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667 mso-para-margin-bottom:.0001pt;
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668 mso-pagination:widow-orphan;
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670 font-family:"Times New Roman";}
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672 {mso-style-name:"Table Grid";
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673 mso-tstyle-rowband-size:0;
\r
674 mso-tstyle-colband-size:0;
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675 border:solid windowtext 1.0pt;
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676 mso-border-alt:solid windowtext .5pt;
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677 mso-padding-alt:0in 5.4pt 0in 5.4pt;
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678 mso-border-insideh:.5pt solid windowtext;
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679 mso-border-insidev:.5pt solid windowtext;
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681 mso-para-margin-bottom:.0001pt;
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684 font-family:"Times New Roman";}
\r
689 <body lang=EN-US link=blue vlink=purple style='tab-interval:.25in'>
\r
691 <div class=Section1>
\r
693 <p class=MsoNormal><o:p> </o:p></p>
\r
695 <p class=MsoNormal><o:p> </o:p></p>
\r
697 <p class=MsoNormal><o:p> </o:p></p>
\r
699 <p class=MsoNormal><o:p> </o:p></p>
\r
701 <p class=MsoNormal align=right style='text-align:right'><span style='font-size:
\r
702 24.0pt;font-family:"Arial Black"'>MUSCLE User Guide<o:p></o:p></span></p>
\r
704 <p class=MsoNormal align=right style='text-align:right'><u> <o:p></o:p></u></p>
\r
706 <p class=MsoNormal align=right style='text-align:right'><b><span
\r
707 style='font-family:Arial'><o:p> </o:p></span></b></p>
\r
709 <p class=MsoNormal><span style='font-family:Arial'><o:p> </o:p></span></p>
\r
711 <p class=MsoNormal><span style='font-family:Arial'><o:p> </o:p></span></p>
\r
713 <p class=MsoNormal><span style='font-family:Arial'><o:p> </o:p></span></p>
\r
715 <p class=MsoNormal><span style='font-family:Arial'><o:p> </o:p></span></p>
\r
717 <p class=MsoNormal><span style='font-family:Arial'><o:p> </o:p></span></p>
\r
719 <p class=MsoNormal><span style='font-family:Arial'>Multiple sequence comparison
\r
720 by log-expectation<o:p></o:p></span></p>
\r
722 <p class=MsoNormal><span class=GramE><span style='font-family:Arial'>by</span></span><span
\r
723 style='font-family:Arial'> Robert C. Edgar<o:p></o:p></span></p>
\r
725 <p class=MsoNormal><span style='font-family:Arial'><o:p> </o:p></span></p>
\r
727 <p class=MsoNormal><span style='font-family:Arial'>Version 3.6<o:p></o:p></span></p>
\r
729 <p class=MsoNormal><span style='font-family:Arial'>September 2005<o:p></o:p></span></p>
\r
731 <p class=MsoNormal><span style='font-family:Arial'><o:p> </o:p></span></p>
\r
733 <p class=MsoNormal><span style='font-family:Arial'><o:p> </o:p></span></p>
\r
735 <p class=MsoNormal><span style='font-family:Arial'><a
\r
736 href="http://www.drive5.com/muscle">http://www.drive5.com/muscle</a><o:p></o:p></span></p>
\r
738 <p class=MsoNormal><span class=GramE><span style='font-family:Arial'>email</span></span><span
\r
739 style='font-family:Arial'>: muscle (at) drive5.com<o:p></o:p></span></p>
\r
741 <p class=MsoNormal><span style='font-family:Arial'><o:p> </o:p></span></p>
\r
743 <p class=MsoNormal><span style='font-family:Arial'>MUSCLE is updated regularly.
\r
744 Send me an e-mail if you would like to be notified of new releases.<o:p></o:p></span></p>
\r
746 <p class=MsoNormal><span style='font-family:Arial'><span
\r
747 style='mso-spacerun:yes'>Â </span><o:p></o:p></span></p>
\r
749 <p class=MsoNormal><span style='font-family:Arial'><o:p> </o:p></span></p>
\r
751 <p class=MsoNormal><i><span style='font-family:Arial'>Citation:<o:p></o:p></span></i></p>
\r
753 <p class=MsoNormal><span style='font-family:Arial'><o:p> </o:p></span></p>
\r
755 <p class=MsoNormal><span style='font-family:Arial'><a
\r
756 href="http://nar.oupjournals.org/cgi/content/full/32/5/1792?ijkey=48Nmt1tta0fMg&keytype=ref">Edgar,
\r
757 Robert C. (2004), MUSCLE: multiple sequence alignment with high accuracy and
\r
758 high throughput, <i>Nucleic Acids Research</i> <b>32</b>(5), 1792-97</a>.<o:p></o:p></span></p>
\r
760 <p class=MsoNormal><span style='font-family:Arial'><o:p> </o:p></span></p>
\r
762 <p class=MsoNormal><i><span style='font-family:Arial'>For a complete
\r
763 description of the algorithm, see also:<o:p></o:p></span></i></p>
\r
765 <p class=MsoNormal><span style='font-family:Arial'><o:p> </o:p></span></p>
\r
767 <p class=MsoNormal><span style='font-family:Arial'><a
\r
768 href="http://www.biomedcentral.com/1471-2105/5/113">Edgar, Robert C (2004), <span
\r
769 style='mso-bidi-font-weight:bold'>MUSCLE: a multiple sequence alignment method
\r
770 with reduced time and <span class=GramE>space</span> complexity</span>. <i
\r
771 style='mso-bidi-font-style:normal'>BMC Bioinformatics</i>, <b style='mso-bidi-font-weight:
\r
772 normal'>5</b>(1):113</a>.<br clear=all style='page-break-before:always'>
\r
773 </span><b><span style='font-size:16.0pt;font-family:Arial'>Table of Contents<o:p></o:p></span></b></p>
\r
775 <p class=MsoToc1 style='tab-stops:right dotted 431.5pt'><!--[if supportFields]><span
\r
776 style='font-family:Arial'><span style='mso-element:field-begin'></span><span
\r
777 style='mso-spacerun:yes'>Â </span>TOC \o "1-3" \h \z \u <span
\r
778 style='mso-element:field-separator'></span></span><![endif]--><span
\r
779 class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954755">1
\r
780 Introduction<span style='color:windowtext;display:none;mso-hide:screen;
\r
781 text-decoration:none;text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
782 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
783 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
784 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
785 text-underline:none'> PAGEREF _Toc113954755 \h </span><span style='color:windowtext;
\r
786 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
787 style='mso-element:field-separator'></span></span><![endif]--><span
\r
788 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
789 text-underline:none'>3</span><span style='color:windowtext;display:none;
\r
790 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
791 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700350035000000</w:data>
\r
792 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
793 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
794 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
795 style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>
\r
797 <p class=MsoToc1 style='tab-stops:right dotted 431.5pt'><span
\r
798 class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954756">2
\r
799 Quick Start<span style='color:windowtext;display:none;mso-hide:screen;
\r
800 text-decoration:none;text-underline:none'><span style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span
\r
801 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
802 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
803 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
804 text-underline:none'> PAGEREF _Toc113954756 \h </span><span style='color:windowtext;
\r
805 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
806 style='mso-element:field-separator'></span></span><![endif]--><span
\r
807 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
808 text-underline:none'>3</span><span style='color:windowtext;display:none;
\r
809 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
810 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700350036000000</w:data>
\r
811 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
812 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
813 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
814 style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>
\r
816 <p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span
\r
817 class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954757">2.1
\r
818 Installation<span style='color:windowtext;display:none;mso-hide:screen;
\r
819 text-decoration:none;text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
820 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
821 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
822 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
823 text-underline:none'> PAGEREF _Toc113954757 \h </span><span style='color:windowtext;
\r
824 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
825 style='mso-element:field-separator'></span></span><![endif]--><span
\r
826 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
827 text-underline:none'>3</span><span style='color:windowtext;display:none;
\r
828 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
829 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700350037000000</w:data>
\r
830 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
831 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
832 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
833 style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>
\r
835 <p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span
\r
836 class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954758">2.2
\r
837 Making an alignment<span style='color:windowtext;display:none;mso-hide:screen;
\r
838 text-decoration:none;text-underline:none'><span style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span
\r
839 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
840 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
841 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
842 text-underline:none'> PAGEREF _Toc113954758 \h </span><span style='color:windowtext;
\r
843 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
844 style='mso-element:field-separator'></span></span><![endif]--><span
\r
845 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
846 text-underline:none'>3</span><span style='color:windowtext;display:none;
\r
847 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
848 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700350038000000</w:data>
\r
849 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
850 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
851 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
852 style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>
\r
854 <p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span
\r
855 class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954759">2.3
\r
856 Large alignments<span style='color:windowtext;display:none;mso-hide:screen;
\r
857 text-decoration:none;text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
858 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
859 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
860 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
861 text-underline:none'> PAGEREF _Toc113954759 \h </span><span style='color:windowtext;
\r
862 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
863 style='mso-element:field-separator'></span></span><![endif]--><span
\r
864 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
865 text-underline:none'>3</span><span style='color:windowtext;display:none;
\r
866 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
867 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700350039000000</w:data>
\r
868 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
869 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
870 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
871 style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>
\r
873 <p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span
\r
874 class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954760">2.4
\r
875 Faster speed<span style='color:windowtext;display:none;mso-hide:screen;
\r
876 text-decoration:none;text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
877 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
878 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
879 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
880 text-underline:none'> PAGEREF _Toc113954760 \h </span><span style='color:windowtext;
\r
881 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
882 style='mso-element:field-separator'></span></span><![endif]--><span
\r
883 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
884 text-underline:none'>4</span><span style='color:windowtext;display:none;
\r
885 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
886 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700360030000000</w:data>
\r
887 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
888 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
889 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
890 style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>
\r
892 <p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span
\r
893 class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954761">2.5
\r
894 Huge alignments<span style='color:windowtext;display:none;mso-hide:screen;
\r
895 text-decoration:none;text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
896 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
897 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
898 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
899 text-underline:none'> PAGEREF _Toc113954761 \h </span><span style='color:windowtext;
\r
900 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
901 style='mso-element:field-separator'></span></span><![endif]--><span
\r
902 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
903 text-underline:none'>4</span><span style='color:windowtext;display:none;
\r
904 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
905 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700360031000000</w:data>
\r
906 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
907 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
908 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
909 style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>
\r
911 <p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span
\r
912 class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954762">2.6
\r
913 Accuracy: caveat emptor<span style='color:windowtext;display:none;mso-hide:
\r
914 screen;text-decoration:none;text-underline:none'><span style='mso-tab-count:
\r
915 1 dotted'> </span></span><!--[if supportFields]><span style='color:windowtext;
\r
916 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
917 style='mso-element:field-begin'></span></span><span style='color:windowtext;
\r
918 display:none;mso-hide:screen;text-decoration:none;text-underline:none'> PAGEREF
\r
919 _Toc113954762 \h </span><span style='color:windowtext;display:none;mso-hide:
\r
920 screen;text-decoration:none;text-underline:none'><span style='mso-element:field-separator'></span></span><![endif]--><span
\r
921 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
922 text-underline:none'>4</span><span style='color:windowtext;display:none;
\r
923 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
924 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700360032000000</w:data>
\r
925 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
926 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
927 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
928 style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>
\r
930 <p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span
\r
