(Ax,By)=Min(weight(A),
14029 weight(B))*res_score(Ax, By)</p>
14030
14031 <p class=flagdescription>These are very simple weights. Their main goal is to
14032 prevent a single sequence present in many copies to dominate the alignment.</p>
14033
14034 <p class=Note><span style='mso-ansi-language:EN-US'>Note: The library output by
14035 -out_lib is the un-weighted<span style="mso-spacerun: yes">&nbsp;
14036 </span>library. <o:p></o:p></span></p>
14037
14038 <p class=Note><span style='mso-ansi-language:EN-US'>Note: Weights can be output
14039 using the -outseqweight flag.<o:p></o:p></span></p>
14040
14041 <p class=Note><span style='mso-ansi-language:EN-US'>Note: You can use your own
14042 weights (see the format section). <o:p></o:p></span></p>
14043
14044 <p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>
14045
14046 <h3><a name="_Toc101065285"></a><a name="_Toc102494376"></a><a
14047 name="_Toc102494819"></a><a name="_Toc151732332"><span style='mso-bookmark:
14048 _Toc102494819'><span style='mso-bookmark:_Toc102494376'><span style='mso-bookmark:
14049 _Toc101065285'>Multiple Alignment Computation</span></span></span></a></h3>
14050
14051 <p class=flag><a name="_Toc101065286"></a><a name="_Toc102494820"></a><a
14052 name="_Toc151732333"><span style='mso-bookmark:_Toc102494820'><span
14053 style='mso-bookmark:_Toc101065286'><span lang=AF>-msa_mode</span></span></span></a></p>
14054
14055 <p class=flagusage><span lang=FR>Usage:
14056 -msa_mode=&lt;tree,graph,precomputed&gt;</span></p>
14057
14058 <p class=instruction>Default: -evaluate_mode=tree</p>
14059
14060 <p class=flagdescription>Unsupported</p>
14061
14062 <p class=flag><a name="_Toc101065287"></a><a name="_Toc102494821"></a><a
14063 name="_Toc151732334"><span style='mso-bookmark:_Toc102494821'><span
14064 style='mso-bookmark:_Toc101065287'><span lang=AF>-one2all</span></span></span></a><span
14065 style='mso-bookmark:_Toc102494821'><span style='mso-bookmark:_Toc101065287'></span></span></p>
14066
14067 <p class=flagusage><span style='mso-bookmark:_Toc102494821'><span
14068 style='mso-bookmark:_Toc101065287'><span lang=FR>Usage: -one2all=&lt;name&gt;</span></span></span></p>
14069
14070 <p class=instruction><span style='mso-bookmark:_Toc102494821'><span
14071 style='mso-bookmark:_Toc101065287'>Default: not used</span></span></p>
14072
14073 <p class=flagdescription><span style='mso-bookmark:_Toc102494821'><span
14074 style='mso-bookmark:_Toc101065287'>Will generate a one to all library with
14075 respect to the specified sequence and will then align all the sequences in turn
14076 to that sequence, in a sequence determined by the order in which the sequences
14077 were provided.<span style="mso-spacerun: yes">&nbsp; </span></span></span></p>
14078
14079 <p class=flagdescription><span style='mso-bookmark:_Toc102494821'><span
14080 style='mso-bookmark:_Toc101065287'><b style='mso-bidi-font-weight:normal'>&#8211;profile_comparison
14081 =profile</b>, the MSAs provided via &#8211;profile are vectorized and the
14082 function specified by &#8211;profile_comparison is used to make profile profile
14083 alignments. In that case, the complexity is NL^2</span></span></p>
14084
14085 <p class=flag><span style='mso-bookmark:_Toc102494821'><span style='mso-bookmark:
14086 _Toc101065287'><a name="_Toc151732335"><span lang=AF>-profile</span></a></span></span><span
14087 style='mso-bookmark:_Toc151732335'><span lang=AF>_comparison</span></span></p>
14088
14089 <p class=flagusage><span lang=FR>Usage: -profile_mode=&lt;fullN,profile&gt;</span></p>
14090
14091 <p class=instruction>Default: -profile_mode=full50</p>
14092
14093 <p class=flagdescription>The profile mode flag controls the multiple profile
14094 alignments in T-Coffee. There are two instances where t_coffee can make
14095 multiple profile alignments:</p>
14096
14097 <p class=flagdescription>1-When N, the number of sequences is higher than <b
14098 style='mso-bidi-font-weight:normal'>&#8211;maxnseq, </b>the program switches to
14099 its multiple profile alignment mode (t_coffee_dpa).</p>
14100
14101 <p class=flagdescription>2-When MSAs are provided via the <b style='mso-bidi-font-weight:
14102 normal'>&#8211;profile</b> flag or via <b style='mso-bidi-font-weight:normal'>&#8211;profile1</b>
14103 and <b style='mso-bidi-font-weight:normal'>&#8211;profile2</b>. </p>
14104
14105 <p class=flagdescription>In these situations, the &#8211;profile_mode value
14106 influences the alignment computation, these values are:</p>
14107
14108 <p class=flagdescription><b style='mso-bidi-font-weight:normal'>&#8211;profile_comparison
14109 =profile</b>, the MSAs provided via &#8211;profile are vectorized and the
14110 function specified by &#8211;profile_comparison is used to make profile profile
14111 alignments. In that case, the complexity is NL^2</p>
14112
14113 <p class=flagdescription><span class=ListChar><b style='mso-bidi-font-weight:
14114 normal'><span style='font-size:12.0pt;mso-bidi-font-size:10.0pt'>-profile_comparison=fullN</span></b></span>,
14115 N is an integer value that can omitted. <i style='mso-bidi-font-style:normal'>Full</i>
14116 indicates that given two profiles, the alignment will be based on a library
14117 that includes every possible pair of sequences between the two profiles. If N
14118 is set, then the library will be restricted to the N most similar pairs of
14119 sequences between the two profiles, as judged from a measure made on a pairwise
14120 alignment of these two profiles.</p>
14121
14122 <p class=flag><a name="_Toc101065288"></a><a name="_Toc102494822"></a><a
14123 name="_Toc151732336"><span style='mso-bookmark:_Toc102494822'><span
14124 style='mso-bookmark:_Toc101065288'><span lang=AF>-profile_</span></span></span><span
14125 lang=AF>mode</span></a></p>
14126
14127 <p class=flagusage><span lang=FR>Usage: -profile_mode=&lt;cw_profile_profile,
14128 muscle_profile_profile, multi_channel&gt;</span></p>
14129
14130 <p class=instruction>Default: -profile_mode=cw_profile_profile</p>
14131
14132 <p class=flagdescription>When <b style='mso-bidi-font-weight:normal'>&#8211;profile_comparison=profile</b>,
14133 this flag selects a profile scoring function.</p>
14134
14135 <h3><a name="_Toc101065289"></a><a name="_Toc102494377"></a><a
14136 name="_Toc102494823"></a><a name="_Toc151732337"><span style='mso-bookmark:
14137 _Toc102494823'><span style='mso-bookmark:_Toc102494377'><span style='mso-bookmark:
14138 _Toc101065289'>Alignment Post-Processing</span></span></span></a></h3>
14139
14140 <p class=flag><a name="_Toc101065290"></a><a name="_Toc102494824"></a><a
14141 name="_Toc151732338"><span style='mso-bookmark:_Toc102494824'><span
14142 style='mso-bookmark:_Toc101065290'><span lang=AF>-clean_aln</span></span></span></a></p>
14143
14144 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
14145 </span>-clean_aln<span style="mso-spacerun: yes">&nbsp; </span></span></p>
14146
14147 <p class=instruction>Default:-clean_aln</p>
14148
14149 <p class=flagdescription>This flag causes T-Coffee to post-process the multiple
14150 alignment. Residues that have a reliability score smaller or equal to
14151 -clean_threshold (as given by an evaluation that uses
14152 -clean_evaluate_mode)<span style="mso-spacerun: yes">&nbsp; </span>are
14153 realigned to the rest of the alignment. Residues with a score higher than the
14154 threshold constitute a rigid framework that cannot be altered.</p>
14155
14156 <p class=flagdescription>The cleaning algorithm is greedy. It starts from the
14157 top left segment of low constituency residues and works its way left to right,
14158 top to bottom along the alignment. You can require this operation to be carried
14159 out for several cycles using the -clean_iterations flag.</p>
14160
14161 <p class=flagdescription>The rationale behind this operation is mostly
14162 cosmetic. In order to ensure a decent looking alignment, the gop is set to -20
14163 and the gep to -1. There is no penalty for terminal gaps, and the matrix is
14164 blosum62mt.</p>
14165
14166 <p class=Note><span style='mso-ansi-language:EN-US'>Note: Gaps are always
14167 considered to have a reliability score of 0.<o:p></o:p></span></p>
14168
14169 <p class=Note><span class=WarningChar>Note: The use of the cleaning option can
14170 result in memory overflow when aligning large</span><span style='mso-ansi-language:
14171 EN-US'> </span><span class=WarningChar>sequences,<o:p></o:p></span></p>
14172
14173 <p class=flag><a name="_Toc101065291"></a><a name="_Toc102494825"></a><a
14174 name="_Toc151732339"><span style='mso-bookmark:_Toc102494825'><span
14175 style='mso-bookmark:_Toc101065291'><span lang=AF>-clean_threshold</span></span></span></a></p>
14176
14177 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
14178 </span>-clean_threshold=&lt;0-9&gt;<span style="mso-spacerun: yes">&nbsp;
14179 </span></span></p>
14180
14181 <p class=flagusage><span lang=FR>Default:-clean_aln=1</span></p>
14182
14183 <p class=MyNormal><span lang=AF>See -clean_aln for details.</span></p>
14184
14185 <p class=flag><a name="_Toc101065292"></a><a name="_Toc102494826"></a><a
14186 name="_Toc151732340"><span style='mso-bookmark:_Toc102494826'><span
14187 style='mso-bookmark:_Toc101065292'><span lang=AF>-clean_iteration</span></span></span></a></p>
14188
14189 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
14190 </span>-clean_iteration=&lt;value between 1 and &gt;<span style="mso-spacerun:
14191 yes">&nbsp; </span></span></p>
14192
14193 <p class=instruction>Default:-clean_iteration=1</p>
14194
14195 <p class=MyNormal><span lang=AF>See -clean_aln for details.</span></p>
14196
14197 <p class=flag><a name="_Toc101065293"></a><a name="_Toc102494827"></a><a
14198 name="_Toc151732341"><span style='mso-bookmark:_Toc102494827'><span
14199 style='mso-bookmark:_Toc101065293'><span lang=AF>-clean_evaluation_mode</span></span></span></a></p>
14200
14201 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
14202 </span>-clean_iteration=&lt;evaluation_mode &gt;<span style="mso-spacerun:
14203 yes">&nbsp; </span></span></p>
14204
14205 <p class=instruction>Default:-clean_iteration=t_coffee_non_extended</p>
14206
14207 <p class=flagdescription>Indicates the mode used for the evaluation that will
14208 indicate the segments that should be realigned. See -evaluation_mode for the
14209 list of accepted modes.</p>
14210
14211 <p class=flag><a name="_Toc101065294"></a><a name="_Toc102494828"></a><a
14212 name="_Toc151732342"><span style='mso-bookmark:_Toc102494828'><span
14213 style='mso-bookmark:_Toc101065294'><span lang=AF>-iterate</span></span></span></a></p>
14214
14215 <p class=flagusage><span lang=FR>Usage: -iterate=&lt;integer&gt;</span></p>
14216
14217 <p class=instruction>Default: -iterate=0</p>
14218
14219 <p class=flagdescription>Sequences are extracted in turn and realigned to the
14220 MSA. If iterate is set to -1, each sequence is realigned, otherwise the number
14221 of iterations is set by &#8211;iterate.</p>
14222
14223 <h2><a name="_Toc101065295"></a><a name="_Toc102494378"></a><a
14224 name="_Toc102494829"></a><a name="_Toc151732343"><span style='mso-bookmark:
14225 _Toc102494829'><span style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:
14226 _Toc101065295'>BLAST Template Selection Parameters</span></span></span></a><span
14227 style='mso-bookmark:_Toc102494829'><span style='mso-bookmark:_Toc102494378'><span
14228 style='mso-bookmark:_Toc101065295'></span></span></span></h2>
14229
14230 <p class=MsoBodyText><span style='mso-bookmark:_Toc102494829'><span
14231 style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:_Toc101065295'>These
14232 parameters are used by T-Coffee when running expresso, accurate and psicoffee</span></span></span></p>
14233
14234 <p class=flag><span style='mso-bookmark:_Toc102494829'><span style='mso-bookmark:
14235 _Toc102494378'><span style='mso-bookmark:_Toc101065295'><a name="_Toc151732344"><span
14236 lang=AF>-blast_server</span></a><span lang=AF> </span></span></span></span></p>
14237
14238 <p class=flagusage><span style='mso-bookmark:_Toc102494829'><span
14239 style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:_Toc101065295'><span
14240 style='mso-ansi-language:EN-US'>Usage:<span style="mso-spacerun: yes">&nbsp;
14241 </span>-blast_server=</span> <span lang=FR>EBI, NCBI or LOCAL_BLAST</span></span></span></span><span
14242 style='mso-bookmark:_Toc102494829'><span style='mso-bookmark:_Toc102494378'><span
14243 style='mso-bookmark:_Toc101065295'><span style='mso-ansi-language:EN-US'><o:p></o:p></span></span></span></span></p>
14244
14245 <p class=instruction><span style='mso-bookmark:_Toc102494829'><span
14246 style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:_Toc101065295'>Default:
14247 EBI</span></span></span></p>
14248
14249 <p class=instruction style='text-indent:28.25pt'><span style='mso-bookmark:
14250 _Toc102494829'><span style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:
14251 _Toc101065295'><span style='mso-bidi-font-weight:bold'>Defines whih way BLAST
14252 will be used<o:p></o:p></span></span></span></span></p>
14253
14254 <p class=flag><span style='mso-bookmark:_Toc102494829'><span style='mso-bookmark:
14255 _Toc102494378'><span style='mso-bookmark:_Toc101065295'><a name="_Toc151732345"><span
14256 lang=AF>-prot_min_sim</span></a><span lang=AF> </span></span></span></span></p>
14257
14258 <p class=flagusage><span style='mso-bookmark:_Toc102494829'><span
14259 style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:_Toc101065295'><span
14260 lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp; </span>-prot_min_sim= &lt;percent_id&gt;</span></span></span></span></p>
14261
14262 <p class=instruction><span style='mso-bookmark:_Toc102494829'><span
14263 style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:_Toc101065295'>Default:
14264 40</span></span></span></p>
14265
14266 <p class=instruction style='text-indent:28.25pt'><span style='mso-bookmark:
14267 _Toc102494829'><span style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:
14268 _Toc101065295'><span style='mso-bidi-font-weight:bold'>Minimum id for inclusion
14269 of a sequence in a psi-blast profile<o:p></o:p></span></span></span></span></p>
14270
14271 <p class=flag><span style='mso-bookmark:_Toc102494829'><span style='mso-bookmark:
14272 _Toc102494378'><span style='mso-bookmark:_Toc101065295'><a name="_Toc151732346"><span
14273 lang=AF>-prot_max_sim</span></a><span lang=AF> </span></span></span></span></p>
14274
14275 <p class=flagusage><span style='mso-bookmark:_Toc102494829'><span
14276 style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:_Toc101065295'><span
14277 lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp; </span>-prot_max_sim= &lt;percent_id&gt;</span></span></span></span></p>
14278
14279 <p class=instruction><span style='mso-bookmark:_Toc102494829'><span
14280 style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:_Toc101065295'>Default:
14281 90</span></span></span></p>
14282
14283 <p class=instruction style='text-indent:28.25pt'><span style='mso-bookmark:
14284 _Toc102494829'><span style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:
14285 _Toc101065295'><span style='mso-bidi-font-weight:bold'>Maximum id for inclusion
14286 of a sequence in a psi-blast profile.<o:p></o:p></span></span></span></span></p>
14287
14288 <p class=flag><span style='mso-bookmark:_Toc102494829'><span style='mso-bookmark:
14289 _Toc102494378'><span style='mso-bookmark:_Toc101065295'><a name="_Toc151732347"><span
14290 lang=AF>-prot_min_cov</span></a><span lang=AF> </span></span></span></span></p>
14291
14292 <p class=flagusage><span style='mso-bookmark:_Toc102494829'><span
14293 style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:_Toc101065295'><span
14294 lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp; </span>-prot_min_cov= &lt;percent&gt;</span></span></span></span></p>
14295
14296 <p class=instruction><span style='mso-bookmark:_Toc102494829'><span
14297 style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:_Toc101065295'>Default:
14298 40</span></span></span></p>
14299
14300 <p class=instruction style='text-indent:28.25pt'><span style='mso-bookmark:
14301 _Toc102494829'><span style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:
14302 _Toc101065295'><span style='mso-bidi-font-weight:bold'>Minimum coverage for
14303 inclusion of a sequence in a psi-blast profile<o:p></o:p></span></span></span></span></p>
14304
14305 <p class=flag><span style='mso-bookmark:_Toc102494829'><span style='mso-bookmark:
14306 _Toc102494378'><span style='mso-bookmark:_Toc101065295'><a name="_Toc151732348"><span
14307 lang=AF>-protein_db</span></a><span lang=AF> </span></span></span></span></p>
14308
14309 <p class=flagusage><span style='mso-bookmark:_Toc102494829'><span
14310 style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:_Toc101065295'><span
14311 lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp; </span>-protein_db= &lt;BLAST
14312 database&gt;</span></span></span></span></p>
14313
14314 <p class=instruction><span style='mso-bookmark:_Toc102494829'><span
14315 style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:_Toc101065295'>Default:
14316 nr</span></span></span></p>
14317
14318 <p class=instruction style='text-indent:28.25pt'><span style='mso-bookmark:
14319 _Toc102494829'><span style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:
14320 _Toc101065295'><span style='mso-bidi-font-weight:bold'>Database used for
14321 construction of psi-blast profiles</span></span></span></span></p>
14322
14323 <p class=flag><span style='mso-bookmark:_Toc102494829'><span style='mso-bookmark:
14324 _Toc102494378'><span style='mso-bookmark:_Toc101065295'><a name="_Toc151732349"><span
14325 lang=AF>-pdb_min_sim</span></a><span lang=AF> </span></span></span></span></p>
14326
14327 <p class=flagusage><span style='mso-bookmark:_Toc102494829'><span
14328 style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:_Toc101065295'><span
14329 lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp; </span>-pdb_min_sim= &lt;percent_id&gt;</span></span></span></span></p>
14330
14331 <p class=instruction><span style='mso-bookmark:_Toc102494829'><span
14332 style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:_Toc101065295'>Default:
14333 35</span></span></span></p>
14334
14335 <p class=instruction style='text-indent:28.25pt'><span style='mso-bookmark:
14336 _Toc102494829'><span style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:
14337 _Toc101065295'><span style='mso-bidi-font-weight:bold'>Minimum id for a PDB
14338 template to be selected by expresso<o:p></o:p></span></span></span></span></p>
14339
14340 <p class=flag><span style='mso-bookmark:_Toc102494829'><span style='mso-bookmark:
14341 _Toc102494378'><span style='mso-bookmark:_Toc101065295'><a name="_Toc151732350"><span
14342 lang=AF>-pdb_max_sim</span></a><span lang=AF> </span></span></span></span></p>
14343
14344 <p class=flagusage><span style='mso-bookmark:_Toc102494829'><span
14345 style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:_Toc101065295'><span
14346 lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp; </span>-pdb_max_sim= &lt;percent_id&gt;</span></span></span></span></p>
14347
14348 <p class=instruction><span style='mso-bookmark:_Toc102494829'><span
14349 style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:_Toc101065295'>Default:
14350 100</span></span></span></p>
14351
14352 <p class=instruction style='text-indent:28.25pt'><span style='mso-bookmark:
14353 _Toc102494829'><span style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:
14354 _Toc101065295'><span style='mso-bidi-font-weight:bold'>Maximum id for a PDB
14355 template to be selected by expresso <o:p></o:p></span></span></span></span></p>
14356
14357 <p class=flag><span style='mso-bookmark:_Toc102494829'><span style='mso-bookmark:
14358 _Toc102494378'><span style='mso-bookmark:_Toc101065295'><a name="_Toc151732351"><span
14359 lang=AF>-pdb_min_cov</span></a><span lang=AF> </span></span></span></span></p>
14360
14361 <p class=flagusage><span style='mso-bookmark:_Toc102494829'><span
14362 style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:_Toc101065295'><span
14363 lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp; </span>-pdb_min_cov= &lt;percent&gt;</span></span></span></span></p>
14364
14365 <p class=instruction><span style='mso-bookmark:_Toc102494829'><span
14366 style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:_Toc101065295'>Default:
14367 50</span></span></span></p>
14368
14369 <p class=instruction style='text-indent:28.25pt'><span style='mso-bookmark:
14370 _Toc102494829'><span style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:
14371 _Toc101065295'><span style='mso-bidi-font-weight:bold'>Minimum coverage for a
14372 PDB template to be selected by expresso. <o:p></o:p></span></span></span></span></p>
14373
14374 <p class=flag><span style='mso-bookmark:_Toc102494829'><span style='mso-bookmark:
14375 _Toc102494378'><span style='mso-bookmark:_Toc101065295'><a name="_Toc151732352"><span
14376 lang=AF>-pdb_db</span></a><span lang=AF> </span></span></span></span></p>
14377
14378 <p class=flagusage><span style='mso-bookmark:_Toc102494829'><span
14379 style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:_Toc101065295'><span
14380 lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp; </span>-protein_db= &lt;BLAST
14381 database&gt;</span></span></span></span></p>
14382
14383 <p class=instruction><span style='mso-bookmark:_Toc102494829'><span
14384 style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:_Toc101065295'>Default:
14385 pdb</span></span></span></p>
14386
14387 <p class=instruction style='text-indent:28.25pt'><span style='mso-bookmark:
14388 _Toc102494829'><span style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:
14389 _Toc101065295'><span style='mso-bidi-font-weight:bold'>Database for PDB
14390 template to be selected by expresso.</span></span></span></span></p>
14391
14392 <p class=flag><span style='mso-bookmark:_Toc102494829'><span style='mso-bookmark:
14393 _Toc102494378'><span style='mso-bookmark:_Toc101065295'><a name="_Toc151732353"><span
14394 lang=AF>-pdb_type</span></a><span lang=AF> </span></span></span></span></p>
14395
14396 <p class=flagusage><span style='mso-bookmark:_Toc102494829'><span
14397 style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:_Toc101065295'><span
14398 lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp; </span>-pdb_type= d,n,m,dnm,dn</span></span></span></span></p>
14399
14400 <p class=instruction><span style='mso-bookmark:_Toc102494829'><span
14401 style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:_Toc101065295'>Default:
14402 d</span></span></span></p>
14403
14404 <p class=instruction style='text-indent:28.25pt'><span style='mso-bookmark:
14405 _Toc102494829'><span style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:
14406 _Toc101065295'><span style='mso-bidi-font-weight:bold'>d: diffraction<o:p></o:p></span></span></span></span></p>
14407
14408 <p class=instruction style='text-indent:28.25pt'><span style='mso-bookmark:
14409 _Toc102494829'><span style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:
14410 _Toc101065295'><span style='mso-bidi-font-weight:bold'>n: NMR<o:p></o:p></span></span></span></span></p>
14411
14412 <p class=instruction style='text-indent:28.25pt'><span style='mso-bookmark:
14413 _Toc102494829'><span style='mso-bookmark:_Toc102494378'><span style='mso-bookmark:
14414 _Toc101065295'><span style='mso-bidi-font-weight:bold'>m: model</span></span></span></span></p>
14415
14416 <h2><span style='mso-bookmark:_Toc102494829'><span style='mso-bookmark:_Toc102494378'><span
14417 style='mso-bookmark:_Toc101065295'><a name="_Toc151732354">CPU Control</a></span></span></span></h2>
14418
14419 <h3><a name="_Toc101065296"></a><a name="_Toc102494379"></a><a
14420 name="_Toc102494830"></a><a name="_Toc151732355"><span style='mso-bookmark:
14421 _Toc102494830'><span style='mso-bookmark:_Toc102494379'><span style='mso-bookmark:
14422 _Toc101065296'>Multithreading</span></span></span></a></h3>
14423
14424 <p class=flag><a name="_Toc101065297"></a><a name="_Toc102494831"></a><a
14425 name="_Toc151732356"><span style='mso-bookmark:_Toc102494831'><span
14426 style='mso-bookmark:_Toc101065297'><span lang=AF>-multi_core</span></span></span></a><span
14427 style='mso-bookmark:_Toc102494831'><span style='mso-bookmark:_Toc101065297'><span
14428 lang=AF> </span></span></span></p>
14429
14430 <p class=flagusage><span style='mso-ansi-language:EN-US'>Usage:<span
14431 style="mso-spacerun: yes">&nbsp; </span>-multi_core=</span><span lang=FR>
14432 templates_jobs_relax_msa</span><span style='mso-ansi-language:EN-US'><o:p></o:p></span></p>
14433
14434 <p class=instruction>Default: 0</p>
14435
14436 <p class=instruction style='text-indent:28.25pt'><span style='mso-bidi-font-weight:
14437 bold'>template: </span>fetch the templates in a parallel way</p>
14438
14439 <p class=instruction style='text-indent:28.25pt'><span style='mso-bidi-font-weight:
14440 bold'>jobs:</span> compute the library</p>
14441
14442 <p class=instruction style='text-indent:28.25pt'><span style='mso-bidi-font-weight:
14443 bold'>relax:</span> extend the library in a parallel way</p>
14444
14445 <p class=instruction style='text-indent:28.25pt'><span style='mso-bidi-font-weight:
14446 bold'>msa:</span> compute the msa in a parallel way</p>
14447
14448 <p class=instruction><o:p>&nbsp;</o:p></p>
14449
14450 <p class=flagdescription>Specifies that the steps of T-Coffee that should be
14451 multi threaded. by default all relevant steps are parallelized.</p>
14452
14453 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
14454 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
14455 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
14456 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
14457
14458 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
14459 sample_seq2.fasta -multi_core jobs</p>
14460
14461 </div>
14462
14463 <p class=flagdescription><a name="_Toc101065298"></a><a name="_Toc102494380"></a><a
14464 name="_Toc102494832"><span style='mso-bookmark:_Toc102494380'><span
14465 style='mso-bookmark:_Toc101065298'>In order to prevent the use of the parallel
14466 mode it is possible to use:</span></span></a></p>
14467
14468 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
14469 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
14470 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
14471 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
14472
14473 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
14474 style='mso-bookmark:_Toc102494832'><span style='mso-bookmark:_Toc102494380'><span
14475 style='mso-bookmark:_Toc101065298'>PROMPT: t_coffee sample_seq2.fasta
14476 -multi_core no</span></span></span></p>
14477
14478 </div>
14479
14480 <p class=flag><span style='mso-bookmark:_Toc102494832'><span style='mso-bookmark:
14481 _Toc102494380'><span style='mso-bookmark:_Toc101065298'><span lang=AF><o:p>&nbsp;</o:p></span></span></span></span></p>
14482
14483 <p class=flag><span style='mso-bookmark:_Toc102494832'><span style='mso-bookmark:
14484 _Toc102494380'><span style='mso-bookmark:_Toc101065298'><a name="_Toc151732357"><span
14485 lang=AF>-n_core</span></a><span lang=AF> </span></span></span></span></p>
14486
14487 <p class=flagusage><span style='mso-bookmark:_Toc102494832'><span
14488 style='mso-bookmark:_Toc102494380'><span style='mso-bookmark:_Toc101065298'><span
14489 style='mso-ansi-language:EN-US'>Usage:<span style="mso-spacerun: yes">&nbsp;
14490 </span>-n_core=</span> <span lang=FR>&lt;number of cores&gt;</span></span></span></span><span
14491 style='mso-bookmark:_Toc102494832'><span style='mso-bookmark:_Toc102494380'><span
14492 style='mso-bookmark:_Toc101065298'><span style='mso-ansi-language:EN-US'><o:p></o:p></span></span></span></span></p>
14493
14494 <p class=instruction><span style='mso-bookmark:_Toc102494832'><span
14495 style='mso-bookmark:_Toc102494380'><span style='mso-bookmark:_Toc101065298'>Default:
14496 0</span></span></span></p>
14497
14498 <p class=flagdescription><span style='mso-bookmark:_Toc102494832'><span
14499 style='mso-bookmark:_Toc102494380'><span style='mso-bookmark:_Toc101065298'>Default
14500 indicates that all cores will be used, as indicated by the environment via:</span></span></span></p>
14501
14502 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
14503 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
14504 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
14505 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
14506
14507 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
14508 style='mso-bookmark:_Toc102494832'><span style='mso-bookmark:_Toc102494380'><span
14509 style='mso-bookmark:_Toc101065298'>PROMPT: t_coffee sample_seq2.fasta -multi_core
14510 jobs</span></span></span></p>
14511
14512 </div>
14513
14514 <h3><span style='mso-bookmark:_Toc102494832'><span style='mso-bookmark:_Toc102494380'><span
14515 style='mso-bookmark:_Toc101065298'><o:p>&nbsp;</o:p></span></span></span></h3>
14516
14517 <h3><span style='mso-bookmark:_Toc102494832'><span style='mso-bookmark:_Toc102494380'><span
14518 style='mso-bookmark:_Toc101065298'><a name="_Toc151732358">Limits</a></span></span></span></h3>
14519
14520 <p class=flag><a name="_Toc101065299"></a><a name="_Toc102494833"></a><a
14521 name="_Toc151732359"><span style='mso-bookmark:_Toc102494833'><span
14522 style='mso-bookmark:_Toc101065299'><span lang=AF>-mem_mode</span></span></span></a></p>
14523
14524 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
14525 </span>deprecated</span><span lang=FR style='mso-bidi-font-weight:bold'><o:p></o:p></span></p>
14526
14527 <p class=flag><a name="_Toc101065300"></a><a name="_Toc102494834"></a><a
14528 name="_Toc151732360"><span style='mso-bookmark:_Toc102494834'><span
14529 style='mso-bookmark:_Toc101065300'><span lang=AF>-ulimit</span></span></span></a></p>
14530
14531 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
14532 </span>-ulimit=&lt;value&gt;</span></p>
14533
14534 <p class=instruction>Default: -ulimit=0</p>
14535
14536 <p class=flagdescription>Specifies the upper limit of memory usage (in
14537 Megabytes). Processes exceeding this limit will automatically exit. A value 0
14538 indicates that no limit applies.</p>
14539
14540 <p class=flag><a name="_Toc101065301"></a><a name="_Toc102494835"></a><a
14541 name="_Toc151732361"><span style='mso-bookmark:_Toc102494835'><span
14542 style='mso-bookmark:_Toc101065301'><span lang=AF>-maxlen</span></span></span></a></p>
14543
14544 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
14545 </span>-maxlen=&lt;value, 0=nolimit&gt;</span></p>
14546
14547 <p class=instruction>Default: -maxlen=1000<span style='mso-bidi-font-weight:
14548 bold'><o:p></o:p></span></p>
14549
14550 <p class=flagdescription>Indicates the maximum length of the sequences. <a
14551 name="_Toc101065302"></a></p>
14552
14553 <h3><span style='mso-bookmark:_Toc101065302'><a name="_Toc102494381"></a><a
14554 name="_Toc102494836"></a><a name="_Toc151732362"><span style='mso-bookmark:
14555 _Toc102494836'><span style='mso-bookmark:_Toc102494381'>Aligning more than 100
14556 sequences with DPA</span></span></a></span></h3>
14557
14558 <p class=flag><a name="_Toc101065303"></a><a name="_Toc102494837"></a><a
14559 name="_Toc151732363"><span style='mso-bookmark:_Toc102494837'><span
14560 style='mso-bookmark:_Toc101065303'><span lang=AF>-maxnseq</span></span></span></a></p>
14561
14562 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
14563 </span>-maxnseq=&lt;value, 0=nolimit&gt;</span></p>
14564
14565 <p class=instruction>Default: -maxnseq=50</p>
14566
14567 <p class=flagdescription>Indicates the maximum number of sequences before
14568 triggering the use of t_coffee_dpa.</p>
14569
14570 <p class=flag><a name="_Toc101065304"></a><a name="_Toc102494838"></a><a
14571 name="_Toc151732364"><span style='mso-bookmark:_Toc102494838'><span
14572 style='mso-bookmark:_Toc101065304'><span lang=AF>-dpa_master_aln</span></span></span></a></p>
14573
14574 <p class=flagusage><span lang=FR>Usage: -dpa_master_aln=&lt;File, method&gt;</span></p>
14575
14576 <p class=instruction>Default: -dpa_master_aln=NO</p>
14577
14578 <p class=flagdescription>When using dpa, t_coffee needs a seed alignment that
14579 can be computed using any appropriate method. By default, t_coffee computes a
14580 fast approximate alignment.</p>
14581
14582 <p class=flagdescription>A pre-alignment can be provided through this flag, as
14583 well as any program using the following syntax:</p>
14584
14585 <p class=example2>your_script &#8211;in &lt;fasta_file&gt; -out
14586 &lt;file_name&gt;</p>
14587
14588 <p class=flag><a name="_Toc101065305"></a><a name="_Toc102494839"></a><a
14589 name="_Toc151732365"><span style='mso-bookmark:_Toc102494839'><span
14590 style='mso-bookmark:_Toc101065305'><span lang=AF>-dpa_maxnseq</span></span></span></a></p>
14591
14592 <p class=flagusage><span lang=FR>Usage: -dpa_maxnseq=&lt;integer value&gt;</span></p>
14593
14594 <p class=instruction>Default: -dpa_maxnseq=30</p>
14595
14596 <p class=flagdescription>Maximum number of sequences aligned simultaneously
14597 when DPA is ran. Given the tree computed from the master alignment, a node is
14598 sent to computation if it controls more than <b style='mso-bidi-font-weight:
14599 normal'>&#8211;dpa_maxnseq</b> OR if it controls a pair of sequences having
14600 less than <b style='mso-bidi-font-weight:normal'>&#8211;dpa_min_score2</b>
14601 percent ID.<a name="_Toc101065306"></a></p>
14602
14603 <p class=flag><span style='mso-bookmark:_Toc101065306'><a name="_Toc102494840"></a><a
14604 name="_Toc151732366"><span style='mso-bookmark:_Toc102494840'><span lang=AF>-dpa_min_score1</span></span></a></span></p>
14605
14606 <p class=flagusage><span lang=FR>Usage: -dpa_min_score1=&lt;integer value&gt;</span></p>
14607
14608 <p class=instruction>Default: -dpa_min_score1=95</p>
14609
14610 <p class=flagdescription>Threshold for not realigning the sequences within the
14611 master alignment. Given this alignment and the associated tree, sequences below
14612 a node are not realigned if none of them has less than<b style='mso-bidi-font-weight:
14613 normal'> &#8211;dpa_min_score1</b> % identity.<a name="_Toc101065307"></a></p>
14614
14615 <p class=flag><span style='mso-bookmark:_Toc101065307'><a name="_Toc102494841"></a><a
14616 name="_Toc151732367"><span style='mso-bookmark:_Toc102494841'><span lang=AF>-dpa_min_score2</span></span></a></span></p>
14617
14618 <p class=flagusage><span lang=FR>Usage: -dpa_min_score2</span></p>
14619
14620 <p class=instruction>Default: -dpa_min_score2</p>
14621
14622 <p class=flagdescription>Maximum number of sequences aligned simultaneously
14623 when DPA is ran. Given the tree computed from the master alignment, a node is
14624 sent to computation if it controls more than <b style='mso-bidi-font-weight:
14625 normal'>&#8211;dpa_maxnseq</b> OR if it controls a pair of sequences having
14626 less than <b style='mso-bidi-font-weight:normal'>&#8211;dpa_min_score2</b>
14627 percent ID.<a name="_Toc101065308"></a></p>
14628
14629 <p class=flag><span style='mso-bookmark:_Toc101065308'><a name="_Toc102494842"></a><a
14630 name="_Toc151732368"><span style='mso-bookmark:_Toc102494842'><span lang=AF>-dap_tree