931 class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954763">2.7
\r
932 Pipelining<span style='color:windowtext;display:none;mso-hide:screen;
\r
933 text-decoration:none;text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
934 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
935 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
936 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
937 text-underline:none'> PAGEREF _Toc113954763 \h </span><span style='color:windowtext;
\r
938 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
939 style='mso-element:field-separator'></span></span><![endif]--><span
\r
940 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
941 text-underline:none'>4</span><span style='color:windowtext;display:none;
\r
942 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
943 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700360033000000</w:data>
\r
944 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
945 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
946 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
947 style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>
\r
949 <p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span
\r
950 class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954764">2.8
\r
951 Refining an existing alignment<span style='color:windowtext;display:none;
\r
952 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
953 style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span
\r
954 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
955 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
956 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
957 text-underline:none'> PAGEREF _Toc113954764 \h </span><span style='color:windowtext;
\r
958 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
959 style='mso-element:field-separator'></span></span><![endif]--><span
\r
960 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
961 text-underline:none'>4</span><span style='color:windowtext;display:none;
\r
962 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
963 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700360034000000</w:data>
\r
964 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
965 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
966 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
967 style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>
\r
969 <p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span
\r
970 class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954765">2.9
\r
971 Using a pre-computed guide tree<span style='color:windowtext;display:none;
\r
972 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
973 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
974 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
975 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
976 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
977 text-underline:none'> PAGEREF _Toc113954765 \h </span><span style='color:windowtext;
\r
978 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
979 style='mso-element:field-separator'></span></span><![endif]--><span
\r
980 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
981 text-underline:none'>4</span><span style='color:windowtext;display:none;
\r
982 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
983 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700360035000000</w:data>
\r
984 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
985 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
986 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
987 style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>
\r
989 <p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span
\r
990 class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954766">2.10
\r
991 Profile-profile alignment<span style='color:windowtext;display:none;mso-hide:
\r
992 screen;text-decoration:none;text-underline:none'><span style='mso-tab-count:
\r
993 1 dotted'> </span></span><!--[if supportFields]><span style='color:windowtext;
\r
994 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
995 style='mso-element:field-begin'></span></span><span style='color:windowtext;
\r
996 display:none;mso-hide:screen;text-decoration:none;text-underline:none'> PAGEREF
\r
997 _Toc113954766 \h </span><span style='color:windowtext;display:none;mso-hide:
\r
998 screen;text-decoration:none;text-underline:none'><span style='mso-element:field-separator'></span></span><![endif]--><span
\r
999 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1000 text-underline:none'>5</span><span style='color:windowtext;display:none;
\r
1001 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
1002 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700360036000000</w:data>
\r
1003 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
1004 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
1005 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
1006 style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>
\r
1008 <p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span
\r
1009 class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954767">2.11
\r
1010 Adding sequences to an existing alignment<span style='color:windowtext;
\r
1011 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
1012 style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span
\r
1013 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1014 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
1015 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1016 text-underline:none'> PAGEREF _Toc113954767 \h </span><span style='color:windowtext;
\r
1017 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
1018 style='mso-element:field-separator'></span></span><![endif]--><span
\r
1019 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1020 text-underline:none'>5</span><span style='color:windowtext;display:none;
\r
1021 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
1022 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700360037000000</w:data>
\r
1023 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
1024 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
1025 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
1026 style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>
\r
1028 <p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span
\r
1029 class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954768">2.12
\r
1030 Sequence clustering<span style='color:windowtext;display:none;mso-hide:screen;
\r
1031 text-decoration:none;text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
1032 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1033 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
1034 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1035 text-underline:none'> PAGEREF _Toc113954768 \h </span><span style='color:windowtext;
\r
1036 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
1037 style='mso-element:field-separator'></span></span><![endif]--><span
\r
1038 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1039 text-underline:none'>5</span><span style='color:windowtext;display:none;
\r
1040 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
1041 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700360038000000</w:data>
\r
1042 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
1043 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
1044 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
1045 style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>
\r
1047 <p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span
\r
1048 class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954769">2.13
\r
1049 Specifying a substitution matrix<span style='color:windowtext;display:none;
\r
1050 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
1051 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
1052 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1053 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
1054 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1055 text-underline:none'> PAGEREF _Toc113954769 \h </span><span style='color:windowtext;
\r
1056 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
1057 style='mso-element:field-separator'></span></span><![endif]--><span
\r
1058 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1059 text-underline:none'>6</span><span style='color:windowtext;display:none;
\r
1060 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
1061 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700360039000000</w:data>
\r
1062 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
1063 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
1064 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
1065 style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>
\r
1067 <p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span
\r
1068 class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954770">2.14
\r
1069 Refining a long alignment<span style='color:windowtext;display:none;mso-hide:
\r
1070 screen;text-decoration:none;text-underline:none'><span style='mso-tab-count:
\r
1071 1 dotted'> </span></span><!--[if supportFields]><span style='color:windowtext;
\r
1072 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
1073 style='mso-element:field-begin'></span></span><span style='color:windowtext;
\r
1074 display:none;mso-hide:screen;text-decoration:none;text-underline:none'> PAGEREF
\r
1075 _Toc113954770 \h </span><span style='color:windowtext;display:none;mso-hide:
\r
1076 screen;text-decoration:none;text-underline:none'><span style='mso-element:field-separator'></span></span><![endif]--><span
\r
1077 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1078 text-underline:none'>6</span><span style='color:windowtext;display:none;
\r
1079 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
1080 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700370030000000</w:data>
\r
1081 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
1082 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
1083 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
1084 style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>
\r
1086 <p class=MsoToc1 style='tab-stops:right dotted 431.5pt'><span
\r
1087 class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954771">3
\r
1088 File Formats<span style='color:windowtext;display:none;mso-hide:screen;
\r
1089 text-decoration:none;text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
1090 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1091 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
1092 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1093 text-underline:none'> PAGEREF _Toc113954771 \h </span><span style='color:windowtext;
\r
1094 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
1095 style='mso-element:field-separator'></span></span><![endif]--><span
\r
1096 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1097 text-underline:none'>6</span><span style='color:windowtext;display:none;
\r
1098 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
1099 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700370031000000</w:data>
\r
1100 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
1101 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
1102 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
1103 style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>
\r
1105 <p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span
\r
1106 class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954772">3.1
\r
1107 Input files<span style='color:windowtext;display:none;mso-hide:screen;
\r
1108 text-decoration:none;text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
1109 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1110 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
1111 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1112 text-underline:none'> PAGEREF _Toc113954772 \h </span><span style='color:windowtext;
\r
1113 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
1114 style='mso-element:field-separator'></span></span><![endif]--><span
\r
1115 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1116 text-underline:none'>6</span><span style='color:windowtext;display:none;
\r
1117 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
1118 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700370032000000</w:data>
\r
1119 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
1120 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
1121 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
1122 style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>
\r
1124 <p class=MsoToc3 style='tab-stops:right dotted 431.5pt'><span
\r
1125 class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954773">3.1.1
\r
1126 Amino acid sequences<span style='color:windowtext;display:none;mso-hide:screen;
\r
1127 text-decoration:none;text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
1128 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1129 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
1130 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1131 text-underline:none'> PAGEREF _Toc113954773 \h </span><span style='color:windowtext;
\r
1132 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
1133 style='mso-element:field-separator'></span></span><![endif]--><span
\r
1134 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1135 text-underline:none'>6</span><span style='color:windowtext;display:none;
\r
1136 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
1137 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700370033000000</w:data>
\r
1138 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
1139 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
1140 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
1141 style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>
\r
1143 <p class=MsoToc3 style='tab-stops:right dotted 431.5pt'><span
\r
1144 class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954774">3.1.2
\r
1145 Nucleotide sequences<span style='color:windowtext;display:none;mso-hide:screen;
\r
1146 text-decoration:none;text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
1147 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1148 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
1149 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1150 text-underline:none'> PAGEREF _Toc113954774 \h </span><span style='color:windowtext;
\r
1151 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
1152 style='mso-element:field-separator'></span></span><![endif]--><span
\r
1153 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1154 text-underline:none'>6</span><span style='color:windowtext;display:none;
\r
1155 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
1156 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700370034000000</w:data>
\r
1157 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
1158 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
1159 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
1160 style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>
\r
1162 <p class=MsoToc3 style='tab-stops:right dotted 431.5pt'><span
\r
1163 class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954775">3.1.3
\r
1164 Determining sequence type<span style='color:windowtext;display:none;mso-hide:
\r
1165 screen;text-decoration:none;text-underline:none'><span style='mso-tab-count:
\r