14631 [NOT IMPLEMENTED]</span></span></a></span></p>
14632
14633 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
14634 </span>-dpa_tree=&lt;filename&gt;</span></p>
14635
14636 <p class=instruction>Default: -unset</p>
14637
14638 <p class=flagdescription>Guide tree used in DPA. This is a newick tree where
14639 the distance associated with each node is set to the minimum pairwise distance
14640 among all considered sequences.</p>
14641
14642 <h2><a name="_Toc101065309"></a><a name="_Toc102494382"></a><a
14643 name="_Toc102494843"></a><a name="_Toc151732369"><span style='mso-bookmark:
14644 _Toc102494843'><span style='mso-bookmark:_Toc102494382'><span style='mso-bookmark:
14645 _Toc101065309'>Using Structures</span></span></span></a><a name="_Toc101065310"></a></h2>
14646
14647 <h3><span style='mso-bookmark:_Toc101065310'><a name="_Toc102494383"></a><a
14648 name="_Toc102494844"></a><a name="_Toc151732370"><span style='mso-bookmark:
14649 _Toc102494844'><span style='mso-bookmark:_Toc102494383'>Generic</span></span></a></span></h3>
14650
14651 <p class=flag><a name="_Toc151732371"><span lang=AF>-mode</span></a></p>
14652
14653 <p class=flagusage><span lang=FR>Usage: -mode=3dcoffee</span></p>
14654
14655 <p class=instruction>Default: turned off</p>
14656
14657 <p class=flagdescription>Runs t_coffee with the 3dcoffee mode (cf next
14658 section).</p>
14659
14660 <p class=flag><a name="_Toc101065312"></a><a name="_Toc102494846"></a><a
14661 name="_Toc151732372"><span style='mso-bookmark:_Toc102494846'><span
14662 style='mso-bookmark:_Toc101065312'><span lang=AF>-check_pdb_status</span></span></span></a></p>
14663
14664 <p class=flagusage><span lang=FR>Usage: -check_pdb_status</span></p>
14665
14666 <p class=instruction>Default: turned off</p>
14667
14668 <p class=flagdescription>Forces t_coffee to run extract_from_pdb to check the
14669 pdb status of each sequence. This can considerably slow down the program.</p>
14670
14671 <p class=flagdescription><o:p>&nbsp;</o:p></p>
14672
14673 <h3><a name="_Toc101065313"></a><a name="_Toc102494384"></a><a
14674 name="_Toc102494847"></a><a name="_Toc151732373"><span style='mso-bookmark:
14675 _Toc102494847'><span style='mso-bookmark:_Toc102494384'><span style='mso-bookmark:
14676 _Toc101065313'>3D Coffee: Using SAP</span></span></span></a></h3>
14677
14678 <p class=flagdescription>It is possible to use t_coffee to compute multiple structural
14679 alignments. To do so, ensure that you have the sap program installed.</p>
14680
14681 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
14682 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
14683 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
14684 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
14685
14686 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
14687 &#8211;pdb=struc1.pdb,struc2.pdb,struc3.pdb -method sap_pair</p>
14688
14689 </div>
14690
14691 <p class=flagdescription>Will combine the pairwise alignments produced by
14692 SAP.<span style="mso-spacerun: yes">&nbsp; </span>There are currently four
14693 methods that can be interfaced with t_coffee:</p>
14694
14695 <p class=flagdescription>sap_pair: that uses the sap algorithm</p>
14696
14697 <p class=flagdescription>align_pdb: uses a t_coffee implementation of sap, not
14698 as accurate.</p>
14699
14700 <p class=flagdescription>tmaliagn_pair
14701 (http://zhang.bioinformatics.ku.edu/TM-align/)</p>
14702
14703 <p class=flagdescription>mustang_pair (http://www.cs.mu.oz.au/~arun/mustang)</p>
14704
14705 <p class=flagdescription>When providing a PDB file, the computation is only
14706 carried out on the first chain of this file. If your original file contains
14707 several chain, you should extract the chain you want to work on. You can use <b
14708 style='mso-bidi-font-weight:normal'>t_coffee &#8211;other_pg extract_from_pdb </b>or
14709 any pdb handling program.</p>
14710
14711 <p class=flagdescription>If you are working with public PDB files, you can use
14712 the PDB identifier and specify the chain by adding its index to the identifier
14713 (i.e. 1pdbC). If your structure is an NMR structure, you are advised to provide
14714 the program with one structure only.</p>
14715
14716 <p class=flagdescription>If you wish to align only a portion of the structure,
14717 you should extract it yourself from the pdb file, using <b style='mso-bidi-font-weight:
14718 normal'>t_coffee &#8211;other_pg extract_from_pdb </b>or any pdb handling
14719 program.</p>
14720
14721 <p class=flagdescription>You can provide t_coffee with a mixture of sequences
14722 and structure. In this case, you should use the special mode:</p>
14723
14724 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
14725 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
14726 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
14727 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
14728
14729 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
14730 &#8211;mode 3dcoffee &#8211;seq 3d_sample3.fasta -template_file
14731 template_file.template</p>
14732
14733 </div>
14734
14735 <h3><a name="_Toc101065314"></a><a name="_Toc102494385"></a><a
14736 name="_Toc102494848"></a><a name="_Toc151732374"><span style='mso-bookmark:
14737 _Toc102494848'><span style='mso-bookmark:_Toc102494385'><span style='mso-bookmark:
14738 _Toc101065314'>Using/finding PDB templates for the Sequences</span></span></span></a></h3>
14739
14740 <p class=flag><a name="_Toc101065315"></a><a name="_Toc102494849"></a><a
14741 name="_Toc151732375"><span style='mso-bookmark:_Toc102494849'><span
14742 style='mso-bookmark:_Toc101065315'><span lang=AF>-template_file</span></span></span></a></p>
14743
14744 <p class=flagusage><span lang=FR style='mso-bidi-font-weight:bold'>Usage</span><span
14745 lang=FR>: -template_file =</span></p>
14746
14747 <p class=flagusage><span lang=FR>&lt;filename, </span></p>
14748
14749 <p class=flagusage><span lang=FR>SCRIPT_scriptame, </span></p>
14750
14751 <p class=flagusage><span lang=FR>SELF_TAG </span></p>
14752
14753 <p class=flagusage><span lang=FR>SEQFILE_TAG_filename,</span></p>
14754
14755 <p class=flagusage><span lang=FR>no&gt;</span></p>
14756
14757 <p class=instruction>Default: no</p>
14758
14759 <p class=flagdescription>This flag instructs t_coffee on the templates that
14760 will be used when combining several types of information. For instance, when
14761 using structural information, this file will indicate the structural template
14762 that corresponds to your sequences. The identifier T indicates that the file
14763 should be a FASTA like file, formatted as follows. There are several ways to
14764 pass the templates:</p>
14765
14766 <p class=flagheading2>Predefined Modes</p>
14767
14768 <p class=MyNormaBoldl><span lang=AF>EXPRESSO: will use the EBI server to find
14769 _P_ templates</span></p>
14770
14771 <p class=MyNormaBoldl><span lang=AF>PSIBLAST: will use the EBI sever to find
14772 profiles </span></p>
14773
14774 <p class=MyNormaBoldl><span lang=AF><o:p>&nbsp;</o:p></span></p>
14775
14776 <p class=flagheading2>File name</p>
14777
14778 <p class=flagdescription>This file contains the sequence/template association
14779 it uses a FASTA-like format, as follows:</p>
14780
14781 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
14782 mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
14783 background:#E6E6E6'>
14784
14785 <p class=examplefileCxSpFirst>&gt;&lt;sequence name&gt; _P_ &lt;pdb
14786 template&gt;</p>
14787
14788 <p class=examplefileCxSpMiddle>&gt;&lt;sequence name&gt; _G_ &lt;gene
14789 template&gt;</p>
14790
14791 <p class=examplefileCxSpMiddle>&gt;&lt;sequence name&gt; _R_ &lt;MSA
14792 template&gt;</p>
14793
14794 <p class=examplefileCxSpMiddle>&gt;&lt;sequence name&gt; _F_ &lt;RNA Secondary
14795 Structure&gt;</p>
14796
14797 <p class=examplefileCxSpMiddle>&gt;&lt;sequence name&gt; _T_ &lt;Transmembrane
14798 Secondary Structure&gt;</p>
14799
14800 <p class=examplefileCxSpMiddle>&gt;&lt;sequence name&gt; _E_ &lt;Protein
14801 Secondary Structure&gt;</p>
14802
14803 <p class=examplefileCxSpLast><o:p>&nbsp;</o:p></p>
14804
14805 </div>
14806
14807 <p class=flagdescription>Each template will be used in place of the sequence
14808 with the appropriate method. For instance, structural templates will be aligned
14809 with sap_pair and the information thus generated will be transferred onto the
14810 alignment.</p>
14811
14812 <p class=flagdescription>Note the following rule:</p>
14813
14814 <p class=flagdescription><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>-Each
14815 sequence can have one template of each type (structural, genomics\85)</p>
14816
14817 <p class=flagdescription><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>-Each
14818 sequence can only have one template of a given type</p>
14819
14820 <p class=flagdescription><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>-Several
14821 sequences can share the same template</p>
14822
14823 <p class=flagdescription><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>-All
14824 the sequences do not need to have a template</p>
14825
14826 <p class=flagdescription>The type of template on which a method works is
14827 declared with the SEQ_TYPE parameter in the method configuration file:</p>
14828
14829 <p class=flagdescription><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>SEQ_TYPE<span
14830 style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>S: a method
14831 that uses sequences </p>
14832
14833 <p class=flagdescription><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>SEQ_TYPE<span
14834 style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>PS: a
14835 pairwise method that aligns sequences and structures</p>
14836
14837 <p class=flagdescription><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>SEQ_TYPE<span
14838 style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>P: a method
14839 that aligns structures (sap for instance)</p>
14840
14841 <p class=flagdescription>There are 4 tags identifying the template type:</p>
14842
14843 <p class=flagdescription>_P_<span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp; </span>Structural
14844 templates: a pdb identifier OR a pdb file</p>
14845
14846 <p class=flagdescription>_G_<span style='mso-tab-count:1'>&nbsp;&nbsp; </span>Genomic
14847 templates: a protein sequence where boundary amino-acid have been recoded with
14848 ( o:0, i:1, j:2)</p>
14849
14850 <p class=flagdescription>_R_<span style='mso-tab-count:1'>&nbsp;&nbsp; </span>Profile
14851 Templates: a file containing a multiple sequence alignment</p>
14852
14853 <p class=flagdescription>_F_<span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp; </span>RNA
14854 secondary Structures</p>
14855
14856 <p class=flagdescription><o:p>&nbsp;</o:p></p>
14857
14858 <p class=flagdescription>More than one template file can be provided. There is
14859 no need to have one template for every sequence in the dataset. </p>
14860
14861 <p class=flagdescription>_P_, _G_, and _R_ are known as <b style='mso-bidi-font-weight:
14862 normal'>template TAGS<o:p></o:p></b></p>
14863
14864 <p class=flagheading2>2-SCRIPT_&lt;scriptname&gt;</p>
14865
14866 <p class=flagdescription>Indicates that filename is a script that will be used
14867 to generate a valid template file. The script will run on a file containing all
14868 your sequences using the following syntax:</p>
14869
14870 <p class=example2>scriptname &#8211;infile=&lt;your sequences&gt;
14871 -outfile=&lt;template_file&gt;</p>
14872
14873 <p class=flagdescription>It is also possible to pass some parameters, use @ as
14874 a separator and # in place of the = sign. For instance, if you want to call the
14875 a script named blast.pl with the foloowing parameters;</p>
14876
14877 <p class=example2>blast.pl -db=pdb -dir=/local/test</p>
14878
14879 <p class=flagdescription>Use</p>
14880
14881 <p class=example2>SCRIPT_blast.pl@db#pdb@dir#/local/test</p>
14882
14883 <p class=flagdescription>Bear in mind that the input output flags will then be
14884 concatenated to this command line so that t_coffee ends up calling the program
14885 using the following system call:</p>
14886
14887 <p class=example2>blast.pl -db=pdb -dir=/local/test -infile=&lt;some tmp
14888 file&gt; -outfile=&lt;another tmp file&gt;</p>
14889
14890 <p class=flagdescription><o:p>&nbsp;</o:p></p>
14891
14892 <p class=flagheading2>3-SELF_TAG</p>
14893
14894 <p class=flagdescription>TAG can take the value of any of the known TAGS (_S_,
14895 _G_, _P_). SELF indicates that the original name of the sequence will be used to
14896 fetch the template: </p>
14897
14898 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
14899 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
14900 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
14901 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
14902
14903 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
14904 3d_sample2.fasta &#8211;template_file SELF_P_</p>
14905
14906 </div>
14907
14908 <p class=flagdescription>The previous command will work because the sequences
14909 in 3d_sample3 are named </p>
14910
14911 <p class=flagheading2>4-SEQFILE_TAG_filename</p>
14912
14913 <p class=flagdescription>Use this flag if your templates are in filename, and
14914 are named according to the sequences. For instance, if your protein sequences
14915 have been recoded with Exon/Intron information, you should have the recoded
14916 sequences names according to the original:</p>
14917
14918 <p class=example2>SEQFILE_G_recodedprotein.fasta<span style='mso-tab-count:
14919 1'> </span></p>
14920
14921 <p class=flag><a name="_Toc101065316"></a><a name="_Toc102494850"></a><a
14922 name="_Toc151732376"><span style='mso-bookmark:_Toc102494850'><span
14923 style='mso-bookmark:_Toc101065316'><span lang=AF>-struc_to_use</span></span></span></a></p>
14924
14925 <p class=flagusage><span lang=FR>Usage: -struc_to_use=&lt;struc1, struc2\85&gt;</span></p>
14926
14927 <p class=instruction>Default: -struc_to_use=NULL</p>
14928
14929 <p class=flagdescription>Restricts the 3Dcoffee to a set of pre-defined
14930 structures.</p>
14931
14932 <h2><a name="_Toc101065317"></a><a name="_Toc102494386"></a><a
14933 name="_Toc102494851"></a><a name="_Toc151732377"><span style='mso-bookmark:
14934 _Toc102494851'><span style='mso-bookmark:_Toc102494386'><span style='mso-bookmark:
14935 _Toc101065317'>Multiple Local Alignments</span></span></span></a></h2>
14936
14937 <p class=MyNormal><span lang=AF>It is possible to compute multiple local
14938 alignments, using the moca routine. MOCA is a routine that allows extracting
14939 all the local alignments that show some similarity with another predefined
14940 fragment.</span></p>
14941
14942 <p class=MyNormal><span lang=AF>'mocca' is a perl script that calls t-coffee
14943 and provides it with the appropriate parameters.</span></p>
14944
14945 <p class=flag><a name="_Toc101065318"></a><a name="_Toc102494852"></a><a
14946 name="_Toc151732378"><span style='mso-bookmark:_Toc102494852'><span
14947 style='mso-bookmark:_Toc101065318'><span lang=AF>-domain</span></span><span
14948 lang=AF>/-mocca</span></span></a></p>
14949
14950 <p class=flagusage><span lang=FR>Usage: -domain</span></p>
14951
14952 <p class=instruction>Default: not set</p>
14953
14954 <p class=flagdescription>This flag indicates that t_coffee will run using the
14955 domain mode. All the sequences will be concatenated, and the resulting sequence
14956 will be compared to itself using lalign_rs_s_pair mode (lalign of the sequence
14957 against itself using keeping the lalign raw score). This step is the most
14958 computer intensive, and it is advisable to save the resulting file.</p>
14959
14960 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
14961 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
14962 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
14963 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
14964
14965 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
14966 -in Ssample_seq1.fasta,Mlalign_rs_s_pair -out_lib=sample_lib1.mocca_lib -domain
14967 -start=100 -len=50 </p>
14968
14969 </div>
14970
14971 <p class=flagdescription>This instruction will use the fragment 100-150 on the
14972 concatenated sequences, as a template for the extracted repeats. The extraction
14973 will only be made once. The library will be placed in the file &lt;lib
14974 name&gt;.</p>
14975
14976 <p class=flagdescription><o:p>&nbsp;</o:p></p>
14977
14978 <p class=flagdescription>If you want, you can test other coordinates for the
14979 repeat, such as </p>
14980
14981 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
14982 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
14983 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
14984 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
14985
14986 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
14987 -in sample_lib1.mocca_lib -domain -start=100 -len=60 </p>
14988
14989 </div>
14990
14991 <p class=flagdescription>This run will use the fragment 100-160, and will be
14992 much faster because it does not need to re-compute the lalign library. </p>
14993
14994 <p class=flag><a name="_Toc101065319"></a><a name="_Toc102494853"></a><a
14995 name="_Toc151732379"><span style='mso-bookmark:_Toc102494853'><span
14996 style='mso-bookmark:_Toc101065319'><span lang=AF>-start</span></span></span></a></p>
14997
14998 <p class=flagusage><span lang=FR>Usage: -start=&lt;int value&gt;</span></p>
14999
15000 <p class=instruction>Default: not set</p>
15001
15002 <p class=flagdescription>This flag indicates the starting position of the
15003 portion of sequence that will be used as a template for the repeat extraction.
15004 The value assumes that all the sequences have been concatenated, and is given
15005 on the resulting sequence.</p>
15006
15007 <p class=flag><a name="_Toc101065320"></a><a name="_Toc102494854"></a><a
15008 name="_Toc151732380"><span style='mso-bookmark:_Toc102494854'><span
15009 style='mso-bookmark:_Toc101065320'><span lang=AF>-len</span></span></span></a></p>
15010
15011 <p class=flagusage><span lang=FR>Usage: -len=&lt;int value&gt;</span></p>
15012
15013 <p class=instruction>Default: not set</p>
15014
15015 <p class=flagdescription>This flag indicates the length of the portion of
15016 sequence that will be used as a template.</p>
15017
15018 <p class=flag><a name="_Toc101065321"></a><a name="_Toc102494855"></a><a
15019 name="_Toc151732381"><span style='mso-bookmark:_Toc102494855'><span
15020 style='mso-bookmark:_Toc101065321'><span lang=AF>-scale</span></span></span></a></p>
15021
15022 <p class=flagusage><span lang=FR>Usage: -scale=&lt;int value&gt;</span></p>
15023
15024 <p class=instruction>Default: -scale=-100</p>
15025
15026 <p class=flagdescription>This flag indicates the value of the threshold for
15027 extracting the repeats. The actual threshold is equal to:</p>
15028
15029 <p class=flagdescription><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>motif_len*scale</p>
15030
15031 <p class=flagdescription>Increase the scale <span style='font-family:Wingdings;
15032 mso-ascii-font-family:"Times New Roman";mso-hansi-font-family:"Times New Roman";
15033 mso-char-type:symbol;mso-symbol-font-family:Wingdings'><span style='mso-char-type:
15034 symbol;mso-symbol-font-family:Wingdings'>ó</span></span>Increase sensitivity <span
15035 style='font-family:Wingdings;mso-ascii-font-family:"Times New Roman";
15036 mso-hansi-font-family:"Times New Roman";mso-char-type:symbol;mso-symbol-font-family:
15037 Wingdings'><span style='mso-char-type:symbol;mso-symbol-font-family:Wingdings'>ó</span></span>
15038 More alignments( i.e. -50).</p>
15039
15040 <p class=flag><a name="_Toc101065322"></a><a name="_Toc102494856"></a><a
15041 name="_Toc151732382"><span style='mso-bookmark:_Toc102494856'><span
15042 style='mso-bookmark:_Toc101065322'><span lang=AF>-domain_interactive [Examples]</span></span></span></a></p>
15043
15044 <p class=flagusage><span lang=FR>Usage: -domain_interactive</span></p>
15045
15046 <p class=instruction>Default: unset</p>
15047
15048 <p class=flagdescription>Launches an interactive mocca session.</p>
15049
15050 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
15051 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
15052 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
15053 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
15054
15055 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
15056 -in Lsample_lib3.tc_lib,Mlalign_rs_s_pair -domain -start=100 -len=60</p>
15057
15058 </div>
15059
15060 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
15061 mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
15062 background:#E6E6E6;margin-left:0cm;margin-right:1.0cm'>
15063
15064 <p class=examplefilesmallCxSpFirst>TOLB_ECOLI_212_26<span style='mso-tab-count:
15065 3'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><span
15066 style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp; </span>211 SKLAYVTFESGR--SALVIQTLANGAVRQV-ASFPRHNGAPAFSPDGSKLAFA</p>
15067
15068 <p class=examplefilesmallCxSpMiddle>TOLB_ECOLI_165_218<span
15069 style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp; </span>164
15070 TRIAYVVQTNGGQFPYELRVSDYDGYNQFVVHRSPQPLMSPAWSPDGSKLAYV</p>
15071
15072 <p class=examplefilesmallCxSpMiddle>TOLB_ECOLI_256_306<span
15073 style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp; </span>255
15074 SKLAFALSKTGS--LNLYVMDLASGQIRQV-TDGRSNNTEPTWFPDSQNLAFT</p>
15075
15076 <p class=examplefilesmallCxSpMiddle>TOLB_ECOLI_307_350<span
15077 style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp; </span>306 -------DQAGR--PQVYKVNINGGAPQRI-TWEGSQNQDADVSSDGKFMVMV</p>
15078
15079 <p class=examplefilesmallCxSpMiddle>TOLB_ECOLI_351_393<span
15080 style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp; </span>350
15081 -------SNGGQ--QHIAKQDLATGGV-QV-LSSTFLDETPSLAPNGTMVIYS<span style="mso-spacerun:
15082 yes">&nbsp; </span></p>
15083
15084 <p class=examplefilesmallCxSpMiddle><span style="mso-spacerun:
15085 yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
15086 </span>1<span style="mso-spacerun:
15087 yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>*<span
15088 style="mso-spacerun:
15089 yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
15090 </span>*<span style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp; </span>:<span
15091 style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
15092 </span>.<span style="mso-spacerun: yes">&nbsp;&nbsp; </span>.:.<span
15093 style="mso-spacerun: yes">&nbsp; </span>:<span style="mso-spacerun:
15094 yes">&nbsp;&nbsp;&nbsp; </span></p>
15095
15096 <p class=examplefilesmallCxSpMiddle><o:p>&nbsp;</o:p></p>
15097
15098 <p class=examplefilesmallCxSpMiddle><span style="mso-spacerun:
15099 yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>MENU: Type Letter
15100 Flag[number] and Return: ex |10</p>
15101
15102 <p class=examplefilesmallCxSpMiddle><span style="mso-spacerun:
15103 yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>|x<span
15104 style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>--&gt;Set<span
15105 style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp; </span>the START to x</p>
15106
15107 <p class=examplefilesmallCxSpMiddle><span style="mso-spacerun:
15108 yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>&gt;x<span
15109 style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>--&gt;Set<span
15110 style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp; </span>the LEN<span
15111 style="mso-spacerun: yes">&nbsp;&nbsp; </span>to x</p>
15112
15113 <p class=examplefilesmallCxSpMiddle><span style="mso-spacerun:
15114 yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Cx<span
15115 style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>--&gt;Set<span
15116 style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp; </span>the sCale to x</p>
15117
15118 <p class=examplefilesmallCxSpMiddle><span style="mso-spacerun:
15119 yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Sname<span
15120 style="mso-spacerun: yes">&nbsp;&nbsp; </span>--&gt;Save<span
15121 style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp; </span>the<span
15122 style="mso-spacerun: yes">&nbsp; </span>Alignment </p>
15123
15124 <p class=examplefilesmallCxSpMiddle><span style="mso-spacerun:
15125 yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Bx<span
15126 style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>--&gt;Save<span
15127 style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp; </span>Goes back x it </p>
15128
15129 <p class=examplefilesmallCxSpMiddle><span style="mso-spacerun:
15130 yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>return<span
15131 style="mso-spacerun: yes">&nbsp; </span>--&gt;Compute the<span
15132 style="mso-spacerun: yes">&nbsp; </span>Alignment</p>
15133
15134 <p class=examplefilesmallCxSpMiddle><span style="mso-spacerun:
15135 yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>X<span
15136 style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
15137 </span>--&gt;eXit</p>
15138
15139 <p class=examplefilesmallCxSpMiddle><o:p>&nbsp;</o:p></p>
15140
15141 <p class=examplefilesmallCxSpMiddle>[ITERATION<span style="mso-spacerun:
15142 yes">&nbsp;&nbsp; </span>1] [START=211] [LEN= 50] [SCALE=-100]<span
15143 style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>YOUR CHOICE:</p>
15144
15145 <p class=examplefilesmallCxSpMiddle>For instance, to set the length of the
15146 domain to 40, type: </p>
15147
15148 <p class=examplefilesmallCxSpMiddle><o:p>&nbsp;</o:p></p>
15149
15150 <p class=examplefilesmallCxSpMiddle>[ITERATION<span style="mso-spacerun:
15151 yes">&nbsp;&nbsp; </span>1] [START=211] [LEN= 50] [SCALE=-100]<span
15152 style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>YOUR
15153 CHOICE:&gt;40[return]</p>
15154
15155 <p class=examplefilesmallCxSpMiddle>[return]</p>
15156
15157 <p class=examplefilesmallCxSpMiddle><o:p>&nbsp;</o:p></p>
15158
15159 <p class=examplefilesmallCxSpMiddle>Which will generate:</p>
15160
15161 <p class=examplefilesmallCxSpMiddle><o:p>&nbsp;</o:p></p>
15162
15163 <p class=examplefilesmallCxSpMiddle>TOLB_ECOLI_212_252<span
15164 style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp; </span>211
15165 SKLAYVTFESGRSALVIQTLANGAVRQVASFPRHNGAPAF<span style="mso-spacerun: yes">&nbsp;
15166 </span>251</p>
15167
15168 <p class=examplefilesmallCxSpMiddle>TOLB_ECOLI_256_296<span
15169 style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp; </span>255
15170 SKLAFALSKTGSLNLYVMDLASGQIRQVTDGRSNNTEPTW<span style="mso-spacerun: yes">&nbsp;
15171 </span>295</p>
15172
15173 <p class=examplefilesmallCxSpMiddle>TOLB_ECOLI_300_340<span
15174 style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp; </span>299
15175 QNLAFTSDQAGRPQVYKVNINGGAPQRITWEGSQNQDADV<span style="mso-spacerun: yes">&nbsp;
15176 </span>339</p>
15177
15178 <p class=examplefilesmallCxSpMiddle>TOLB_ECOLI_344_383<span
15179 style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp; </span>343 KFMVMVSSNGGQQHIAKQDLATGGV-QVLSSTFLDETPSL<span
15180 style="mso-spacerun: yes">&nbsp; </span>382</p>
15181
15182 <p class=examplefilesmallCxSpMiddle>TOLB_ECOLI_387_427<span
15183 style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp; </span>386
15184 TMVIYSSSQGMGSVLNLVSTDGRFKARLPATDGQVKFPAW<span style="mso-spacerun: yes">&nbsp;
15185 </span>426</p>
15186
15187 <p class=examplefilesmallCxSpMiddle><span style="mso-spacerun:
15188 yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
15189 </span>1<span style="mso-spacerun: yes">&nbsp;&nbsp; </span>:<span
15190 style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp; </span>:<span
15191 style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp; </span>:<span
15192 style="mso-spacerun:
15193 yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>::<span
15194 style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
15195 </span>.<span style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp; </span>40</p>
15196
15197 <p class=examplefilesmallCxSpMiddle><o:p>&nbsp;</o:p></p>
15198
15199 <p class=examplefilesmallCxSpMiddle><o:p>&nbsp;</o:p></p>
15200
15201 <p class=examplefilesmallCxSpMiddle><o:p>&nbsp;</o:p></p>
15202
15203 <p class=examplefilesmallCxSpMiddle><o:p>&nbsp;</o:p></p>
15204
15205 <p class=examplefilesmallCxSpMiddle><span style="mso-spacerun:
15206 yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>MENU: Type Letter
15207 Flag[number] and Return: ex |10</p>
15208
15209 <p class=examplefilesmallCxSpMiddle><span style="mso-spacerun:
15210 yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><span style="mso-spacerun:
15211 yes">&nbsp;&nbsp;</span>|x<span style="mso-spacerun:
15212 yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>--&gt;Set<span style="mso-spacerun:
15213 yes">&nbsp;&nbsp;&nbsp;&nbsp; </span>the START to x</p>
15214
15215 <p class=examplefilesmallCxSpMiddle><span style="mso-spacerun:
15216 yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>&gt;x<span
15217 style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>--&gt;Set<span
15218 style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp; </span>the LEN<span
15219 style="mso-spacerun: yes">&nbsp;&nbsp; </span>to x</p>
15220
15221 <p class=examplefilesmallCxSpMiddle><span style="mso-spacerun:
15222 yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Cx<span
15223 style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>--&gt;Set<span
15224 style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp; </span>the sCale to x</p>
15225
15226 <p class=examplefilesmallCxSpMiddle><span style="mso-spacerun:
15227 yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Sname<span
15228 style="mso-spacerun: yes">&nbsp;&nbsp; </span>--&gt;Save<span
15229 style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp; </span>the<span
15230 style="mso-spacerun: yes">&nbsp; </span>Alignment </p>
15231
15232 <p class=examplefilesmallCxSpMiddle><span style="mso-spacerun:
15233 yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Bx<span
15234 style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>--&gt;Save<span
15235 style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp; </span>Goes back x it </p>
15236
15237 <p class=examplefilesmallCxSpMiddle><span style="mso-spacerun:
15238 yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>return<span
15239 style="mso-spacerun: yes">&nbsp; </span>--&gt;Compute the<span
15240 style="mso-spacerun: yes">&nbsp; </span>Alignment</p>
15241
15242 <p class=examplefilesmallCxSpMiddle><span style="mso-spacerun:
15243 yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>X<span
15244 style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
15245 </span>--&gt;eXit</p>
15246
15247 <p class=examplefilesmallCxSpMiddle><o:p>&nbsp;</o:p></p>
15248
15249 <p class=examplefilesmallCxSpLast>[ITERATION<span style="mso-spacerun:
15250 yes">&nbsp;&nbsp; </span>3] [START=211] [LEN= 40] [SCALE=-100]<span
15251 style="mso-spacerun: yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>YOUR CHOICE: </p>
15252
15253 </div>
15254
15255 <p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>
15256
15257 <p class=flagdescription>If you want to indicate the coordinates, relative to a
15258 specific sequence, type:</p>
15259
15260 <p class=example2><span style='mso-tab-count:1'>&nbsp; </span>|&lt;seq_name&gt;:start</p>
15261
15262 <p class=flagdescription>Type S&lt;your name&gt; to save the current alignment,
15263 and extract a new motif. </p>
15264
15265 <p class=flagdescription>Type X when you are done.</p>
15266
15267 <h2><a name="_Toc101065323"></a><a name="_Toc102494387"></a><a
15268 name="_Toc102494857"></a><a name="_Toc151732383"><span style='mso-bookmark:
15269 _Toc102494857'><span style='mso-bookmark:_Toc102494387'><span style='mso-bookmark:
15270 _Toc101065323'>Output Control</span></span></span></a></h2>
15271
15272 <h3><a name="_Toc101065324"></a><a name="_Toc102494388"></a><a
15273 name="_Toc102494858"></a><a name="_Toc151732384"><span style='mso-bookmark:
15274 _Toc102494858'><span style='mso-bookmark:_Toc102494388'><span style='mso-bookmark:
15275 _Toc101065324'>Generic</span></span></span></a></h3>
15276
15277 <p class=flag><a name="_Toc102494859"></a><a name="_Toc151732385"><span
15278 style='mso-bookmark:_Toc102494859'><span lang=AF>Conventions Regarding
15279 Filenames</span></span></a></p>
15280
15281 <p class=MyNormal><span lang=AF>stdout, stderr, stdin, no, /dev/null are valid
15282 filenames. They cause the corresponding file to be output in stderr or stdout,
15283 for an input file, stdin causes the program to requests the corresponding file
15284 through pipe. No causes a suppression of the output, as does /dev/null.</span></p>
15285
15286 <p class=flag><a name="_Toc102494860"></a><a name="_Toc151732386"><span
15287 style='mso-bookmark:_Toc102494860'><span lang=AF>Identifying the Output files
15288 automatically</span></span></a></p>
15289
15290 <p class=MyNormal><span lang=AF>In the t_coffee output, each output appears in
15291 a line:</span></p>
15292
15293 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
15294 mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
15295 background:#E6E6E6'>
15296
15297 <p class=examplefile>##### FILENAME &lt;name&gt; TYPE &lt;Type&gt; FORMAT
15298 &lt;Format&gt;</p>
15299
15300 </div>
15301
15302 <p class=flag><a name="_Toc101065325"></a><a name="_Toc102494389"></a><a
15303 name="_Toc102494861"></a><a name="_Toc151732387"><span style='mso-bookmark:
15304 _Toc102494861'><span style='mso-bookmark:_Toc102494389'><span style='mso-bookmark:
15305 _Toc101065325'><span lang=AF>-no_warning</span></span></span></span></a><span
15306 style='mso-bookmark:_Toc102494861'><span style='mso-bookmark:_Toc102494389'><span
15307 style='mso-bookmark:_Toc101065325'></span></span></span></p>
15308
15309 <p class=flagusage><span style='mso-bookmark:_Toc102494861'><span
15310 style='mso-bookmark:_Toc102494389'><span style='mso-bookmark:_Toc101065325'><span
15311 lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp; </span>-no_warning</span></span></span></span></p>
15312
15313 <p class=instruction><span style='mso-bookmark:_Toc102494861'><span
15314 style='mso-bookmark:_Toc102494389'><span style='mso-bookmark:_Toc101065325'>Default:
15315 Switched off</span></span></span></p>
15316
15317 <p class=flagdescription><span style='mso-bookmark:_Toc102494861'><span
15318 style='mso-bookmark:_Toc102494389'><span style='mso-bookmark:_Toc101065325'>Suppresseswarning
15319 output.<i style='mso-bidi-font-style:normal'><o:p></o:p></i></span></span></span></p>