1166 1 dotted'>. </span></span><!--[if supportFields]><span style='color:windowtext;
\r
1167 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
1168 style='mso-element:field-begin'></span></span><span style='color:windowtext;
\r
1169 display:none;mso-hide:screen;text-decoration:none;text-underline:none'> PAGEREF
\r
1170 _Toc113954775 \h </span><span style='color:windowtext;display:none;mso-hide:
\r
1171 screen;text-decoration:none;text-underline:none'><span style='mso-element:field-separator'></span></span><![endif]--><span
\r
1172 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1173 text-underline:none'>7</span><span style='color:windowtext;display:none;
\r
1174 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
1175 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700370035000000</w:data>
\r
1176 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
1177 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
1178 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
1179 style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>
\r
1181 <p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span
\r
1182 class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954776">3.2
\r
1183 Output files<span style='color:windowtext;display:none;mso-hide:screen;
\r
1184 text-decoration:none;text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
1185 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1186 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
1187 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1188 text-underline:none'> PAGEREF _Toc113954776 \h </span><span style='color:windowtext;
\r
1189 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
1190 style='mso-element:field-separator'></span></span><![endif]--><span
\r
1191 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1192 text-underline:none'>7</span><span style='color:windowtext;display:none;
\r
1193 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
1194 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700370036000000</w:data>
\r
1195 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
1196 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
1197 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
1198 style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>
\r
1200 <p class=MsoToc3 style='tab-stops:right dotted 431.5pt'><span
\r
1201 class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954777">3.2.1
\r
1202 Sequence grouping<span style='color:windowtext;display:none;mso-hide:screen;
\r
1203 text-decoration:none;text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
1204 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1205 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
1206 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1207 text-underline:none'> PAGEREF _Toc113954777 \h </span><span style='color:windowtext;
\r
1208 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
1209 style='mso-element:field-separator'></span></span><![endif]--><span
\r
1210 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1211 text-underline:none'>7</span><span style='color:windowtext;display:none;
\r
1212 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
1213 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700370037000000</w:data>
\r
1214 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
1215 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
1216 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
1217 style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>
\r
1219 <p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span
\r
1220 class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954778">3.3
\r
1221 CLUSTALW format<span style='color:windowtext;display:none;mso-hide:screen;
\r
1222 text-decoration:none;text-underline:none'><span style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span
\r
1223 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1224 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
1225 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1226 text-underline:none'> PAGEREF _Toc113954778 \h </span><span style='color:windowtext;
\r
1227 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
1228 style='mso-element:field-separator'></span></span><![endif]--><span
\r
1229 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1230 text-underline:none'>7</span><span style='color:windowtext;display:none;
\r
1231 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
1232 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700370038000000</w:data>
\r
1233 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
1234 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
1235 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
1236 style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>
\r
1238 <p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span
\r
1239 class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954779">3.4
\r
1240 MSF format<span style='color:windowtext;display:none;mso-hide:screen;
\r
1241 text-decoration:none;text-underline:none'><span style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span
\r
1242 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1243 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
1244 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1245 text-underline:none'> PAGEREF _Toc113954779 \h </span><span style='color:windowtext;
\r
1246 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
1247 style='mso-element:field-separator'></span></span><![endif]--><span
\r
1248 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1249 text-underline:none'>7</span><span style='color:windowtext;display:none;
\r
1250 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
1251 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700370039000000</w:data>
\r
1252 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
1253 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
1254 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
1255 style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>
\r
1257 <p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span
\r
1258 class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954780">3.5
\r
1259 HTML format<span style='color:windowtext;display:none;mso-hide:screen;
\r
1260 text-decoration:none;text-underline:none'><span style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span
\r
1261 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1262 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
1263 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1264 text-underline:none'> PAGEREF _Toc113954780 \h </span><span style='color:windowtext;
\r
1265 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
1266 style='mso-element:field-separator'></span></span><![endif]--><span
\r
1267 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1268 text-underline:none'>8</span><span style='color:windowtext;display:none;
\r
1269 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
1270 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700380030000000</w:data>
\r
1271 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
1272 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
1273 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
1274 style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>
\r
1276 <p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span
\r
1277 class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954781">3.6
\r
1278 Phylip format<span style='color:windowtext;display:none;mso-hide:screen;
\r
1279 text-decoration:none;text-underline:none'><span style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span
\r
1280 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1281 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
1282 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1283 text-underline:none'> PAGEREF _Toc113954781 \h </span><span style='color:windowtext;
\r
1284 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
1285 style='mso-element:field-separator'></span></span><![endif]--><span
\r
1286 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1287 text-underline:none'>8</span><span style='color:windowtext;display:none;
\r
1288 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
1289 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700380031000000</w:data>
\r
1290 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
1291 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
1292 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
1293 style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>
\r
1295 <p class=MsoToc1 style='tab-stops:right dotted 431.5pt'><span
\r
1296 class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954782">4
\r
1297 Using MUSCLE<span style='color:windowtext;display:none;mso-hide:screen;
\r
1298 text-decoration:none;text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
1299 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1300 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
1301 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1302 text-underline:none'> PAGEREF _Toc113954782 \h </span><span style='color:windowtext;
\r
1303 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
1304 style='mso-element:field-separator'></span></span><![endif]--><span
\r
1305 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1306 text-underline:none'>8</span><span style='color:windowtext;display:none;
\r
1307 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
1308 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700380032000000</w:data>
\r
1309 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
1310 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
1311 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
1312 style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>
\r
1314 <p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span
\r
1315 class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954783">4.1
\r
1316 How the algorithm works<span style='color:windowtext;display:none;mso-hide:
\r
1317 screen;text-decoration:none;text-underline:none'><span style='mso-tab-count:
\r
1318 1 dotted'>. </span></span><!--[if supportFields]><span style='color:windowtext;
\r
1319 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
1320 style='mso-element:field-begin'></span></span><span style='color:windowtext;
\r
1321 display:none;mso-hide:screen;text-decoration:none;text-underline:none'> PAGEREF
\r
1322 _Toc113954783 \h </span><span style='color:windowtext;display:none;mso-hide:
\r
1323 screen;text-decoration:none;text-underline:none'><span style='mso-element:field-separator'></span></span><![endif]--><span
\r
1324 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1325 text-underline:none'>8</span><span style='color:windowtext;display:none;
\r
1326 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
1327 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700380033000000</w:data>
\r
1328 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
1329 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
1330 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
1331 style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>
\r
1333 <p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span
\r
1334 class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954784">4.2
\r
1335 Command-line options<span style='color:windowtext;display:none;mso-hide:screen;
\r
1336 text-decoration:none;text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
1337 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1338 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
1339 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1340 text-underline:none'> PAGEREF _Toc113954784 \h </span><span style='color:windowtext;
\r
1341 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
1342 style='mso-element:field-separator'></span></span><![endif]--><span
\r
1343 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1344 text-underline:none'>9</span><span style='color:windowtext;display:none;
\r
1345 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
1346 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700380034000000</w:data>
\r
1347 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
1348 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
1349 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
1350 style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>
\r
1352 <p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span
\r
1353 class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954785">4.3
\r
1354 The maxiters option<span style='color:windowtext;display:none;mso-hide:screen;
\r
1355 text-decoration:none;text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
1356 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1357 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
1358 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1359 text-underline:none'> PAGEREF _Toc113954785 \h </span><span style='color:windowtext;
\r
1360 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
1361 style='mso-element:field-separator'></span></span><![endif]--><span
\r
1362 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1363 text-underline:none'>9</span><span style='color:windowtext;display:none;
\r
1364 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
1365 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700380035000000</w:data>
\r
1366 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
1367 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
1368 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
1369 style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>
\r
1371 <p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span
\r
1372 class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954786">4.4
\r
1373 The maxtrees option<span style='color:windowtext;display:none;mso-hide:screen;
\r
1374 text-decoration:none;text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
1375 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1376 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
1377 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1378 text-underline:none'> PAGEREF _Toc113954786 \h </span><span style='color:windowtext;
\r
1379 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
1380 style='mso-element:field-separator'></span></span><![endif]--><span
\r
1381 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1382 text-underline:none'>10</span><span style='color:windowtext;display:none;
\r
1383 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
1384 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700380036000000</w:data>
\r
1385 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
1386 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
1387 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
1388 style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>
\r
1390 <p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span
\r
1391 class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954787">4.5
\r
1392 The maxhours option<span style='color:windowtext;display:none;mso-hide:screen;
\r
1393 text-decoration:none;text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
1394 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1395 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
1396 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1397 text-underline:none'> PAGEREF _Toc113954787 \h </span><span style='color:windowtext;
\r
1398 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
1399 style='mso-element:field-separator'></span></span><![endif]--><span
\r
1400 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1401 text-underline:none'>10</span><span style='color:windowtext;display:none;
\r
1402 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
1403 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700380037000000</w:data>
\r
1404 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
1405 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
1406 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
1407 style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>
\r
1409 <p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span
\r
1410 class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954788">4.6
\r
1411 The maxmb option<span style='color:windowtext;display:none;mso-hide:screen;
\r
1412 text-decoration:none;text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
1413 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1414 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
1415 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1416 text-underline:none'> PAGEREF _Toc113954788 \h </span><span style='color:windowtext;
\r
1417 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
1418 style='mso-element:field-separator'></span></span><![endif]--><span
\r
1419 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1420 text-underline:none'>10</span><span style='color:windowtext;display:none;
\r
1421 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
1422 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700380038000000</w:data>
\r
1423 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
1424 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
1425 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
1426 style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>
\r
1428 <p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span
\r
1429 class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954789">4.7
\r
1430 The profile scoring function<span style='color:windowtext;display:none;
\r
1431 mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
1432 style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
1433 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1434 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
1435 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1436 text-underline:none'> PAGEREF _Toc113954789 \h </span><span style='color:windowtext;
\r
1437 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
1438 style='mso-element:field-separator'></span></span><![endif]--><span
\r
1439 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1440 text-underline:none'>10</span><span style='color:windowtext;display:none;
\r
1441 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
1442 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700380039000000</w:data>
\r
1443 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
1444 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
1445 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
1446 style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>
\r
1448 <p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span
\r
1449 class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954790">4.8
\r
1450 Diagonal optimization<span style='color:windowtext;display:none;mso-hide:screen;
\r
1451 text-decoration:none;text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
1452 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1453 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
1454 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1455 text-underline:none'> PAGEREF _Toc113954790 \h </span><span style='color:windowtext;
\r
1456 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
1457 style='mso-element:field-separator'></span></span><![endif]--><span
\r
1458 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1459 text-underline:none'>10</span><span style='color:windowtext;display:none;
\r
1460 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
1461 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700390030000000</w:data>
\r
1462 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
1463 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
1464 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
1465 style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>
\r
1467 <p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span
\r
1468 class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954791">4.9
\r
1469 Anchor optimization<span style='color:windowtext;display:none;mso-hide:screen;
\r
1470 text-decoration:none;text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
1471 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1472 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
1473 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1474 text-underline:none'> PAGEREF _Toc113954791 \h </span><span style='color:windowtext;
\r
1475 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
1476 style='mso-element:field-separator'></span></span><![endif]--><span
\r
1477 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1478 text-underline:none'>11</span><span style='color:windowtext;display:none;
\r
1479 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
1480 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700390031000000</w:data>
\r
1481 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
1482 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
1483 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
1484 style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>
\r
1486 <p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span
\r
1487 class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954792">4.10
\r
1488 Log file<span style='color:windowtext;display:none;mso-hide:screen;text-decoration:
\r
1489 none;text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
1490 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1491 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
1492 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1493 text-underline:none'> PAGEREF _Toc113954792 \h </span><span style='color:windowtext;
\r
1494 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
1495 style='mso-element:field-separator'></span></span><![endif]--><span
\r
1496 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1497 text-underline:none'>11</span><span style='color:windowtext;display:none;
\r
1498 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
1499 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700390032000000</w:data>
\r
1500 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
1501 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
1502 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
1503 style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>
\r
1505 <p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span
\r
1506 class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954793">4.11
\r
1507 Progress messages<span style='color:windowtext;display:none;mso-hide:screen;
\r
1508 text-decoration:none;text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
1509 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1510 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
1511 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1512 text-underline:none'> PAGEREF _Toc113954793 \h </span><span style='color:windowtext;
\r
1513 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
1514 style='mso-element:field-separator'></span></span><![endif]--><span
\r
1515 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1516 text-underline:none'>11</span><span style='color:windowtext;display:none;
\r
1517 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
1518 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700390033000000</w:data>
\r
1519 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
1520 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
1521 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
1522 style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>
\r
1524 <p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span
\r
1525 class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954794">4.12
\r
1526 Running out of memory<span style='color:windowtext;display:none;mso-hide:screen;
\r
1527 text-decoration:none;text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
1528 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1529 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
1530 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1531 text-underline:none'> PAGEREF _Toc113954794 \h </span><span style='color:windowtext;
\r
1532 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
1533 style='mso-element:field-separator'></span></span><![endif]--><span
\r
1534 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1535 text-underline:none'>12</span><span style='color:windowtext;display:none;
\r
1536 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
1537 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700390034000000</w:data>
\r
1538 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
1539 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
1540 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
1541 style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>
\r
1543 <p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span
\r
1544 class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954795">4.13
\r
1545 Troubleshooting<span style='color:windowtext;display:none;mso-hide:screen;
\r
1546 text-decoration:none;text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
1547 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1548 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
1549 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1550 text-underline:none'> PAGEREF _Toc113954795 \h </span><span style='color:windowtext;
\r
1551 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
1552 style='mso-element:field-separator'></span></span><![endif]--><span
\r
1553 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1554 text-underline:none'>12</span><span style='color:windowtext;display:none;
\r
1555 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
1556 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700390035000000</w:data>
\r
1557 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
1558 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
1559 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
1560 style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>
\r
1562 <p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span
\r
1563 class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954796">4.14
\r
1564 Technical support<span style='color:windowtext;display:none;mso-hide:screen;
\r
1565 text-decoration:none;text-underline:none'><span style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span
\r
1566 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1567 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
1568 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1569 text-underline:none'> PAGEREF _Toc113954796 \h </span><span style='color:windowtext;
\r
1570 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
1571 style='mso-element:field-separator'></span></span><![endif]--><span
\r
1572 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1573 text-underline:none'>12</span><span style='color:windowtext;display:none;
\r
1574 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
1575 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700390036000000</w:data>
\r
1576 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
1577 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
1578 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
1579 style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>
\r
1581 <p class=MsoToc1 style='tab-stops:right dotted 431.5pt'><span
\r
1582 class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954797">5
\r
1583 Command Line Reference<span style='color:windowtext;display:none;mso-hide:screen;
\r
1584 text-decoration:none;text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span
\r
1585 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1586 text-underline:none'><span style='mso-element:field-begin'></span></span><span
\r
1587 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1588 text-underline:none'> PAGEREF _Toc113954797 \h </span><span style='color:windowtext;
\r
1589 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
1590 style='mso-element:field-separator'></span></span><![endif]--><span
\r
1591 style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;
\r
1592 text-underline:none'>13</span><span style='color:windowtext;display:none;
\r
1593 mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>
\r
1594 <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700390037000000</w:data>
\r
1595 </xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;
\r
1596 display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span
\r
1597 style='mso-element:field-end'></span></span><![endif]--></a></span></span><span
\r
1598 style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>
\r
1600 <p class=MsoNormal><!--[if supportFields]><span style='font-family:Arial'><span
\r
1601 style='mso-element:field-end'></span></span><![endif]--><span style='font-family:
\r
1602 Arial'><o:p> </o:p></span></p>
\r
1604 <b><span style='font-size:16.0pt;font-family:Arial;mso-fareast-font-family:
\r
1605 "MS Mincho";mso-bidi-font-family:"Times New Roman";mso-font-kerning:16.0pt;
\r
1606 mso-ansi-language:EN-US;mso-fareast-language:JA;mso-bidi-language:AR-SA'><br
\r
1607 clear=all style='page-break-before:always'>
\r
1610 <h1 style='margin-left:0in;text-indent:0in'><a name="_Toc113954755"><![if !supportLists]><span
\r
1611 style='mso-fareast-font-family:Arial;mso-bidi-font-family:Arial'><span
\r
1612 style='mso-list:Ignore'>1 </span></span><![endif]>Introduction</a></h1>
\r
1614 <p class=MsoNormal>MUSCLE is a program for creating multiple alignments of
\r
1615 amino acid or nucleotide sequences. A range of options is provided that give
\r
1616 you the choice of optimizing accuracy, speed, or some compromise between the
\r
1617 two. Default parameters are those that give the best average accuracy in our
\r
1618 tests. Using versions current at the time of writing, my tests show that MUSCLE
\r
1619 can achieve both better average accuracy and better speed than CLUSTALW or T‑Coffee,
\r
1620 depending on the chosen options. Many command line options are provided to vary
\r
1621 the internals of the algorithm; some of these will primarily be of interest to
\r
1622 algorithm developers who wish to better understand which features of the algorithm
\r
1623 are important in different circumstances.</p>
\r
1625 <h1 style='margin-left:0in;text-indent:0in'><a name="_Toc113954756"><![if !supportLists]><span
\r
1626 style='mso-fareast-font-family:Arial;mso-bidi-font-family:Arial'><span
\r
1627 style='mso-list:Ignore'>2 </span></span><![endif]>Quick Start</a></h1>
\r
1629 <p class=MsoNormal>The MUSCLE algorithm is delivered as a command-line program
\r
1630 called <i>muscle</i>. If you are running under Linux or <span class=GramE>Unix</span>
\r
1631 you will be working at a shell prompt. If you are running under Windows, you should
\r
1632 be in a command window (nostalgically known to us older people as a DOS prompt).