15320
15321 <h3><span style='mso-bookmark:_Toc102494861'><span style='mso-bookmark:_Toc102494389'><span
15322 style='mso-bookmark:_Toc101065325'><o:p>&nbsp;</o:p></span></span></span></h3>
15323
15324 <h3><span style='mso-bookmark:_Toc102494861'><span style='mso-bookmark:_Toc102494389'><span
15325 style='mso-bookmark:_Toc101065325'><a name="_Toc151732388">Alignments</a></span></span></span></h3>
15326
15327 <p class=flag><a name="_Toc101065326"></a><a name="_Toc102494862"></a><a
15328 name="_Toc151732389"><span style='mso-bookmark:_Toc102494862'><span
15329 style='mso-bookmark:_Toc101065326'><span lang=AF>-outfile</span></span></span></a></p>
15330
15331 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
15332 </span>-outfile=&lt;out_aln file,default,no&gt;</span></p>
15333
15334 <p class=MyNormal><span lang=AF>Defau</span><!--[if supportFields]><span
15335 lang=AF><span style='mso-element:field-begin'></span> TOC \o &quot;1-1&quot; <span
15336 style='mso-element:field-separator'></span></span><![endif]--><span lang=AF><b
15337 style='mso-bidi-font-weight:normal'><span style='mso-no-proof:yes'>Word did not
15338 find any entries for your table of contents.</span></b></span><!--[if supportFields]><span
15339 lang=AF><span style='mso-element:field-end'></span></span><![endif]--><span
15340 lang=AF>lt:-outfile=default</span></p>
15341
15342 <p class=flagdescription>Indicates the name of the alignment output by
15343 t_coffee. If the default is used, the alignment is named <i style='mso-bidi-font-style:
15344 normal'>&lt;your sequences&gt;.aln<o:p></o:p></i></p>
15345
15346 <p class=flag><a name="_Toc101065327"></a><a name="_Toc102494863"></a><a
15347 name="_Toc151732390"><span style='mso-bookmark:_Toc102494863'><span
15348 style='mso-bookmark:_Toc101065327'><span lang=AF>-output</span></span></span></a></p>
15349
15350 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
15351 </span>-output=&lt;format1,format2,...&gt; </span></p>
15352
15353 <p class=instruction>Default:-output=clustalw</p>
15354
15355 <p class=flagdescription>Indicates the format used for outputting the -outfile.</p>
15356
15357 <p class=flagdescription>Supported formats are:</p>
15358
15359 <p class=flagdescription><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></p>
15360
15361 <p class=flagdescriptionid1>clustalw_aln, clustalw<span style='mso-tab-count:
15362 1'>&nbsp;&nbsp;&nbsp;&nbsp; </span>: ClustalW format.</p>
15363
15364 <p class=flagdescriptionid1>gcg, msf_aln<span style="mso-spacerun:
15365 yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><span style='mso-tab-count:2'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>:
15366 MSF alignment.</p>
15367
15368 <p class=flagdescriptionid1>pir_aln<span style='mso-tab-count:3'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>:
15369 pir alignment.</p>
15370
15371 <p class=flagdescriptionid1>fasta_aln<span style='mso-tab-count:2'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>:
15372 fasta alignment.</p>
15373
15374 <p class=flagdescriptionid1>phylip<span style='mso-tab-count:3'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>:
15375 Phylip format.</p>
15376
15377 <p class=flagdescriptionid1>pir_seq<span style='mso-tab-count:3'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>:
15378 pir sequences (no gap).</p>
15379
15380 <p class=flagdescriptionid1>fasta_seq<span style='mso-tab-count:2'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>:
15381 fasta sequences (no gap).</p>
15382
15383 <p class=flagdescription><span style='mso-tab-count:2'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></p>
15384
15385 <p class=flagdescription>As well as:</p>
15386
15387 <p class=flagdescription><o:p>&nbsp;</o:p></p>
15388
15389 <p class=flagdescriptionid1>score_ascii<span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>:
15390 causes the output of a reliability flag </p>
15391
15392 <p class=flagdescriptionid1>score_html<span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>:
15393 causes the output to be a reliability plot in HTML</p>
15394
15395 <p class=flagdescriptionid1>score_pdf<span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>:
15396 idem in PDF (if ps2pdf is installed on your system).</p>
15397
15398 <p class=flagdescriptionid1>score_ps<span style='mso-tab-count:2'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>:
15399 idem in postscript.</p>
15400
15401 <p class=flagdescription><o:p>&nbsp;</o:p></p>
15402
15403 <p class=flagdescription>More than one format can be indicated:</p>
15404
15405 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
15406 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
15407 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
15408 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
15409
15410 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
15411 sample_seq1.fasta -output=clustalw,gcg, score_html </p>
15412
15413 </div>
15414
15415 <p class=flagdescription>A publication describing the CORE index is available
15416 on:</p>
15417
15418 <p class=MyNormal><span lang=AF><a
15419 href="http://www.tcoffee.org/Publications/Pdf/core.pp.pdf"><span lang=EN-US
15420 style='mso-ansi-language:EN-US'>http://www.tcoffee.org/Publications/Pdf/core.pp.pdf</span></a></span></p>
15421
15422 <p class=flag><a name="_Toc101065328"></a><a name="_Toc102494864"></a><a
15423 name="_Toc151732391"><span style='mso-bookmark:_Toc102494864'><span
15424 style='mso-bookmark:_Toc101065328'><span lang=AF>-outseqweight</span></span></span></a></p>
15425
15426 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
15427 </span>-outseqweight=&lt;filename&gt;</span></p>
15428
15429 <p class=instruction>Default: not used</p>
15430
15431 <p class=flagdescription>Indicates the name of the file in which the sequences
15432 weights should be saved..</p>
15433
15434 <p class=flag><a name="_Toc101065329"></a><a name="_Toc102494865"></a><a
15435 name="_Toc151732392"><span style='mso-bookmark:_Toc102494865'><span
15436 style='mso-bookmark:_Toc101065329'><span lang=AF>-case</span></span></span></a></p>
15437
15438 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
15439 </span>-case=&lt;keep,upper,lower&gt;</span></p>
15440
15441 <p class=instruction>Default: -case=keep</p>
15442
15443 <p class=MyNormal><span lang=AF>Instructs the program on the case to be used in
15444 the output file (Clustalw uses upper case). The default keeps the case and
15445 makes it possible to maintain a mixture of upper and lower case residues.</span></p>
15446
15447 <p class=MyNormal><span lang=AF>If you need to change the case of your file,
15448 you can use seq_reformat:</span></p>
15449
15450 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
15451 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
15452 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
15453 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
15454
15455 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
15456 &#8211;other_pg seq_reformat &#8211;in sample_aln1.aln &#8211;action +lower
15457 &#8211;output clustalw </p>
15458
15459 </div>
15460
15461 <p class=flag><a name="_Toc101065330"></a><a name="_Toc102494866"></a><a
15462 name="_Toc151732393"><span style='mso-bookmark:_Toc102494866'><span
15463 style='mso-bookmark:_Toc101065330'><span lang=AF>-cpu</span></span></span></a></p>
15464
15465 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
15466 </span>deprecated</span></p>
15467
15468 <p class=flag><a name="_Toc102494867"></a><a name="_Toc151732394"><span
15469 style='mso-bookmark:_Toc102494867'><span lang=AF>-outseqweight</span></span></a></p>
15470
15471 <p class=MyNormal><span lang=AF>Usage: -outseqweight=&lt;name of the file
15472 containing the weights applied&gt;</span></p>
15473
15474 <p class=MyNormal><span lang=AF>Default: -outseqweight=no</span></p>
15475
15476 <p class=MyNormal><span lang=AF>Will cause the program to output the weights
15477 associated with every sequence in the dataset.</span></p>
15478
15479 <p class=flag><a name="_Toc101065331"></a><a name="_Toc102494868"></a><a
15480 name="_Toc151732395"><span style='mso-bookmark:_Toc102494868'><span
15481 style='mso-bookmark:_Toc101065331'><span lang=AF>-outorder [cw]</span></span></span></a></p>
15482
15483 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
15484 </span>-outorder=&lt;input OR aligned OR filename&gt; </span></p>
15485
15486 <p class=instruction>Default:-outorder=input</p>
15487
15488 <p class=flagdescription>Sets the order of the sequences in the output
15489 alignment: <b>-outorder=input</b> means the sequences are kept in the original
15490 order. <b>-outorder=aligned</b> means the sequences come in the order indicated
15491 by the tree. This order can be seen as a one-dimensional projection of the tree
15492 distances. <b style='mso-bidi-font-weight:normal'>&#8211;outdorder=&lt;filename&gt;</b>Filename
15493 is a legal fasta file, whose order will be used in the final alignment.</p>
15494
15495 <p class=flag><a name="_Toc151732396"><span lang=AF>-inorder [cw]</span></a></p>
15496
15497 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
15498 </span>-inorder=&lt;input OR aligned&gt; </span></p>
15499
15500 <p class=instruction>Default:-inorder=aligned</p>
15501
15502 <p class=flagdescription>Multiple alignments based on dynamic programming
15503 depend slightly on the order in which the incoming sequences are provided. To
15504 prevent this effect sequences are arbitrarily sorted at the beginning of the
15505 program (-inorder=aligned). However, this affects the sequence order within the
15506 library. You can switch this off by ststing &#8211;inorder=input.</p>
15507
15508 <p class=flag><a name="_Toc102494869"></a><a name="_Toc151732397"><span
15509 style='mso-bookmark:_Toc102494869'><span lang=AF>-seqnos</span></span></a></p>
15510
15511 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
15512 </span>-seqnos=&lt;on or off&gt; </span></p>
15513
15514 <p class=instruction>Default:-seqnos=off</p>
15515
15516 <p class=MyNormal><span lang=AF>Causes the output alignment to contain residue
15517 numbers at the end of each line:</span></p>
15518
15519 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
15520 mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
15521 background:#E6E6E6'>
15522
15523 <p class=examplefileCxSpFirst>T-COFFEE</p>
15524
15525 <p class=examplefileCxSpMiddle>seq1 aaa---aaaa--------aa 9</p>
15526
15527 <p class=examplefileCxSpMiddle>seq2 a-----aa-----------a 4</p>
15528
15529 <p class=examplefileCxSpMiddle><o:p>&nbsp;</o:p></p>
15530
15531 <p class=examplefileCxSpMiddle>seq1 a-----------------a 11</p>
15532
15533 <p class=examplefileCxSpLast>seq2 aaaaaaaaaaaaaaaaaaa 19</p>
15534
15535 </div>
15536
15537 <h3><a name="_Toc101065332"></a><a name="_Toc102494390"></a><a
15538 name="_Toc102494870"></a><a name="_Toc151732398"><span style='mso-bookmark:
15539 _Toc102494870'><span style='mso-bookmark:_Toc102494390'><span style='mso-bookmark:
15540 _Toc101065332'>Libraries</span></span></span></a></h3>
15541
15542 <p class=MyNormal><span lang=AF>Although, it does not necessarily do so
15543 explicitly, T-Coffee always end up combining libraries. Libraries are
15544 collections of pairs of residues. Given a set of libraries, T-Coffee makes an
15545 attempt to assemble the alignment with the highest level of consistence. You
15546 can think of the alignment as a timetable. Each library pair would be a request
15547 from students or teachers, and the job of T-Coffee would be to assemble the
15548 time table that makes as many people as possible happy\85</span></p>
15549
15550 <p class=flag><a name="_Toc102494871"></a><a name="_Toc151732399"><span
15551 style='mso-bookmark:_Toc102494871'><span lang=AF>-out_lib</span></span></a></p>
15552
15553 <p class=MyNormal><span lang=AF>Usage:<span style="mso-spacerun: yes">&nbsp;
15554 </span>-out_lib=&lt;name of the library,default,no&gt; </span></p>
15555
15556 <p class=MyNormal><span lang=AF>Default:-out_lib=default</span></p>
15557
15558 <p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>
15559
15560 <p class=flagdescription>Sets the name of the library output. Default implies
15561 &lt;run_name&gt;.tc_lib</p>
15562
15563 <p class=flag><a name="_Toc101065333"></a><a name="_Toc102494872"></a><a
15564 name="_Toc151732400"><span style='mso-bookmark:_Toc102494872'><span
15565 style='mso-bookmark:_Toc101065333'><span lang=AF>-lib_only</span></span></span></a></p>
15566
15567 <p class=flagusage><span lang=FR>Usage:<span style="mso-spacerun: yes">&nbsp;
15568 </span>-lib_only</span></p>
15569
15570 <p class=instruction>Default: unset</p>
15571
15572 <p class=flagdescription>Causes the program to stop once the library has been
15573 computed. Must be used in conjunction with the flag <b style='mso-bidi-font-weight:
15574 normal'>&#8211;out_lib</b></p>
15575
15576 <h3><a name="_Toc101065334"></a><a name="_Toc102494391"></a><a
15577 name="_Toc102494873"></a><a name="_Toc151732401"><span style='mso-bookmark:
15578 _Toc102494873'><span style='mso-bookmark:_Toc102494391'><span style='mso-bookmark:
15579 _Toc101065334'>Trees</span></span></span></a></h3>
15580
15581 <p class=flag><a name="_Toc101065335"></a><a name="_Toc102494874"></a><a
15582 name="_Toc151732402"><span style='mso-bookmark:_Toc102494874'><span
15583 style='mso-bookmark:_Toc101065335'><span lang=AF>-newtree</span></span></span></a></p>
15584
15585 <p class=flagusage><span lang=FR>Usage: -newtree=&lt;tree file&gt;</span></p>
15586
15587 <p class=instruction>Default: No file specified</p>
15588
15589 <p class=flagdescription>Indicates the name of the file into which the guide
15590 tree will be written. The default will be &lt;sequence_name&gt;.dnd, or
15591 &lt;run_name.dnd&gt;. The tree is written in the parenthesis format known as
15592 newick or New Hampshire and used by Phylips (see the format section).</p>
15593
15594 <div style='mso-element:para-border-div;border:solid windowtext 1.5pt;
15595 padding:0cm 0cm 0cm 0cm;background:#F7CBB7'>
15596
15597 <p class=Warning>Do NOT confuse this guide tree with a phylogenetic tree.</p>
15598
15599 </div>
15600
15601 <h2><a name="_Toc101065336"></a><a name="_Toc102494392"></a><a
15602 name="_Toc102494875"></a><a name="_Toc151732403"><span style='mso-bookmark:
15603 _Toc102494875'><span style='mso-bookmark:_Toc102494392'><span style='mso-bookmark:
15604 _Toc101065336'>Reliability Estimation</span></span></span></a></h2>
15605
15606 <h3><a name="_Toc101065337"></a><a name="_Toc102494393"></a><a
15607 name="_Toc102494876"></a><a name="_Toc151732404"><span style='mso-bookmark:
15608 _Toc102494876'><span style='mso-bookmark:_Toc102494393'><span style='mso-bookmark:
15609 _Toc101065337'>CORE Computation</span></span></span></a></h3>
15610
15611 <p class=MyNormal><span lang=AF>The CORE is an index that indicates the
15612 consistency between the library of piarwise alignments and the final multiple
15613 alignment. Our experiment indicate that the higher this consistency, the more
15614 reliable the alignment. A publication describing the CORE index can be found
15615 on:</span></p>
15616
15617 <p class=MyNormal><a name="_Toc101065338"></a><a name="_Toc102494877"><span
15618 style='mso-bookmark:_Toc101065338'></span></a><a
15619 href="http://www.tcoffee.org/Publications/Pdf/core.pp.pdf"><span
15620 style='mso-bookmark:_Toc102494877'><span style='mso-bookmark:_Toc101065338'><span
15621 style='mso-ansi-language:EN-US'>http://www.tcoffee.org/Publications/Pdf/core.pp.pdf</span></span></span><span
15622 style='mso-bookmark:_Toc102494877'><span style='mso-bookmark:_Toc101065338'></span></span></a><span
15623 style='mso-bookmark:_Toc102494877'><span style='mso-bookmark:_Toc101065338'></span></span></p>
15624
15625 <p class=flag><span style='mso-bookmark:_Toc102494877'><span style='mso-bookmark:
15626 _Toc101065338'><a name="_Toc151732405"><span lang=AF>-evaluate_mode</span></a></span></span></p>
15627
15628 <p class=flagusage><span lang=FR>Usage:
15629 -evaluate_mode=&lt;t_coffee_fast,t_coffee_slow,t_coffee_non_extended &gt;</span></p>
15630
15631 <p class=instruction>Default: -evaluate_mode=t_coffee_fast</p>
15632
15633 <p class=flagdescription>This flag indicates the mode used to normalize the
15634 t_coffee score when computing the reliability score. </p>
15635
15636 <p class=flagdescription><i style='mso-bidi-font-style:normal'>t_coffee_fast</i>:
15637 Normalization is made using the highest score in the MSA. This evaluation mode
15638 was validated and in our hands, pairs of residues with a score of 5 or higher
15639 have 90 % chances to be correctly aligned to one another. </p>
15640
15641 <p class=flagdescription><i style='mso-bidi-font-style:normal'>t_coffee_slow:</i>
15642 Normalization is made using the library. This usually results in lower score
15643 and a scoring scheme more sensitive to the number of sequences in the dataset.