\r
1633 If you don't know how to use command-line programs, you should get help from a
\r
1636 <h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954757"><![if !supportLists]><span
\r
1637 style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>2.1 </span></span><![endif]>Installation</a></h2>
\r
1639 <p class=MsoNormal>Copy the <i>muscle</i> binary file to a directory that is
\r
1640 accessible from your computer. That's it
\97there are no configuration files,
\r
1641 libraries, environment variables or other settings to worry about. If you are
\r
1642 using Windows, then the binary file is named <i>muscle.exe</i>. From now on <i>muscle</i>
\r
1643 should be understood to mean "<i>muscle</i> if you are using Linux or <span
\r
1644 class=GramE>Unix</span>, <i>muscle.exe</i> if you are using Windows".<o:p></o:p></p>
\r
1646 <h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954758"><![if !supportLists]><span
\r
1647 style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>2.2 </span></span><![endif]>Making
\r
1648 an alignment</a></h2>
\r
1650 <p class=MsoNormal>Make a FASTA file containing some sequences. (If you are not
\r
1651 familiar with FASTA format, it is described in detail later in this Guide.) For
\r
1652 now, just to make things fast, limit the number of sequence in the file to no
\r
1653 more than 50 and the sequence length to be no more than 500. Call the input
\r
1654 file <span class=SpellE><i>seqs.fa</i></span>. (An example file named <span
\r
1655 class=SpellE><i>seqs.fa</i></span> is distributed with the standard MUSCLE
\r
1656 package). Make sure the directory containing the <i>muscle</i> binary is in
\r
1657 your path. (If it isn't, you can run it by typing the full path name, and the
\r
1658 following example command lines must be changed accordingly). Now type:</p>
\r
1660 <p class=MsoNormal><o:p> </o:p></p>
\r
1662 <p class=Code>muscle -in seqs.fa -out seqs.afa</p>
\r
1664 <p class=MsoNormal><o:p> </o:p></p>
\r
1666 <p class=MsoNormal>You should see some progress messages. If <i>muscle</i> completes
\r
1667 successfully, it will create a file <span class=SpellE><i>seqs.afa</i></span>
\r
1668 containing the alignment. By default, output is created in "aligned
\r
1669 FASTA" format (hence the <i>.<span class=SpellE>afa</span></i> extension).
\r
1670 This is just like regular FASTA except that gaps are added in order to align
\r
1671 the sequences. This is a nice format for computers but not very readable for
\r
1672 people, so to look at the alignment you will want an alignment viewer such as <span
\r
1673 class=SpellE>Belvu</span>, or a script that converts FASTA to a more readable format.
\r
1674 You can also use the
\96<span class=SpellE><i>clw</i></span> command-line option
\r
1675 to request output in CLUSTALW format, which is easier to understand for people.
\r
1676 If <i>muscle</i> gives an error message and you don't know how to fix it,
\r
1677 please read the Troubleshooting section.<o:p></o:p></p>
\r
1679 <p class=MsoNormal><o:p> </o:p></p>
\r
1681 <p class=MsoNormal>The default settings are designed to give the best accuracy,
\r
1682 so this may be all you need to know.</p>
\r
1684 <h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954759"><![if !supportLists]><span
\r
1685 style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>2.3 </span></span><![endif]>Large
\r
1686 alignments</a></h2>
\r
1688 <p class=MsoNormal>If you have a large number of sequences (a few thousand), or
\r
1689 they are very long, then the default settings of may be too slow for practical
\r
1690 use. A good compromise between speed and accuracy is to run just the first two
\r
1691 iterations of the algorithm. On average, this gives accuracy comparable to
\r
1692 T-Coffee and speeds much faster than CLUSTALW. This is done by the option <i>
\96maxiters
\r
1693 2</i>, as in the following example.</p>
\r
1695 <p class=MsoNormal><o:p> </o:p></p>
\r
1697 <p class=Code>muscle -in seqs.fa -out seqs.afa -maxiters 2</p>
\r
1699 <h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954760"><![if !supportLists]><span
\r
1700 style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>2.4 </span></span><![endif]>Faster
\r
1703 <p class=MsoNormal>The <i>
\96<span class=SpellE>diags</span></i> option enables
\r
1704 an optimization for speed by finding common words (6-mers in a compressed amino
\r
1705 acid alphabet) between the two sequences as seeds for diagonals. This is
\r
1706 related to optimizations in programs such as BLAST and FASTA: you get faster speed,
\r
1707 but sometimes lower average accuracy. For large numbers of closely related
\r
1708 sequences, this option works very well.</p>
\r
1710 <p class=MsoNormal><o:p> </o:p></p>
\r
1712 <p class=MsoNormal>If you want the fastest possible speed, then the following
\r
1713 example shows the applicable options for proteins.</p>
\r
1715 <p class=MsoNormal><o:p> </o:p></p>
\r
1717 <p class=Code>muscle -in seqs.fa -out seqs.afa -maxiters 1 -diags -sv
\r
1718 -distance1 kbit20_3</p>
\r
1720 <p class=Code><o:p> </o:p></p>
\r
1722 <p class=MsoNormal>For nucleotides, use:</p>
\r
1724 <p class=MsoNormal><o:p> </o:p></p>
\r
1726 <p class=Code>muscle -in seqs.fa -out seqs.afa -maxiters 1 -diags</p>
\r
1728 <p class=MsoNormal><o:p> </o:p></p>
\r
1730 <p class=MsoNormal>At the time of writing, <i>muscle</i> with these options is faster
\r
1731 than any other multiple sequence alignment <span class=GramE>program</span>
\r
1732 that I have tested. The alignments are not bad, especially when the sequences
\r
1733 are closely related. However, as you might expect, this blazing speed comes at
\r
1734 the cost of the lowest average accuracy of the options that <i>muscle</i>
\r
1737 <h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954761"><![if !supportLists]><span
\r
1738 style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>2.5 </span></span><![endif]>Huge
\r
1739 alignments</a></h2>
\r
1741 <p class=MsoNormal>If you have a <i>very</i> large number of sequences (several
\r
1742 thousand), or they are very long, then the <i>kbit20_3</i> option may cause
\r
1743 problems because it needs a relatively large amount of memory. Better is to use
\r
1744 the default distance measure, which is roughly 2× or 3× slower but needs less
\r
1745 memory, like this:</p>
\r
1747 <p class=MsoNormal><o:p> </o:p></p>
\r
1749 <p class=Code>muscle -in seqs.fa -out seqs.afa -maxiters 1 -diags1 -sv</p>
\r
1751 <h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954762"><![if !supportLists]><span
\r
1752 style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>2.6 </span></span><![endif]>Accuracy:
\r
1753 caveat emptor</a></h2>
\r
1755 <p class=MsoNormal>Why do I keep using the clumsy phrase "average
\r
1756 accuracy" instead of just saying "accuracy"? That's because the
\r
1757 quality of alignments produced by MUSCLE varies, as do those produced other programs
\r
1758 such as CLUSTALW and T-Coffee. The state of the art leaves plenty of room for
\r
1759 improvement. Sometimes the fastest speed options to <i>muscle</i> give
\r
1760 alignments that are better than T-Coffee, though the reverse will more often be
\r
1761 the case. With challenging sets of sequences, it is a good idea to make several
\r
1762 different alignments using different <i>muscle</i> options and to try other programs
\r
1763 too. Regions where different alignments agree are more believable than regions
\r
1764 where they disagree. <o:p></o:p></p>
\r
1766 <h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954763"><![if !supportLists]><span
\r
1767 style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>2.7 </span></span><![endif]>Pipelining</a></h2>
\r
1769 <p class=MsoNormal>Input can be taken from standard input, and output can be
\r
1770 written to standard output. This is the default, so our first example would
\r
1771 also work like this:</p>
\r
1773 <p class=MsoNormal><o:p> </o:p></p>
\r
1775 <p class=Code>muscle < seqs.fa > seqs.afa</p>
\r
1777 <h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954764"><![if !supportLists]><span
\r
1778 style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>2.8 </span></span><![endif]>Refining
\r
1779 an existing alignment</a></h2>
\r
1781 <p class=MsoNormal>You can ask <i>muscle</i> to try to improve an existing
\r
1782 alignment by using the
\96<i>refine</i> option. The input file must then be a
\r
1783 FASTA file containing an alignment. All sequences must be of equal length, gaps
\r
1784 can be specified using dots "." or dashes "
\96". For example:</p>
\r
1786 <p class=MsoNormal><o:p> </o:p></p>
\r
1788 <p class=Code>muscle -in seqs.afa -out refined.afa -refine</p>
\r
1790 <h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954765"><![if !supportLists]><span
\r
1791 style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>2.9 </span></span><![endif]>Using
\r
1792 a pre-computed guide tree</a></h2>
\r
1794 <p class=MsoNormal>The
\96<span class=SpellE><i>usetree</i></span> option allows
\r
1795 you to provide your own guide tree. For example,</p>
\r
1797 <p class=MsoNormal><o:p> </o:p></p>
\r
1799 <p class=Code>muscle -in seqs.fa -out seqs.afa -usetree mytree.phy</p>
\r
1801 <p class=MsoNormal><o:p> </o:p></p>
\r
1803 <p class=MsoNormal>The tree must by in <span class=SpellE>Newick</span> format,
\r
1804 as used by the <span class=SpellE>Phylip</span> package (hence the <i>.<span
\r
1805 class=SpellE>phy</span></i> extension). The <span class=SpellE>Newick</span>
\r
1806 format is described here:</p>
\r
1808 <p class=MsoNormal><o:p> </o:p></p>
\r
1810 <p class=MsoNormal><span style='mso-tab-count:1'>Â Â Â Â Â Â Â </span><a
\r
1811 href="http://evolution.genetics.washington.edu/phylip/newicktree.html">http://evolution.genetics.washington.edu/phylip/newicktree.html</a></p>
\r
1813 <p class=MsoNormal><o:p> </o:p></p>
\r
1815 <p class=MsoNormal><span class=GramE><b>WARNING</b>.</span> Do not use this
\r
1816 option just because you believe that you have an accurate evolutionary tree for
\r
1817 your sequences. The best guide tree for multiple <span class=GramE>alignment</span>
\r
1818 is <i>not</i> in general the correct evolutionary tree. This can be understood
\r
1819 by the following argument. Alignment accuracy decreases with lower sequence
\r
1820 identity. It follows that given a set of <span class=GramE>profiles,</span> the
\r
1821 two that can be aligned most accurately will tend to be the pair with the
\r
1822 highest identity, i.e. at the shortest evolutionary distance. This is exactly
\r
1823 the pair selected by the nearest-neighbor criterion which MUSCLE uses by
\r
1824 default. When mutation rates are variable, the <i>evolutionary </i>neighbor may
\r
1825 not be the <i>nearest </i>neighbor. This explains why a nearest-neighbor tree
\r
1826 may be superior to the true evolutionary tree for guiding a progressive alignment.</p>
\r
1828 <p class=MsoNormal><o:p> </o:p></p>
\r
1830 <p class=MsoNormal>You will get a warning if you use the
\96<span class=SpellE><i>usetree</i></span>
\r
1831 option. To disable the warning, use
\ad<i>
\96<span class=SpellE>usetree_nowarn</span></i>
\r
1834 <p class=MsoNormal>e.g.:</p>
\r
1836 <p class=MsoNormal><o:p> </o:p></p>
\r
1838 <p class=Code>muscle -in seqs.fa -out seqs.afa -usetree_nowarn mytree.phy</p>
\r
1840 <h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954766"><![if !supportLists]><span
\r
1841 style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>2.10 </span></span><![endif]>Profile-profile
\r
1842 alignment</a></h2>
\r
1844 <p class=MsoNormal>A fundamental step in the MUSCLE algorithm is aligning two
\r
1845 multiple sequence alignments. This operation is sometimes called
\r
1846 "profile-profile alignment". If you have two existing alignments of
\r
1847 related sequences you can use the <i>
\96profile</i> option of MUSCLE to align
\r
1848 those two sequences. Typical usage is:</p>
\r
1850 <p class=MsoNormal><o:p> </o:p></p>
\r
1852 <p class=Code>muscle -profile -in1 one.afa -in2 two.afa -out both.afa</p>
\r
1854 <p class=MsoNormal><o:p> </o:p></p>
\r
1856 <p class=MsoNormal>The alignments in <span class=SpellE><i>one.afa</i></span>
\r
1857 and <span class=SpellE><i>two.afa</i></span>, which must be in aligned FASTA
\r
1858 format, are aligned to each other, keeping input columns intact and inserting
\r
1859 columns of gaps where needed. Output is stored in <span class=SpellE><i>both.afa</i></span>.</p>
\r
1861 <p class=MsoNormal><o:p> </o:p></p>
\r
1863 <p class=MsoNormal>MUSCLE does not compute a similarity measure or measure of
\r
1864 statistical significance (such as an E-value), so this option is not useful for
\r
1865 discriminating homologs from unrelated sequences. For this task, I recommend <span
\r
1866 class=SpellE>Sadreyev</span> & <span class=SpellE>Grishin's</span> COMPASS
\r
1869 <h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954767"><![if !supportLists]><span
\r
1870 style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>2.11 </span></span><![endif]>Adding
\r
1871 sequences to an existing alignment</a></h2>
\r
1873 <p class=MsoNormal>To add a sequence to an existing alignment that you wish to
\r
1874 keep intact, use profile-profile alignment with the new sequence as a profile.
\r
1875 For example, if you have an existing alignment <span class=SpellE><i>existing_aln.afa</i></span>
\r
1876 and want to add a new sequence in <span class=SpellE><i>new_seq.fa</i></span>,
\r
1877 use the following commands:</p>
\r
1879 <p class=MsoNormal><o:p> </o:p></p>
\r
1881 <p class=Code>muscle -profile -in1 existing_aln.afa -in2 new_seq.fa -out
\r
1882 combined.afa<o:p></o:p></p>
\r
1884 <p class=MsoNormal><o:p> </o:p></p>
\r
1886 <p class=MsoNormal>If you have more than one new <span class=GramE>sequences</span>,
\r
1887 you can align them first then add them, for example:</p>
\r
1889 <p class=MsoNormal><o:p> </o:p></p>
\r
1891 <p class=Code>muscle -in new_seqs.fa -out new_seqs.afa</p>
\r
1893 <p class=Code>muscle -profile -in1 existing_aln.afa -in2 new_seqs.fa -out
\r
1896 <h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954768"><![if !supportLists]><span
\r
1897 style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>2.12 </span></span><![endif]>Sequence
\r
1898 clustering</a></h2>
\r
1900 <p class=MsoNormal>The first stage in MUSCLE is a fast clustering algorithm.
\r
1901 This may be of use in other applications. Typical usage is:</p>
\r
1903 <p class=MsoNormal><o:p> </o:p></p>
\r
1905 <p class=Code>muscle -cluster -in seqs.fa -tree1 tree.phy -maxiters 1</p>
\r
1907 <p class=MsoNormal><o:p> </o:p></p>
\r
1909 <p class=MsoNormal>The sequences will be clustered, and a tree written to <span
\r
1910 class=SpellE><i>tree.phy</i></span>. Options
\96<i>weight1</i>,
\96<i>distance1</i>,
\r
1911 \96<i>cluster1</i> and
\96<i>root1</i> can be applied if desired. Note that by
\r
1912 default, UPGMA clustering is used. You can use</p>
\r
1914 <p class=MsoNormal><span style='mso-spacerun:yes'>Â </span><span class=GramE>
\96<span
\r
1915 class=SpellE><i>neighborjoining</i></span> if you prefer, but note that this is
\r
1916 substantially slower than UPGMA for large numbers of sequences, and is also
\r
1917 slightly less accurate.</span> See discussion of
\96<span class=SpellE><i>usetree</i></span>
\r
1920 <h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954769"><![if !supportLists]><span
\r
1921 style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>2.13 </span></span><![endif]>Specifying
\r
1922 a substitution matrix</a></h2>
\r
1924 <p class=MsoNormal>You can specify your own substitution matrix by using the <i>-matrix</i>
\r
1925 option. This reads a protein substitution matrix in NCBI or WU-BLAST format.
\r
1926 The alphabet is assumed to be amino acid, and sum-of-pairs scoring is used. The
\r
1927 \ad<i>-<span class=SpellE>gapopen</span></i>, <i>-<span class=SpellE>gapextend</span></i>
\r
1928 and -<i>center</i> parameters should be specified; normally you will specify a
\r
1929 zero value for the center. Note that gap penalties MUST be negative. The
\r
1930 environment variable MUSCLE_MXPATH can be used to specify a path where the
\r
1931 matrices are stored. For example,</p>
\r
1933 <p class=MsoNormal><o:p> </o:p></p>
\r
1935 <p class=Code>muscle -in seqs.fa -out seqs.afa -matrix blosum62 -gapopen -12.0</p>
\r
1937 <p class=Code><span style='mso-tab-count:1'>Â Â </span><span
\r
1938 style='mso-spacerun:yes'>Â </span>-gapextend -1.0 -center 0.0</p>
\r
1940 <p class=MsoNormal><o:p> </o:p></p>
\r
1942 <p class=MsoNormal>You can hack a nucleotide matrix by pretending that AGCT are
\r
1943 amino acids and making a 20x20 matrix out of the original 4x4 matrix. Let me
\r
1944 know if this isn't clear, I can help you through it.<o:p></o:p></p>
\r
1946 <h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954770"><![if !supportLists]><span
\r
1947 style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>2.14 </span></span><![endif]>Refining
\r
1948 a long alignment</a></h2>
\r
1950 <p class=MsoNormal>A long alignment can be refined using the
\96<span
\r
1951 class=SpellE><i>refinew</i></span> option, which is primarily designed for
\r
1952 refining whole-genome nucleotide alignments. Usage is:</p>
\r
1954 <p class=MsoNormal><o:p> </o:p></p>
\r
1956 <p class=Code>muscle -in input.afa -out output.afa</p>
\r
1958 <p class=MsoNormal><o:p> </o:p></p>
\r
1960 <p class=MsoNormal>MUSCLE divides the input alignment into non-overlapping
\r
1961 windows and re-aligns each window from scratch, i.e. all gap characters are
\r
1962 discarded. The
\96<span class=SpellE><i>refinewindow</i></span> option may be
\r
1963 used to change the window length, which <span class=GramE>is</span> 200 columns
\r
1964 by default.<o:p></o:p></p>
\r
1966 <h1 style='margin-left:0in;text-indent:0in'><a name="_Toc113954771"><![if !supportLists]><span
\r
1967 style='mso-fareast-font-family:Arial;mso-bidi-font-family:Arial'><span
\r
1968 style='mso-list:Ignore'>3 </span></span><![endif]>File Formats</a></h1>
\r
1970 <p class=MsoNormal>MUSCLE uses FASTA format for both input and output. For
\r
1971 output only, it also offers CLUSTALW, MSF, HTML, <span class=SpellE>Phylip</span>
\r
1972 sequential and <span class=SpellE>Phylip</span> interleaved formats. See the
\r
1973 following command-line options: ‑<span class=SpellE><i>clw</i></span>, ‑<span
\r
1974 class=SpellE><i>clwstrict</i></span><i>, </i>
\96<span class=SpellE><i>msf</i></span>,
\r
1975 \96<i>html</i>,
\96<i>phys</i>,
\96<span class=SpellE><i>phyi</i></span><i>,</i> ‑<span
\r
1976 class=SpellE><i>clwout</i></span>, ‑<span class=SpellE><i>clwstrictout</i></span><i>,
\r
1977 </i>
\96<span class=SpellE><i>msfout</i></span>,
\96<span class=SpellE><i>htmlout</i></span>,
\r
1978 \96<span class=SpellE><i>physout</i></span><i> </i>and
\96<span class=SpellE><i>phyiout</i></span>.<o:p></o:p></p>
\r
1980 <p class=MsoNormal><o:p> </o:p></p>
\r
1982 <h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954772"><![if !supportLists]><span
\r
1983 style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>3.1 </span></span><![endif]>Input
\r
1986 <p class=MsoNormal>Input files must be in FASTA format. These are plain text
\r
1987 files (word processing files such as Word documents are not understood!). <span
\r
1988 class=GramE>Unix</span>, Windows and DOS text files are supported (end-of-line
\r
1989 may be NL or CR NL). There is no explicit limit on the length of a sequence,
\r
1990 however if you are running a 32-bit version of <i>muscle</i> then the maximum
\r
1991 will be very roughly 10,000 letters due to maximum addressable size of tables
\r
1992 required in memory. Each sequence starts with an annotation line, which is
\r
1993 recognized by having a greater-than symbol ">" as its first
\r
1994 character. There is no limit on the length of an annotation line (this is new
\r
1995 as of version 3.5), and there is no requirement that the annotation be unique. The
\r
1996 sequence itself follows on one or more subsequent lines, and is terminated
\r
1997 either by the next annotation line or by the end of the file. </p>
\r
1999 <h3 style='margin-left:0in;text-indent:0in'><a name="_Toc113954773"><![if !supportLists]><span
\r
2000 style='mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:"Times New Roman"'><span
\r
2001 style='mso-list:Ignore'>3.1.1 </span></span><![endif]>Amino acid sequences</a></h3>
\r
2003 <p class=MsoNormal>The standard single-letter amino acid alphabet is used. Upper
\r
2004 and lower case is allowed, the case is not significant. The special characters