15644 Note that this scoring scheme is not any more slower, thanks to the
15645 implementation of a faster heuristic algorithm. </p>
15646
15647 <p class=flagdescription><i style='mso-bidi-font-style:normal'>t_coffee_non_extended:</i>
15648 the score of each residue is the ratio between the sum of its non extended
15649 scores with the column and the sum of all its possible non extended scores.</p>
15650
15651 <p class=flagdescription>These modes will be useful when generating colored
15652 version of the output, with the <b style='mso-bidi-font-weight:normal'>&#8211;output</b>
15653 flag:</p>
15654
15655 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
15656 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
15657 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
15658 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
15659
15660 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
15661 sample_seq1.fasta &#8211;evaluate_mode t_coffee_slow &#8211;output score_ascii,
15662 score_html </p>
15663
15664 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
15665 sample_seq1.fasta &#8211;evaluate_mode t_coffee_fast &#8211;output score_ascii,
15666 score_html </p>
15667
15668 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
15669 sample_seq1.fasta &#8211;evaluate_mode t_coffee_non_extended &#8211;output
15670 score_ascii, score_html </p>
15671
15672 </div>
15673
15674 <h2><a name="_Toc101065339"></a><a name="_Toc102494394"></a><a
15675 name="_Toc102494878"></a><a name="_Toc151732406"><span style='mso-bookmark:
15676 _Toc102494878'><span style='mso-bookmark:_Toc102494394'><span style='mso-bookmark:
15677 _Toc101065339'>Generic Output</span></span></span></a></h2>
15678
15679 <p class=flag><a name="_Toc102494879"></a><a name="_Toc151732407"><span
15680 style='mso-bookmark:_Toc102494879'><span lang=AF>-run_name</span></span></a></p>
15681
15682 <p class=flagusage><span lang=FR>Usage: -run_name=&lt;your run name&gt;</span></p>
15683
15684 <p class=instruction>Default: no default set</p>
15685
15686 <p class=MyNormal><span lang=AF>This flag causes the prefix &lt;your
15687 sequences&gt; to be replaced by &lt;your run name&gt; when renaming the default
15688 output files.</span></p>
15689
15690 <p class=flag><a name="_Toc101065340"></a><a name="_Toc102494880"></a><a
15691 name="_Toc151732408"><span style='mso-bookmark:_Toc102494880'><span
15692 style='mso-bookmark:_Toc101065340'><span lang=AF>-quiet</span></span></span></a></p>
15693
15694 <p class=flagusage><span lang=FR>Usage: -quiet=&lt;stderr,stdout,file name OR
15695 nothing&gt;.</span></p>
15696
15697 <p class=instruction>Default:-quiet=stderr</p>
15698
15699 <p class=flagdescription>Redirects the standard output to either a file. <b>-quiet</b>
15700 on its own redirect the output to /dev/null.</p>
15701
15702 <p class=flag><a name="_Toc102494881"></a><a name="_Toc151732409"><span
15703 style='mso-bookmark:_Toc102494881'><span lang=AF>-align [CW]</span></span></a></p>
15704
15705 <p class=MyNormal><span lang=AF>This flag indicates that the program must
15706 produce the alignment. It is here for compatibility with ClustalW.</span></p>
15707
15708 <h2><a name="_Toc151732410">APDB, iRMSD and tRMSD Parameters</a></h2>
15709
15710 <p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>
15711
15712 <div style='mso-element:para-border-div;border:solid windowtext 1.5pt;
15713 padding:0cm 0cm 0cm 0cm;background:#F7CBB7'>
15714
15715 <p class=Warning>Warning: These flags will only work within the APDB package
15716 that can be invoked via the &#8211;other_pg parameter of T-Coffee:</p>
15717
15718 <p class=Warning><span style='mso-tab-count:2'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span><span
15719 style="mso-spacerun: yes">&nbsp;</span>t_coffee &#8211;other_pg apdb &#8211;aln
15720 &lt;your aln&gt;</p>
15721
15722 <p class=Warning><o:p>&nbsp;</o:p></p>
15723
15724 </div>
15725
15726 <p class=flag><a name="_Toc151732411"><span lang=AF>-quiet [Same as T-Coffee]</span></a></p>
15727
15728 <p class=flag><a name="_Toc151732412"><span lang=AF>-run_name [Same as
15729 T-Coffee]</span></a></p>
15730
15731 <p class=flag><a name="_Toc151732413"><span lang=AF>-aln</span></a></p>
15732
15733 <p class=flagusage><span lang=FR>Usage: -aln=&lt;file_name&gt;.</span></p>
15734
15735 <p class=instruction>Default:none</p>
15736
15737 <p class=flagdescription>Indicates the name of the file containing the
15738 sequences that need to be evaluated. The sequences whose structure is meant to
15739 be used must be named according to their PDB identifier. </p>
15740
15741 <p class=flagdescription>The format can be FASTA, CLUSTAL or any of the formats
15742 supported by T-Coffee. APDB only evaluates residues in capital and ignores
15743 those in lower case. If your sequences are in lower case, you can upper case
15744 them using seq_reformat:</p>
15745
15746 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
15747 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
15748 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
15749 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
15750
15751 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
15752 &#8211;other_pg seq_reformat &#8211;in 3d_sample4.aln &#8211;action +upper
15753 &#8211;output clustalw &gt; 3d_sample4.cw_aln</p>
15754
15755 </div>
15756
15757 <p class=flagdescription>The alignment can then be evaluated using the defaultr
15758 of APDB:</p>
15759
15760 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
15761 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
15762 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
15763 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
15764
15765 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
15766 &#8211;other_pg apdb &#8211;aln 3d_sample4.aln</p>
15767
15768 </div>
15769
15770 <p class=flagdescription>The alignment can contain as many structures as you
15771 wish.</p>
15772
15773 <p class=flag><a name="_Toc151732414"><span lang=AF>-n_excluded_nb</span></a></p>
15774
15775 <p class=flagusage><span lang=FR>Usage: -n_excluded_nb=&lt;integer&gt;.</span></p>
15776
15777 <p class=instruction>Default:1</p>
15778
15779 <p class=flagdescription>When evaluating the local score of a pair of aligned
15780 residues, the residues immediately next to that column should not contribute to
15781 the measure. By default the first to the left and first to the right are
15782 excluded.</p>
15783
15784 <p class=flag><a name="_Toc151732415"><span lang=AF>-maximum_distance</span></a></p>
15785
15786 <p class=flagusage><span lang=FR>Usage: -maximum_distance=&lt;float&gt;.</span></p>
15787
15788 <p class=instruction>Default:10</p>
15789
15790 <p class=flagdescription>Size of the neighborhood considered around every
15791 residue. If .-local_mode is set to sphere, -maximum_distance is the radius of a
15792 sphere centered around each residue. If &#8211;local_mode is set to window,
15793 then &#8211;maximum_distance is the size of the half window (i.e. window_size=-maximum_distance*2+1).</p>
15794
15795 <p class=flag><a name="_Toc151732416"><span lang=AF>-similarity_threshold</span></a></p>
15796
15797 <p class=flagusage><span lang=FR>Usage: -similarity_threshold=&lt;integer&gt;.</span></p>
15798
15799 <p class=instruction>Default:70</p>
15800
15801 <p class=flagdescription>Fraction of the neighborhood that must be supportive
15802 for a pair of residue to be considered correct in APDB. The neighborhood is a
15803 sphere defined by &#8211;maximum_distance, and the support is defined by
15804 &#8211;md_threshold.</p>
15805
15806 <p class=flag><a name="_Toc151732417"><span lang=AF>-local_mode</span></a></p>
15807
15808 <p class=flagusage><span lang=FR>Usage: -local_mode=&lt;sphere,window&gt;.</span></p>
15809
15810 <p class=instruction>Default:sphere</p>
15811
15812 <p class=flagdescription>Defines the shape of a neighborhood, either as a
15813 sphere or as a window.</p>
15814
15815 <p class=flag><a name="_Toc151732418"><span lang=AF>-filter</span></a></p>
15816
15817 <p class=flagusage><span lang=FR>Usage: -filter=&lt;0.00-1.00&gt;.</span></p>
15818
15819 <p class=instruction>Default:1.00</p>
15820
15821 <p class=flagdescription>Defines the centiles that should be kept when making
15822 the local measure. Foir instance, -filter=0.90 means that the the 10 last
15823 centiles will be removed from the evaluation. The filtration is carried out on
15824 the iRMSD values.</p>
15825
15826 <p class=flag><a name="_Toc151732419"><span lang=AF>-print_rapdb [Unsupported]</span></a></p>
15827
15828 <p class=flagusage><span lang=FR>Usage: -print_rapdb (FLAG)</span></p>
15829
15830 <p class=instruction>Default:off</p>
15831
15832 <p class=flagdescription>This causes the prints out of the exact neighborhood
15833 of every considered pair of residues.</p>
15834
15835 <p class=flag><a name="_Toc151732420"><span lang=AF>-outfile [Same as T-Coffee]</span></a></p>
15836
15837 <p class=MyNormal><span lang=AF>This flag is meant to control the output name
15838 of the colored APDB output. This file will either display the local APDB score
15839 or the local iRMD, depending on the value of &#8211;color_mode. The default
15840 format is defined by &#8211;ouptut and is score_html.</span></p>
15841
15842 <p class=flag><a name="_Toc151732421"><span lang=AF>-color_mode</span></a></p>
15843
15844 <p class=flagusage><span lang=FR>Usage: -color_mode=&lt;apdb, irmsd&gt;</span></p>
15845
15846 <p class=instruction>Default:apdb</p>
15847
15848 <p class=MyNormal><span lang=AF>This flag is meant to control the colored APDB
15849 output (local score). This file will either display the local APDB score or the
15850 local iRMD.</span></p>
15851
15852 <div style='mso-element:para-border-div;border:solid windowtext 3.0pt;
15853 padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#CCCCCC;margin-left:0cm;margin-right:
15854 4.25pt'>
15855
15856 <p class=ChapterTitle>Building a Server</p>
15857
15858 </div>
15859
15860 <p class=MyNormal><span lang=AF>We maintain a T-Coffee server
15861 (www.tcoffee.org). We will be pleased to provide anyone who wants to set up a
15862 similar service with the sources</span></p>
15863
15864 <h3><a name="_Toc102494396"></a><a name="_Toc102494884"></a><a
15865 name="_Toc151732422"><span style='mso-bookmark:_Toc102494884'><span
15866 style='mso-bookmark:_Toc102494396'>Environment Variables</span></span></a><span
15867 style='mso-bookmark:_Toc102494884'><span style='mso-bookmark:_Toc102494396'></span></span></h3>
15868
15869 <p class=MyNormal><span style='mso-bookmark:_Toc102494884'><span
15870 style='mso-bookmark:_Toc102494396'><span lang=AF>T-Coffee stores a lots of
15871 information in locations that may be unsuitable when running a server. </span></span></span></p>
15872
15873 <p class=MyNormal><span style='mso-bookmark:_Toc102494884'><span
15874 style='mso-bookmark:_Toc102494396'><span lang=AF>By default, T-Coffee will
15875 generate and rely on the follwing directory structure:</span></span></span></p>
15876
15877 <p class=example><span style='mso-bookmark:_Toc102494884'><span
15878 style='mso-bookmark:_Toc102494396'>/home/youraccount/<span style='mso-tab-count:
15879 2'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>#HOME_4_TCOFFEE</span></span></p>
15880
15881 <p class=example><span style='mso-bookmark:_Toc102494884'><span
15882 style='mso-bookmark:_Toc102494396'>HOME_4_TCOFFEE/.t_coffee/ <span
15883 style='mso-tab-count:1'>&nbsp; </span>#DIR_4_TCOFFEE</span></span></p>
15884
15885 <p class=example><span style='mso-bookmark:_Toc102494884'><span
15886 style='mso-bookmark:_Toc102494396'>DIR_4_TCOFFEE/cache<span style='mso-tab-count:
15887 2'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>#CACHE_4_TCOFFEE</span></span></p>
15888
15889 <p class=example><span style='mso-bookmark:_Toc102494884'><span
15890 style='mso-bookmark:_Toc102494396'>DIR_4_TCOFFEE/tmp<span style='mso-tab-count:
15891 2'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>#TMP_4_TCOFFEE</span></span></p>
15892
15893 <p class=example><span style='mso-bookmark:_Toc102494884'><span
15894 style='mso-bookmark:_Toc102494396'>DIR_4_TCOFFEE/methods<span style='mso-tab-count:
15895 2'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>#METHOS_4_TCOFFEE</span></span></p>
15896
15897 <p class=example><span style='mso-bookmark:_Toc102494884'><span
15898 style='mso-bookmark:_Toc102494396'>DIR_4_TCOFFEE/mcoffee<span style='mso-tab-count:
15899 2'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>#MCOFFEE_4_TCOFFEE</span></span></p>
15900
15901 <p class=MyNormal><span style='mso-bookmark:_Toc102494884'><span
15902 style='mso-bookmark:_Toc102494396'><span lang=AF><o:p>&nbsp;</o:p></span></span></span></p>
15903
15904 <p class=MyNormal><span style='mso-bookmark:_Toc102494884'><span
15905 style='mso-bookmark:_Toc102494396'><span lang=AF>By default, all these
15906 directories are automatically created, following the dependencies suggested
15907 here. </span></span></span></p>
15908
15909 <p class=MyNormal><span style='mso-bookmark:_Toc102494884'><span
15910 style='mso-bookmark:_Toc102494396'><span lang=AF>The first step is the
15911 determination of the HOME. By default the program tries to use HOME_4_TCOFFEE,
15912 then the HOME variable and TMP or TEMP if HOME is not set on your system or
15913 your account. It is your responsibility to make sure that one of these variables
15914 is set to some valid location where the T-Coffee process is allowed to read and
15915 write.</span></span></span></p>
15916
15917 <p class=MyNormal><span style='mso-bookmark:_Toc102494884'><span
15918 style='mso-bookmark:_Toc102494396'><span lang=AF>If no valid location can be
15919 found for HOME_4_TCOFFEE, the program exits. If you are running T-Coffee on a
15920 server, we recommend to hard set the following locations, where your scratch is
15921 a valid location. </span></span></span></p>
15922
15923 <p class=MyNormal><span style='mso-bookmark:_Toc102494884'><span
15924 style='mso-bookmark:_Toc102494396'><span lang=AF><o:p>&nbsp;</o:p></span></span></span></p>
15925
15926 <p class=example><span style='mso-bookmark:_Toc102494884'><span
15927 style='mso-bookmark:_Toc102494396'>HOME_4_TCOFFEE=\94your scratch\94</span></span></p>
15928
15929 <p class=example><span style='mso-bookmark:_Toc102494884'><span
15930 style='mso-bookmark:_Toc102494396'>TMP_4_TCOFFEE=\94your scratch\94</span></span></p>
15931
15932 <p class=example><span style='mso-bookmark:_Toc102494884'><span
15933 style='mso-bookmark:_Toc102494396'>DIR_4_TCOFFEE=\94your scratch\94</span></span></p>
15934
15935 <p class=example><span style='mso-bookmark:_Toc102494884'><span
15936 style='mso-bookmark:_Toc102494396'>CACHE_4_TCOFFEE=\94your scratch\94</span></span></p>
15937
15938 <p class=example><span style='mso-bookmark:_Toc102494884'><span
15939 style='mso-bookmark:_Toc102494396'>NO_ERROR_REPORT_4_TCOFFEE=1</span></span></p>
15940
15941 <p class=MyNormal><span style='mso-bookmark:_Toc102494884'><span
15942 style='mso-bookmark:_Toc102494396'><span lang=AF>Note that<span
15943 style="mso-spacerun: yes">&nbsp; </span>it is a good idea to have a cron job
15944 that cleans up this scratch area, once in a while. </span></span></span></p>
15945
15946 <p class=MyNormal><span style='mso-bookmark:_Toc102494884'><span
15947 style='mso-bookmark:_Toc102494396'><span lang=AF><o:p>&nbsp;</o:p></span></span></span></p>
15948
15949 <h3><span style='mso-bookmark:_Toc102494884'><span style='mso-bookmark:_Toc102494396'><a
15950 name="_Toc151732423">Output of the .dnd file.</a></span></span></h3>
15951
15952 <p class=MyNormal><span lang=AF>A common source of error when running a server:
15953 T-Coffee MUST output the .dnd file because it re-reads it to carry out the