\r
2005 X, B, Z and U are understood. X means "unknown amino acid", B is D or
\r
2006 N, Z is E or Q. U is understood to be the 21st amino acid <span class=SpellE>Selenocysteine</span>.
\r
2007 White space (spaces, tabs and the end-of-line characters CR and NL) is allowed
\r
2008 inside sequence data. Dots "." and dashes "
\96" in sequences
\r
2009 are allowed and are discarded unless the input is expected to be aligned (e.g.
\r
2010 for the
\96<i>refine</i> option). </p>
\r
2012 <h3 style='margin-left:0in;text-indent:0in'><a name="_Toc113954774"><![if !supportLists]><span
\r
2013 style='mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:"Times New Roman"'><span
\r
2014 style='mso-list:Ignore'>3.1.2 </span></span><![endif]>Nucleotide sequences</a></h3>
\r
2016 <p class=MsoNormal>The usual letters A, G, C, T and U stand for nucleotides.
\r
2017 The letters T and U are equivalent as far as MUSCLE is concerned. N is the
\r
2018 wildcard meaning "unknown nucleotide". R means A or G, Y means C or
\r
2019 T/U. Other wildcards, such as those used by RFAM, are not understood in this
\r
2020 version and will be replaced by Ns. If you would like support for other DNA /
\r
2021 RNA alphabets, please let me know.</p>
\r
2023 <h3 style='margin-left:0in;text-indent:0in'><a name="_Toc113954775"><![if !supportLists]><span
\r
2024 style='mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:"Times New Roman"'><span
\r
2025 style='mso-list:Ignore'>3.1.3 </span></span><![endif]>Determining sequence type</a></h3>
\r
2027 <p class=MsoNormal>By default, MUSCLE looks at the first 100 letters in the
\r
2028 input sequence data (excluding gaps). If 95% or more of those letters are valid
\r
2029 nucleotides (AGCTUN), then the file is treated as nucleotides, otherwise as
\r
2030 amino acids. This method almost always guesses correctly, but you can make sure
\r
2031 by specifying the sequence type on the command line. This is done using the
\96<span
\r
2032 class=SpellE><i>seqtype</i></span> option, which can take the following values:</p>
\r
2034 <p class=MsoNormal><o:p> </o:p></p>
\r
2036 <p class=MsoNormal><span style='mso-tab-count:1'>Â Â Â Â Â Â Â </span>
\96\ad<span
\r
2037 class=SpellE><i>seqtype</i></span><i> protein</i><span style='mso-tab-count:
\r
2038 4'>Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â </span>Amino acid</p>
\r
2040 <p class=MsoNormal><span style='mso-tab-count:1'>Â Â Â Â Â Â Â </span>
\96<span
\r
2041 class=SpellE>s<i>eqtype</i></span><i> <span class=SpellE>nucleo</span></i><span
\r
2042 style='mso-tab-count:4'>Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â </span>Nucleotide</p>
\r
2044 <p class=MsoNormal><span style='mso-tab-count:1'>Â Â Â Â Â Â Â </span><span
\r
2045 class=GramE>
\96<span class=SpellE><i>seqtype</i></span><i> auto</i><span
\r
2046 style='mso-tab-count:4'>Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â </span>Automatic
\r
2047 detection (default).</span><o:p></o:p></p>
\r
2049 <h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954776"><![if !supportLists]><span
\r
2050 style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>3.2 </span></span><![endif]>Output
\r
2053 <p class=MsoNormal>By default, output is also written in FASTA format. All
\r
2054 letters are upper-case and gaps are represented by dashes "
\96". Output
\r
2055 is written to the following destination(s):</p>
\r
2057 <p class=MsoNormal><o:p> </o:p></p>
\r
2059 <p class=MsoNormal><span style='mso-tab-count:1'>Â Â Â Â Â Â Â </span>If no other
\r
2060 output option is given, then standard output.</p>
\r
2062 <p class=MsoNormal><span style='mso-tab-count:1'>Â Â Â Â Â Â Â </span>If <i>-out</i> <i><filename></i>
\r
2063 is given, to the specified file.</p>
\r
2065 <p class=MsoNormal><span style='mso-tab-count:1'>Â Â Â Â Â Â Â </span><span
\r
2066 class=GramE>For all of the <i>-<span class=SpellE>xxxout</span></i> options
\r
2067 (e.g. -<span class=SpellE><i>fastaout</i></span>, -<span class=SpellE><i>clwout</i></span>),
\r
2068 to the specified files.</span><o:p></o:p></p>
\r
2070 <h3 style='margin-left:0in;text-indent:0in'><a name="_Toc113954777"><![if !supportLists]><span
\r
2071 style='mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:"Times New Roman"'><span
\r
2072 style='mso-list:Ignore'>3.2.1 </span></span><![endif]>Sequence grouping</a></h3>
\r
2074 <p class=MsoNormal>By default, MUSCLE re-arranges sequences so that similar
\r
2075 sequences are adjacent in the output file. (This is done by ordering sequences
\r
2076 according to a prefix traversal of the guide tree). This makes the alignment
\r
2077 easier to evaluate by eye. If you want to the sequences to be output in the
\r
2078 same order as the input file, you can use the
\96<i>stable</i> option.</p>
\r
2080 <h3 style='margin-left:0in;text-indent:0in'><![if !supportLists]><span
\r
2081 style='mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:"Times New Roman"'><span
\r
2082 style='mso-list:Ignore'>3.2.2 </span></span><![endif]>Output to multiple file
\r
2085 <p class=MsoNormal>You can request output to more than one file format by using
\r
2086 the -<span class=SpellE><i>xxxout</i></span> options. For example, to get both
\r
2087 FASTA and CLUSTALW formats:</p>
\r
2089 <p class=MsoNormal><o:p> </o:p></p>
\r
2091 <p class=Code>muscle -in seqs.fa -fastaout seqs.afa -clwout seqs.aln<o:p></o:p></p>
\r
2093 <h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954778"><![if !supportLists]><span
\r
2094 style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>3.3 </span></span><![endif]>CLUSTALW
\r
2097 <p class=MsoNormal>You can request CLUSTALW output by using the
\96<span
\r
2098 class=SpellE><i>clw</i></span> option. This should be compatible with CLUSTALW,
\r
2099 with the exception of the program name in the file header. You can ask MUSCLE
\r
2100 to impersonate CLUSTALW by writing "CLUSTAL W (1.81)" as the program
\r
2101 name by using
\96<span class=SpellE><i>clwstrict</i></span> or <i>‑<span
\r
2102 class=SpellE>clwstrictout</span></i>. Note that MUSCLE allows duplicate
\r
2103 sequence labels, while CLUSTALW forbids duplicates. If you use the
\96<i>stable</i>
\r
2104 option of <i>muscle</i>, then the order of the input sequences is preserved and
\r
2105 sequences can be unambiguously identified even if the labels differ. If you
\r
2106 have problems parsing MUSCLE output with scripts designed for CLUSTALW, please
\r
2107 let me know and I'll do my best to provide a fix.<o:p></o:p></p>
\r
2109 <h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954779"><![if !supportLists]><span
\r
2110 style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>3.4 </span></span><![endif]>MSF
\r
2113 <p class=MsoNormal>MSF format, as used in the GCG package, is requested by
\r
2114 using the
\96<span class=SpellE><i>msf</i></span> option. As with CLUSTALW
\r
2115 format, this is easier for people to read than FASTA. As of MUSCLE 3.52, the
\r
2116 MSF format has been tweaked to be more compatible with GCG. The following
\r
2117 differences remain.</p>
\r
2119 <p class=MsoNormal><o:p> </o:p></p>
\r
2121 <p class=MsoNormal>(a) MUSCLE truncates at the first white space or after 63
\r
2122 characters, which ever comes first. The GCG package apparently truncates after
\r
2123 10 characters. If this is a problem for you, please let me know and I'll add an
\r
2124 option to truncate after 10 in a future version.</p>
\r
2126 <p class=MsoNormal><o:p> </o:p></p>
\r
2128 <p class=MsoNormal>(b) MUSCLE allows duplicate sequence labels, while GCG
\r
2129 forbids duplicates. If you use the
\96<i>stable</i> option of <i>muscle</i>, then
\r
2130 the order of the input sequences is preserved and sequences can be
\r
2131 unambiguously identified even if the labels differ.</p>
\r
2133 <p class=MsoNormal><o:p> </o:p></p>
\r
2135 <p class=MsoNormal>Thanks to Eric Martel for help with improving GCG
\r
2136 compatibility.<o:p></o:p></p>
\r
2138 <h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954780"><![if !supportLists]><span
\r
2139 style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>3.5 </span></span><![endif]>HTML