15954 progressive alignment. By default T-Coffee outputs this file in the directory where
15955 the process is running. If the T-Coffee process does not have permission to
15956 write in that directory, the computation will abort...</span></p>
15957
15958 <p class=MyNormal><span lang=AF>To avoid this, simply specify the name of the
15959 output tree: </span></p>
15960
15961 <p class=MyNormal><span lang=AF><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>-newtree=&lt;writable
15962 file (usually in /tmp)&gt;</span></p>
15963
15964 <p class=MyNormal><span lang=AF>Chose the name so that two processes may not
15965 over-write each other dnd file. </span></p>
15966
15967 <h3><a name="_Toc102494397"></a><a name="_Toc102494885"></a><a
15968 name="_Toc151732424"><span style='mso-bookmark:_Toc102494885'><span
15969 style='mso-bookmark:_Toc102494397'>Permissions</span></span></a></h3>
15970
15971 <p class=MyNormal><span lang=AF>The t_coffee process MUST be allowed to write
15972 in some scratch area, even when it is ran by Mr nobody... Make sure the /tmp/
15973 partition is not protected.</span></p>
15974
15975 <h3><a name="_Toc102494398"></a><a name="_Toc102494886"></a><a
15976 name="_Toc151732425"><span style='mso-bookmark:_Toc102494886'><span
15977 style='mso-bookmark:_Toc102494398'>Other Programs</span></span></a></h3>
15978
15979 <p class=MyNormal><span lang=AF>T-Coffee may call various programs while it
15980 runs (lalign2list by defaults). Make sure your process knows where to find
15981 these executables.</span></p>
15982
15983 <div style='mso-element:para-border-div;border:solid windowtext 3.0pt;
15984 padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#CCCCCC;margin-left:0cm;margin-right:
15985 4.25pt'>
15986
15987 <p class=ChapterTitle><a name="_Toc101065353"></a><a name="_Toc102494887"><span
15988 style='mso-bookmark:_Toc101065353'>F</span></a>ormats</p>
15989
15990 </div>
15991
15992 <h2><a name="_Toc101065354"></a><a name="_Toc102494399"></a><a
15993 name="_Toc102494888"></a><a name="_Toc151732426"><span style='mso-bookmark:
15994 _Toc102494888'><span style='mso-bookmark:_Toc102494399'><span style='mso-bookmark:
15995 _Toc101065354'>Parameter files</span></span></span></a></h2>
15996
15997 <p class=MyNormal><span lang=AF>Parameter files used with -parameters,
15998 -t_coffee_defaults, -dali_defaults... Must contain a valid parameter string
15999 where line breaks are allowed. These files cannot contain any comment, the
16000 recommended format is one parameter per line:</span></p>
16001
16002 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
16003 mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
16004 background:#E6E6E6'>
16005
16006 <p class=examplefileCxSpFirst><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>&lt;parameter
16007 name&gt;=&lt;value1&gt;,&lt;value2&gt;....</p>
16008
16009 <p class=examplefileCxSpLast><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>&lt;parameter
16010 name&gt;=.....</p>
16011
16012 </div>
16013
16014 <h2><a name="_Toc101065355"></a><a name="_Toc102494400"></a><a
16015 name="_Toc102494889"></a><a name="_Toc151732427"><span style='mso-bookmark:
16016 _Toc102494889'><span style='mso-bookmark:_Toc102494400'><span style='mso-bookmark:
16017 _Toc101065355'>Sequence Name Handling</span></span></span></a></h2>
16018
16019 <p class=MyNormal><span lang=AF>Sequence name handling is meant to be fully
16020 consistent with ClustalW (Version 1.75). This implies that in some cases the
16021 names of your sequences may be edited when coming out of the program. Five
16022 rules apply:</span></p>
16023
16024 <p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>
16025
16026 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
16027 mso-border-alt:solid windowtext .5pt;padding:1.0pt 1.0pt 1.0pt 1.0pt'>
16028
16029 <p class=Noteboxtitle style='border:none;mso-border-alt:solid windowtext .5pt;
16030 padding:0cm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'>Naming Your Sequences the
16031 Right Way</p>
16032
16033 <p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;
16034 padding:0cm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'>1-No Space</p>
16035
16036 <p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;
16037 padding:0cm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'>Names that do contain
16038 spaces, for instance:</p>
16039
16040 <p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;
16041 padding:0cm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'><span style='mso-tab-count:
16042 1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>&gt;seq1
16043 human_myc</p>
16044
16045 <p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;
16046 padding:0cm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'>will be turned into</p>
16047
16048 <p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;
16049 padding:0cm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'><span style='mso-tab-count:
16050 1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>&gt;seq1</p>
16051
16052 <p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;
16053 padding:0cm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'>It is your responsibility
16054 to make sure that the names you provide are not ambiguous after such an
16055 editing. This editing is consistent with Clustalw (Version 1.75)</p>
16056
16057 <p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;
16058 padding:0cm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'><o:p>&nbsp;</o:p></p>
16059
16060 <p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;
16061 padding:0cm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'>2-No Strange Character</p>
16062
16063 <p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;
16064 padding:0cm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'>Some non alphabetical characters
16065 are replaced with underscores. These are: ';:()'</p>
16066
16067 <p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;
16068 padding:0cm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'>Other characters are legal
16069 and will be kept unchanged. This editing is meant to keep in line with Clustalw
16070 (Version 1.75).</p>
16071
16072 <p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;
16073 padding:0cm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'><o:p>&nbsp;</o:p></p>
16074
16075 <p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;
16076 padding:0cm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'>3-&gt; is NEVER legal
16077 (except as a header token in a FASTA file)</p>
16078
16079 <p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;
16080 padding:0cm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'><o:p>&nbsp;</o:p></p>
16081
16082 <p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;
16083 padding:0cm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'>4-Name length must be
16084 below 100 characters, although 15 is recommended for compatibility with other
16085 programs.</p>
16086
16087 <p class=noteboxbody style='border:none;mso-border-alt:solid windowtext .5pt;
16088 padding:0cm;mso-padding-alt:1.0pt 1.0pt 1.0pt 1.0pt'>5-Duplicated sequences
16089 will be renamed (i.e. sequences with the same name in the same dataset) are
16090 allowed but will be renamed according to their original order. When sequences
16091 come from multiple sources via the &#8211;in flag, consistency of the renaming
16092 is not guaranteed. You should avoid duplicated sequences as they will cause
16093 your input to differ from your output thus making it difficult to track data.</p>
16094
16095 </div>
16096
16097 <h2><a name="_Toc101065356"></a><a name="_Toc102494401"></a><a
16098 name="_Toc102494890"></a><a name="_Toc151732428"><span style='mso-bookmark:
16099 _Toc102494890'><span style='mso-bookmark:_Toc102494401'><span style='mso-bookmark:
16100 _Toc101065356'>Automatic Format Recognition</span></span></span></a></h2>
16101
16102 <p class=MyNormal><span lang=AF>Most common formats are automatically
16103 recognized by t_coffee. See -in and the next section for more details. If your
16104 format is not recognized, use readseq or clustalw to switch to another format.
16105 We recommend Fasta.</span></p>
16106
16107 <h2><a name="_Toc101065357"></a><a name="_Toc102494402"></a><a
16108 name="_Toc102494891"></a><a name="_Toc151732429"><span style='mso-bookmark:
16109 _Toc102494891'><span style='mso-bookmark:_Toc102494402'><span style='mso-bookmark:
16110 _Toc101065357'>Structures</span></span></span></a></h2>
16111
16112 <p class=MyNormal><span lang=AF>PDB format is recognized by T-Coffee. T-Coffee
16113 uses extract_from_pdb (cf &#8211;other_pg flag). extract_from_pdb is a small
16114 embeded module that can be used on its own to extract information from pdb
16115 files.</span></p>
16116
16117 <h2><a name="_Toc151732430">RNA Structures</a></h2>
16118
16119 <p class=MyNormal><span lang=AF>RNA structures can either be coded as T-Coffee
16120 libraries, with each line indicating two paired residues, or as alifold output.
16121 The selex format is also partly supported (see the seq_reformat tutorial on RNA
16122 sequences handling).</span></p>
16123
16124 <h2><a name="_Toc101065358"></a><a name="_Toc102494403"></a><a
16125 name="_Toc102494892"></a><a name="_Toc151732431"><span style='mso-bookmark:
16126 _Toc102494892'><span style='mso-bookmark:_Toc102494403'><span style='mso-bookmark:
16127 _Toc101065358'>Sequences</span></span></span></a></h2>
16128
16129 <p class=MyNormal><span lang=AF>Sequences can come in the following formats:
16130 fasta, pir, swiss-prot, clustal aln, msf aln and t_coffee aln. These formats
16131 are the one automatically recognized. Please replace the '*' sign sometimes
16132 used for stop codons with an X.</span></p>
16133
16134 <h2><a name="_Toc101065359"></a><a name="_Toc102494404"></a><a
16135 name="_Toc102494893"></a><a name="_Toc151732432"><span style='mso-bookmark:
16136 _Toc102494893'><span style='mso-bookmark:_Toc102494404'><span style='mso-bookmark:
16137 _Toc101065359'>Alignments</span></span></span></a></h2>
16138
16139 <p class=MyNormal><span lang=AF>Alignments can come in the following formats:
16140 msf, ClustalW, Fasta, Pir and t_coffee. The t_coffee format is very similar to
16141 the ClustalW format, but slightly more flexible. Any interleaved format with
16142 sequence name on each line will be correctly parsed:</span></p>
16143
16144 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
16145 mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
16146 background:#E6E6E6'>
16147
16148 <p class=examplefileCxSpFirst>&lt;empy line&gt; <span style='mso-tab-count:
16149 1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>[Facultative]n</p>
16150
16151 <p class=examplefileCxSpMiddle>&lt;line of text&gt; <span style='mso-tab-count:
16152 1'>&nbsp;&nbsp; </span>[Required]</p>
16153
16154 <p class=examplefileCxSpMiddle>&lt;line of text&gt;<span style='mso-tab-count:
16155 3'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>[Facultative]n</p>
16156
16157 <p class=examplefileCxSpMiddle>&lt;empty line&gt;<span style='mso-tab-count:
16158 3'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>[Required]</p>
16159
16160 <p class=examplefileCxSpMiddle>&lt;empty line&gt;<span style='mso-tab-count:
16161 3'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>[Facultative]n</p>
16162
16163 <p class=examplefileCxSpMiddle>&lt;seq1 name&gt;&lt;space&gt;&lt;seq1&gt;</p>
16164
16165 <p class=examplefileCxSpMiddle>&lt;seq2 name&gt;&lt;space&gt;&lt;seq2&gt;</p>
16166
16167 <p class=examplefileCxSpMiddle>&lt;seq3 name&gt;&lt;space&gt;&lt;seq3&gt;</p>
16168
16169 <p class=examplefileCxSpMiddle>&lt;empty line&gt;<span style='mso-tab-count:
16170 3'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>[Required]</p>
16171
16172 <p class=examplefileCxSpMiddle>&lt;empty line&gt;<span style='mso-tab-count:
16173 3'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>[Facultative]n</p>
16174
16175 <p class=examplefileCxSpMiddle>&lt;seq1 name&gt;&lt;space&gt;&lt;seq1&gt;</p>
16176
16177 <p class=examplefileCxSpMiddle>&lt;seq2 name&gt;&lt;space&gt;&lt;seq2&gt;</p>
16178
16179 <p class=examplefileCxSpMiddle>&lt;seq3 name&gt;&lt;space&gt;&lt;seq3&gt;</p>
16180
16181 <p class=examplefileCxSpMiddle>&lt;empty line&gt;<span style='mso-tab-count:
16182 3'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>[Required]</p>
16183
16184 <p class=examplefileCxSpLast>&lt;empty line&gt;<span style='mso-tab-count:3'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>[Facultative]n</p>
16185
16186 </div>
16187
16188 <p class=MyNormal><span lang=AF>An empty line is a line that does NOT contain
16189 amino-acid. A line that contains the ClustalW annotation (.:*) is empty.</span></p>
16190
16191 <p class=MyNormal><span lang=AF>Spaces are forbidden in the name. When the
16192 alignment is being read, non character signs are ignored in the sequence field
16193 (such as numbers, annotation\85).</span></p>
16194
16195 <p class=Note><span style='mso-ansi-language:EN-US'>Note: a different number of
16196 lines in the different blocks will cause the program to crash or hang.<o:p></o:p></span></p>
16197
16198 <h2><a name="_Toc101065360"></a><a name="_Toc102494405"></a><a
16199 name="_Toc102494894"></a><a name="_Toc151732433"><span style='mso-bookmark:
16200 _Toc102494894'><span style='mso-bookmark:_Toc102494405'><span style='mso-bookmark:
16201 _Toc101065360'>Libraries</span></span></span></a></h2>
16202
16203 <h3><a name="_Toc102494406"></a><a name="_Toc102494895"></a><a
16204 name="_Toc151732434"><span style='mso-bookmark:_Toc102494895'><span
16205 style='mso-bookmark:_Toc102494406'>T-COFFEE_LIB_FORMAT_01</span></span></a></h3>
16206
16207 <p class=MyNormal><span lang=AF>This is currently the only supported format.</span></p>
16208
16209 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
16210 mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
16211 background:#E6E6E6'>
16212
16213 <p class=examplefileCxSpFirst>!&lt;space&gt; TC_LIB_FORMAT_01</p>
16214
16215 <p class=examplefileCxSpMiddle>&lt;nseq&gt;</p>
16216
16217 <p class=examplefileCxSpMiddle>&lt;seq1 name&gt; &lt;seq1 length&gt;
16218 &lt;seq1&gt;</p>
16219
16220 <p class=examplefileCxSpMiddle>&lt;seq2 name&gt; &lt;seq2 length&gt;
16221 &lt;seq2&gt;</p>
16222
16223 <p class=examplefileCxSpMiddle>&lt;seq3 name&gt; &lt;seq3 length&gt;
16224 &lt;seq3&gt;</p>
16225
16226 <p class=examplefileCxSpMiddle>!Comment</p>
16227
16228 <p class=examplefileCxSpMiddle>(!Comment)n</p>
16229
16230 <p class=examplefileCxSpMiddle>#Si1 Si2</p>
16231
16232 <p class=examplefileCxSpMiddle>Ri1 Ri2 V1 (V2, V3)</p>
16233
16234 <p class=examplefileCxSpMiddle>#1 2</p>
16235
16236 <p class=examplefileCxSpMiddle>12 13 99 (12/0 vs 13/1, weight 99)</p>
16237
16238 <p class=examplefileCxSpMiddle>12 14 70</p>
16239
16240 <p class=examplefileCxSpMiddle>15 16 56</p>
16241
16242 <p class=examplefileCxSpMiddle>#1 3</p>
16243
16244 <p class=examplefileCxSpMiddle>12 13 99 </p>
16245
16246 <p class=examplefileCxSpMiddle>12 14 70</p>
16247
16248 <p class=examplefileCxSpMiddle>15 16 56</p>
16249
16250 <p class=examplefileCxSpLast>!&lt;space&gt;SEQ_1_TO_N </p>
16251
16252 </div>
16253
16254 <p class=MyNormal><span lang=AF>Si1: index of Sequence 1</span></p>
16255
16256 <p class=MyNormal><span lang=AF>Ri1: index of residue 1 in seq1</span></p>
16257
16258 <p class=MyNormal><span lang=AF>V1: Integer Value: Weight</span></p>
16259
16260 <p class=MyNormal><span lang=AF>V2, V3: optional values</span></p>
16261
16262 <p class=Note><span style='mso-ansi-language:EN-US'>Note 1: There is a space
16263 between the ! And SEQ_1_TO_N<o:p></o:p></span></p>
16264
16265 <p class=Note><span style='mso-ansi-language:EN-US'>Note 2: The last line (!
16266 SEQ_1_TO_N) indicates that:<o:p></o:p></span></p>
16267
16268 <p class=MyNormal><span lang=AF>Sequences and residues are numbered from 1 to
16269 N, unless the token SEQ_1_TO_N is omitted, in which case the sequences are
16270 numbered from 0 to N-1, and residues are from 1 to N.</span></p>
16271
16272 <p class=MyNormal><span lang=AF>Residues do not need to be sorted, and neither
16273 do the sequences. The same pair can appear several times in the library. For
16274 instance, the following file would be legal:</span></p>
16275
16276 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
16277 mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
16278 background:#E6E6E6'>
16279
16280 <p class=examplefileCxSpFirst>#1 2</p>
16281
16282 <p class=examplefileCxSpMiddle>12 13 99</p>
16283
16284 <p class=examplefileCxSpMiddle>#1 2</p>
16285
16286 <p class=examplefileCxSpMiddle>15 16 99 </p>
16287
16288 <p class=examplefileCxSpMiddle>#1 1</p>
16289
16290 <p class=examplefileCxSpLast>12 14 70</p>
16291
16292 </div>
16293
16294 <p class=MyNormal><a name="_Toc102494407"></a><a name="_Toc102494896"><span
16295 style='mso-bookmark:_Toc102494407'><span lang=AF>It is also poosible to declare
16296 ranges of resdues rather than single pairs. For instance, the following:</span></span></a></p>
16297
16298 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
16299 mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
16300 background:#E6E6E6'>
16301
16302 <p class=examplefileCxSpFirst><span style='mso-bookmark:_Toc102494896'><span
16303 style='mso-bookmark:_Toc102494407'>#0 1</span></span></p>
16304
16305 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494896'><span
16306 style='mso-bookmark:_Toc102494407'>+BLOCK+<span style="mso-spacerun:
16307 yes">&nbsp; </span>10 12 14 99</span></span></p>
16308
16309 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494896'><span
16310 style='mso-bookmark:_Toc102494407'>+BLOCK+<span style="mso-spacerun:
16311 yes">&nbsp; </span>15 30 40 99</span></span></p>
16312
16313 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494896'><span
16314 style='mso-bookmark:_Toc102494407'>#0 2</span></span></p>
16315
16316 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494896'><span
16317 style='mso-bookmark:_Toc102494407'>15 16 99 </span></span></p>
16318
16319 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc102494896'><span
16320 style='mso-bookmark:_Toc102494407'>#0 1</span></span></p>
16321
16322 <p class=examplefileCxSpLast><span style='mso-bookmark:_Toc102494896'><span
16323 style='mso-bookmark:_Toc102494407'>12 14 70</span></span></p>
16324
16325 </div>
16326
16327 <p class=MyNormal><span style='mso-bookmark:_Toc102494896'><span
16328 style='mso-bookmark:_Toc102494407'><span lang=AF>The first statement BLOCK
16329 declares a BLOCK of length 10, that starts on position 12 of sequence 1 and
16330 position 14 of sequence 2 and where each pair of residues within the block has
16331 a score of 99. The second BLOCK starts on residue 30 of 1, residue 40 of 2 and
16332 extends for 15 residues.</span></span></span></p>
16333
16334 <p class=MyNormal><span style='mso-bookmark:_Toc102494896'><span
16335 style='mso-bookmark:_Toc102494407'><span lang=AF>Blocks can overalp and be
16336 incompatible with one another, just like single constraints.</span></span></span></p>
16337
16338 <p class=MyNormal><span style='mso-bookmark:_Toc102494896'><span
16339 style='mso-bookmark:_Toc102494407'><span lang=AF><span style="mso-spacerun:
16340 yes">&nbsp; </span></span></span></span></p>
16341
16342 <h3><span style='mso-bookmark:_Toc102494896'><span style='mso-bookmark:_Toc102494407'><a
16343 name="_Toc151732435">T-COFFEE_LIB_FORMAT_02</a></span></span></h3>
16344
16345 <p class=MyNormal><span lang=AF>A simpler format is being developed, however it
16346 is not yet fully supported and is only mentioned here for development purpose.</span></p>
16347
16348 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
16349 mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
16350 background:#E6E6E6'>
16351
16352 <p class=examplefileCxSpFirst>! TC_LIB_FORMAT_02</p>
16353
16354 <p class=examplefileCxSpMiddle>#S1 SEQ1 [OPTIONAL]</p>
16355
16356 <p class=examplefileCxSpMiddle>#S2 SEQ2 [OPTIONAL]</p>
16357
16358 <p class=examplefileCxSpMiddle>...</p>
16359
16360 <p class=examplefileCxSpMiddle>!comment [OPTIONAL]</p>
16361
16362 <p class=examplefileCxSpMiddle>S1 R1 Ri1 S2 R2 Ri2 V1 (V2 V3)</p>
16363
16364 <p class=examplefileCxSpMiddle>=&gt; N R1 Ri1 S2 R2 Ri2 V1 (V2 V3)</p>
16365
16366 <p class=examplefileCxSpLast>...</p>
16367
16368 </div>
16369
16370 <p class=MyNormal><span lang=AF>S1, S2: name of sequence 1 and 2</span></p>
16371
16372 <p class=MyNormal><span lang=AF>SEQ1: sequence of S1</span></p>
16373
16374 <p class=MyNormal><span lang=AF>Ri1, Ri2: index of the residues in their
16375 respective sequence</span></p>
16376
16377 <p class=MyNormal><span lang=AF>R1, R2: Residue type</span></p>
16378
16379 <p class=MyNormal><span lang=AF>V1, V2, V3: integer Values (V2 and V3 are
16380 optional)</span></p>
16381
16382 <p class=MyNormal><span lang=AF>Value1, Value 2 and Value3 are optional.</span></p>
16383
16384 <h2><a name="_Toc101065361"></a><a name="_Toc102494408"></a><a
16385 name="_Toc102494897"></a><a name="_Toc151732436"><span style='mso-bookmark:
16386 _Toc102494897'><span style='mso-bookmark:_Toc102494408'><span style='mso-bookmark:
16387 _Toc101065361'>Library List</span></span></span></a><span style='mso-bookmark:
16388 _Toc101065361'></span></h2>
16389
16390 <p class=MyNormal><span style='mso-bookmark:_Toc101065361'><span lang=AF>These
16391 are lists of pairs of sequences that must be used to compute a library. The
16392 format is:</span></span></p>
16393
16394 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
16395 mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
16396 background:#E6E6E6'>
16397
16398 <p class=examplefileCxSpFirst><span style='mso-bookmark:_Toc101065361'>&lt;nseq&gt;
16399 &lt;S1&gt; &lt;S2&gt;</span></p>
16400
16401 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065361'>2 hamg2
16402 globav</span></p>
16403
16404 <p class=examplefileCxSpMiddle><span style='mso-bookmark:_Toc101065361'>3 hamgw
16405 hemog singa</span></p>
16406
16407 <p class=examplefileCxSpLast><span style='mso-bookmark:_Toc101065361'>...</span></p>
16408
16409 </div>
16410
16411 <h2><span style='mso-bookmark:_Toc101065361'><a name="_Toc102494409"></a><a
16412 name="_Toc102494898"></a><a name="_Toc151732437"><span style='mso-bookmark:
16413 _Toc102494898'><span style='mso-bookmark:_Toc102494409'>Substitution matrices.</span></span></a></span></h2>
16414
16415 <p class=MyNormal><span lang=AF>If the required substitution matrix is not
16416 available, write your own in a file using the following format:</span></p>
16417
16418 <h3><a name="_Toc101065362"></a><a name="_Toc102494410"></a><a
16419 name="_Toc102494899"></a><a name="_Toc151732438"><span style='mso-bookmark:
16420 _Toc102494899'><span style='mso-bookmark:_Toc102494410'><span style='mso-bookmark:
16421 _Toc101065362'>ClustalW Style</span> [Deprecated]</span></span></a></h3>
16422
16423 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
16424 mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
16425 background:#E6E6E6'>
16426
16427 <p class=examplefileCxSpFirst># CLUSTALW_MATRIX FORMAT</p>
16428
16429 <p class=examplefileCxSpMiddle>$</p>
16430
16431 <p class=examplefileCxSpMiddle>v1</p>
16432
16433 <p class=examplefileCxSpMiddle>v2 v3</p>
16434
16435 <p class=examplefileCxSpMiddle>v4 v5 v6</p>
16436
16437 <p class=examplefileCxSpMiddle>...</p>
16438
16439 <p class=examplefileCxSpLast>$</p>
16440
16441 </div>
16442
16443 <p class=MyNormal><span lang=AF>v1, v2... are integers, possibly negatives.</span></p>
16444
16445 <p class=MyNormal><span lang=AF>The order of the amino acids is:
16446 ABCDEFGHIKLMNQRSTVWXYZ, which means that v1 is the substitution value for A vs
16447 A, v2 for A vs B, v3 for B vs B, v4 for A vs C and so on.</span></p>
16448
16449 <h3><a name="_Toc101065363"></a><a name="_Toc102494411"></a><a
16450 name="_Toc102494900"></a><a name="_Toc151732439"><span style='mso-bookmark:
16451 _Toc102494900'><span style='mso-bookmark:_Toc102494411'><span style='mso-bookmark:
16452 _Toc101065363'>BLAST Format [Recommended]</span></span></span></a></h3>
16453
16454 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
16455 mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
16456 background:#E6E6E6'>
16457
16458 <p class=examplefileCxSpFirst># BLAST_MATRIX FORMAT</p>
16459
16460 <p class=examplefileCxSpMiddle># ALPHABET=AGCT</p>
16461
16462 <p class=examplefileCxSpMiddle><span style="mso-spacerun: yes">&nbsp;</span>A G
16463 C T</p>
16464
16465 <p class=examplefileCxSpMiddle>A 0 1 2 3</p>
16466
16467 <p class=examplefileCxSpMiddle>G 0 2 3 4</p>
16468
16469 <p class=examplefileCxSpMiddle>C 1 1 2 3</p>
16470
16471 <p class=examplefileCxSpLast>...</p>
16472
16473 </div>
16474
16475 <p class=MyNormal><span lang=AF>The alphabet can be freely defined</span></p>
16476
16477 <h2><a name="_Toc101065364"></a><a name="_Toc102494412"></a><a
16478 name="_Toc102494901"></a><a name="_Toc151732440"><span style='mso-bookmark:
16479 _Toc102494901'><span style='mso-bookmark:_Toc102494412'><span style='mso-bookmark:
16480 _Toc101065364'>Sequences Weights</span></span></span></a></h2>
16481
16482 <p class=MyNormal><span lang=AF>Create your own weight file, using the
16483 -seq_weight flag:</span></p>
16484
16485 <div style='mso-element:para-border-div;border:solid windowtext 1.0pt;
16486 mso-border-alt:solid windowtext .5pt;padding:1.0pt 4.0pt 1.0pt 4.0pt;
16487 background:#E6E6E6'>
16488
16489 <p class=examplefileCxSpFirst># SINGLE_SEQ_WEIGHT_FORMAT_01</p>
16490
16491 <p class=examplefileCxSpMiddle>seq_name1 v1</p>
16492
16493 <p class=examplefileCxSpMiddle>seq_name2 v2</p>
16494
16495 <p class=examplefileCxSpLast>...</p>
16496
16497 </div>
16498
16499 <p class=MyNormal><span lang=AF>No duplicate allowed. Sequences not included in
16500 the set of sequences provided to t_coffee will be ignored. Order is free. V1 is
16501 a float. Un-weighted sequences will see their weight set to 1.</span></p>
16502
16503 <span lang=AF style='font-size:11.0pt;font-family:"Times New Roman";mso-fareast-font-family:
16504 "Times New Roman";mso-bidi-font-family:"Courier New";mso-ansi-language:AF;
16505 mso-fareast-language:EN-US'><br clear=ALL style='page-break-before:always'>
16506 </span>
16507
16508 <div style='mso-element:para-border-div;border:solid windowtext 3.0pt;
16509 padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#CCCCCC;margin-left:0cm;margin-right:
16510 4.25pt'>
16511
16512 <p class=ChapterTitle>Known Problems</p>
16513
16514 </div>
16515
16516 <p class=MyNormal><span lang=AF>1-Sensitivity to sequence order: It is
16517 difficult to implement a MSA algorithm totally insensitive to the order of
16518 input of the sequences. In t_coffee, robustness is increased by sorting the
16519 sequences alphabetically before aligning them. Beware that this can result in
16520 confusing output where sequences with similar name are unexpectedly close to
16521 one another in the final alignment.</span></p>
16522
16523 <p class=MyNormal><span lang=AF>2-Nucleotides sequences with long stretches of
16524 Ns will cause problems to lalign, especially when using Mocca. To avoid any
16525 problem, filter out these nucleotides before running mocca.</span></p>
16526
16527 <p class=MyNormal><span lang=AF>3-Stop codons are sometimes coded with '*' in
16528 protein sequences. This will cause the program to crash or hang. Please replace
16529 the '*' signs with an X.</span></p>
16530
16531 <p class=MyNormal><span lang=AF>4-Results can differ from one architecture to
16532 another, due rounding differences. This is caused by the tree estimation
16533 procedcure. If you want to make sure an alignment is reproducible, you should
16534 keep the associated dendrogram.</span></p>
16535
16536 <p class=MyNormal><span lang=AF>5-Deploying the program on a </span></p>
16537
16538 <div style='mso-element:para-border-div;border:solid windowtext 3.0pt;
16539 padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#CCCCCC;margin-left:0cm;margin-right:
16540 4.25pt'>
16541
16542 <p class=ChapterTitle>Technical Notes</p>
16543
16544 </div>
16545
16546 <p class=MyNormal><span lang=AF>These notes are only meant for internal
16547 development.</span></p>
16548
16549 <h2><a name="_Toc102494413"></a><a name="_Toc102494904"></a><a
16550 name="_Toc151732441"><span style='mso-bookmark:_Toc102494904'><span
16551 style='mso-bookmark:_Toc102494413'>Development</span></span></a></h2>
16552
16553 <p class=MyNormal><span lang=AF>The following examples are only meant for
16554 internal development, and are used to insure stability from release to release</span></p>
16555
16556 <h4><a name="_Toc151732442"><span lang=AF>profile2list</span></a></h4>
16557
16558 <p class=MyNormal><span lang=AF>prf1: profile containing one structure</span></p>
16559
16560 <p class=MyNormal><span lang=AF>prf2: profile containing one structure</span></p>
16561
16562 <p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>
16563
16564 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
16565 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
16566 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
16567 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
16568
16569 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT:
16570 t_coffee<span style="mso-spacerun: yes">&nbsp; </span>Rsample_profile1.aln,Rsample_profile2.aln
16571 -mode=3dcoffee -outfile=aligned_prf.aln</p>
16572
16573 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><o:p>&nbsp;</o:p></p>
16574
16575 </div>
16576
16577 <h3><a name="_Toc102494414"></a><a name="_Toc102494905"></a><a
16578 name="_Toc151732443"><span style='mso-bookmark:_Toc102494905'><span
16579 style='mso-bookmark:_Toc102494414'>Command Line List</span></span></a></h3>
16580
16581 <p class=MyNormal><span lang=AF>These command lines have been checked before
16582 every release (along with the other CL in this documentation:</span></p>
16583
16584 <p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>
16585
16586 <p class=MyNormal><span lang=AF>-external methods;</span></p>
16587
16588 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
16589 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
16590 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
16591 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
16592
16593 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'><span
16594 style='mso-tab-count:1'>&nbsp;&nbsp; </span>PROMPT: t_coffee sample_seq1.fasta
16595 &#8211;in=Mclustalw_pair,Mclustalw_msa,Mslow_pair &#8211;outfile=clustal_text</p>
16596
16597 </div>
16598
16599 <p class=MyNormal><span lang=AF>-fugue_client</span></p>
16600
16601 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
16602 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
16603 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
16604 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
16605
16606 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
16607 &#8211;in Ssample_seq5.fasta Pstruc4.pdb Mfugue_pair</p>
16608
16609 </div>
16610
16611 <p class=MyNormal><span lang=AF>-A list of command lines kindly provided by
16612 James Watson (used to crash the pg before version 3.40)</span></p>
16613
16614 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
16615 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
16616 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
16617 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
16618
16619 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
16620 -in Sseq.fas P2PTC Mfugue_pair</p>
16621
16622 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
16623 -in S2seqs.fas Mfugue_pair -template_file SELF_P_</p>
16624
16625 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee -mode
16626 3dcoffee -in Sseq.fas P2PTC</p>
16627
16628 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee -mode
16629 3dcoffee -in S2seqs.fas -template_file SELF_P_</p>
16630
16631 </div>
16632
16633 <p class=MyNormal><span lang=AF>-A list of command lines that crashed the
16634 program before 3.81</span></p>
16635
16636 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
16637 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
16638 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
16639 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
16640
16641 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
16642 sample_seq6.fasta &#8211;in Mfast_pair Msap_pair Mfugue_pair
16643 &#8211;template_file template_file6.template </p>
16644
16645 </div>
16646
16647 <p class=MsoBodyText><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>-A
16648 command line to read \93relaxed\94 pdb files...</p>
16649
16650 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
16651 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
16652 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
16653 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
16654
16655 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
16656 &#8211;in Msap_pair Ssample_seq7.fasta &#8211;template_file template_file7.template
16657 &#8211;weight 1001 &#8211;out_lib test_lib7.tc_lib &#8211;lib_only </p>
16658
16659 </div>
16660
16661 <p class=MsoBodyText><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>-Parsing
16662 of MARNA libraries</p>
16663
16664 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
16665 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
16666 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
16667 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
16668
16669 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
16670 &#8211;in Lmarna.tc_lib &#8211;outfile maran.test</p>
16671
16672 </div>
16673
16674 <p class=MsoBodyText><span style='mso-tab-count:1'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>-Parsing
16675 of long sequence lines:</p>
16676
16677 <div style='mso-element:para-border-div;border-top:solid black 1.0pt;
16678 border-left:none;border-bottom:solid black 1.0pt;border-right:none;mso-border-top-alt:
16679 solid black .25pt;mso-border-bottom-alt:solid black .25pt;padding:10.0pt 0cm 10.0pt 0cm;
16680 background:#FFFFCC;margin-left:2.0cm;margin-right:0cm'>
16681
16682 <p class=MyExample style='margin-left:0cm;background:#FFFFCC'>PROMPT: t_coffee
16683 &#8211;in Asample_aln5.aln &#8211;outfile test.aln</p>
16684
16685 </div>
16686
16687 <p class=MsoBodyText><o:p>&nbsp;</o:p></p>
16688
16689 <div style='mso-element:para-border-div;border:solid windowtext 3.0pt;
16690 padding:1.0pt 4.0pt 1.0pt 4.0pt;background:#CCCCCC;margin-left:0cm;margin-right:
16691 4.25pt'>
16692
16693 <p class=ChapterTitle><a name="_Toc102494906">To D</a>o\85</p>
16694
16695 </div>
16696
16697 <p class=MyNormal><span lang=AF>-implement UPGMA tree computation</span></p>
16698
16699 <p class=MyNormal><span lang=AF>-implement seq2dpa_tree</span></p>
16700
16701 <p class=MyNormal><span lang=AF>-debug dpa</span></p>
16702
16703 <p class=MyNormal><span lang=AF>-Reconciliate sequences and template when
16704 reading the template</span></p>
16705
16706 <p class=MyNormal><span lang=AF>-Add the server command lines to the checking
16707 procedure</span></p>
16708
16709 <p class=MyNormal><span lang=AF><o:p>&nbsp;</o:p></span></p>
16710
16711 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
16712
16713 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
16714
16715 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
16716
16717 <p class=MsoBodyText><o:p>&nbsp;</o:p></p>
16718
16719 </div>
16720
16721 </body>
16722
16723 </html>