\r
2142 <p class=MsoNormal>I've added an experimental feature starting in version 3.4. To
\r
2143 get a Web page as output, use the
\96<i>html</i> option. The alignment is colored
\r
2144 using a color scheme from Eric <span class=SpellE>Sonnhammer's</span> <span
\r
2145 class=SpellE>Belvu</span> editor, which is my personal favorite. A drawback of
\r
2146 this option is that the Web page typically contains a very large number of HTML
\r
2147 tags, which can be slow to display in the Internet Explorer browser. The
\r
2148 Netscape browser works much better. If you have any ideas about good ways to
\r
2149 make Web pages, please let me know.</p>
\r
2151 <h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954781"><![if !supportLists]><span
\r
2152 style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>3.6 </span></span><![endif]></a><span
\r
2153 class=SpellE><span style='mso-bookmark:_Toc113954781'>Phylip</span></span><span
\r
2154 style='mso-bookmark:_Toc113954781'> format</span></h2>
\r
2156 <p class=MsoNormal>The <span class=SpellE>Phylip</span> package supports two
\r
2157 different multiple sequence alignment file formats, called sequential and
\r
2158 interleaved respectively.<o:p></o:p></p>
\r
2160 <h1 style='margin-left:0in;text-indent:0in'><a name="_Toc113954782"><![if !supportLists]><span
\r
2161 style='mso-fareast-font-family:Arial;mso-bidi-font-family:Arial'><span
\r
2162 style='mso-list:Ignore'>4 </span></span><![endif]>Using MUSCLE</a></h1>
\r
2164 <p class=MsoNormal>In this section we give more details of the MUSCLE algorithm
\r
2165 and the more important options offered by the <i>muscle</i> implementation.<o:p></o:p></p>
\r
2167 <h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954783"><![if !supportLists]><span
\r
2168 style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>4.1 </span></span><![endif]>How
\r
2169 the algorithm works</a></h2>
\r
2171 <p class=MsoNormal>I won't give a complete description of the MUSCLE algorithm
\r
2172 here
\97for that, you will have to read the papers. (See citations on title page
\r
2173 above). But hopefully a summary will help explain what some of the command-line
\r
2174 options do and how they might be useful in your work.</p>
\r
2176 <p class=MsoNormal><o:p> </o:p></p>
\r
2178 <p class=MsoNormal>The first step is to calculate a tree. In CLUSTALW, this is
\r
2179 done as follows. Each pair of input sequences is aligned, and used to compute
\r
2180 the pair-wise identity of the pair. Identities are converted to a measure of
\r
2181 distance. Finally, the distance matrix is converted to a tree using a
\r
2182 clustering method (CLUSTALW uses neighbor-joining). If you have 1,000
\r
2183 sequences, there are (1,000 <span style='font-family:Symbol;mso-ascii-font-family:
\r
2184 "Times New Roman";mso-hansi-font-family:"Times New Roman";mso-char-type:symbol;
\r
2185 mso-symbol-font-family:Symbol'><span style='mso-char-type:symbol;mso-symbol-font-family:
\r
2186 Symbol'>´</span></span> 999)/2 = 499,500 pairs, so aligning every pair can take
\r
2187 a while. MUSCLE uses a much faster, but somewhat more approximate, method to
\r
2188 compute distances: it counts the number of short sub-sequences (known as <i>k</i>-<span
\r
2189 class=SpellE>mers</span>, <i>k</i>-<span class=SpellE>tuples</span> or words)
\r
2190 that two sequences have in common, without constructing an alignment. This is
\r
2191 typically around 3,000 times faster that <span class=SpellE>CLUSTALW's</span>
\r
2192 method, but the trees will generally be less accurate. We call this step "<i>k</i>-<span
\r
2193 class=SpellE>mer</span> clustering".<o:p></o:p></p>
\r
2195 <p class=MsoNormal><o:p> </o:p></p>
\r
2197 <p class=MsoNormal>The second step is to use the tree to construct what is
\r
2198 known as a progressive alignment. At each node of the binary tree, a pair-wise
\r
2199 alignment is constructed, progressing from the leaves towards the root. The
\r
2200 first alignment will be made from two sequences. Later alignments will be one
\r
2201 of the three following types: sequence-sequence, profile-sequence or
\r
2202 profile-profile, where "profile" means the multiple <span
\r
2203 class=GramE>alignment</span> of the sequences under a given internal node of
\r
2204 the tree. This is very similar to what CLUSTALW does once it has built a tree.</p>
\r
2206 <p class=MsoNormal><o:p> </o:p></p>
\r
2208 <p class=MsoNormal style='page-break-after:avoid'>Now we have a multiple
\r
2209 alignment, which has been built very quickly compared with conventional
\r
2210 methods, mainly because of the distance calculation using <i>k</i>-<span
\r
2211 class=SpellE>mers</span> rather than alignments. The quality of this alignment
\r
2212 is typically pretty good
\97it will often tie or beat a T-Coffee alignment on our
\r
2213 tests. However, on average, we find that it can be improved by proceeding
\r
2214 through the following steps.</p>
\r
2216 <p class=MsoNormal style='page-break-after:avoid'><o:p> </o:p></p>
\r
2218 <p class=MsoNormal style='page-break-after:avoid'>From the multiple <span
\r
2219 class=GramE>alignment</span>, we can now compute the pair-wise identities of
\r
2220 each pair of sequences. This gives us a new distance matrix, from which we
\r
2221 estimate a new tree. We compare the old and new trees, and re-align subgroups
\r
2222 where needed to produce a progressive multiple alignment from the new tree. If
\r
2223 the two trees are identical, there is nothing to do; if there are no subtrees
\r
2224 that agree (very unusual), then the whole progressive alignment procedure must
\r
2225 be repeated from scratch. Typically we find that the tree is pretty stable near
\r
2226 the leaves, but some re-alignments are needed closer the root. This procedure
\r
2227 (compute pair-wise identities, estimate new tree, compare trees, re-align) is
\r
2228 iterated until the tree stabilizes or until a specified maximum number of
\r
2229 iterations has been done. We call this process "tree refinement",
\r
2230 although it also tends to improve the alignment.</p>
\r
2232 <p class=MsoNormal style='page-break-after:avoid'><o:p> </o:p></p>
\r
2234 <p class=MsoNormal style='page-break-after:avoid'>We now keep the tree fixed
\r
2235 and move to a new procedure which is designed to improve the multiple
\r
2236 alignment. The set of sequences is divided into two subsets (i.e., we make a
\r
2237 bipartition on the set of sequences). A profile is constructed for each of the
\r
2238 two subsets based on the current multiple <span class=GramE>alignment</span>.
\r
2239 These two profiles are then re-aligned to each other using the same pair-wise
\r
2240 alignment algorithm as used in the progressive stage. If this improves an
\r
2241 "objective score" that measures the quality of the alignment, then
\r
2242 the new multiple <span class=GramE>alignment</span> is kept, otherwise it is
\r
2243 discarded. By default, the objective score is the classic sum-of-pairs score
\r
2244 that takes the (sequence weighted) average of the pair-wise alignment score of
\r
2245 every pair of sequences in the alignment. Bipartitions are chosen by deleting
\r
2246 an edge in the guide tree, each of the two resulting subtrees defines a subset
\r
2247 of sequences. This procedure is called "tree dependent refinement". <span
\r
2248 class=GramE>One iteration</span> of tree dependent refinement tries
\r
2249 bipartitions produced by deleting every edge of the tree in depth order moving
\r
2250 from the leaves towards the center of the tree. Iterations continue until
\r
2251 convergence or up to a specified maximum.</p>
\r
2253 <p class=MsoNormal style='page-break-after:avoid'><o:p> </o:p></p>
\r
2255 <p class=MsoNormal style='page-break-after:avoid'>For convenience, the major
\r
2256 steps in MUSCLE are described as "iterations", though the first three
\r
2257 iterations all do quite different things and may take very different lengths of
\r
2258 time to complete. The tree-dependent refinement iterations 3, 4 ... are true
\r
2259 iterations and will take similar lengths of time. </p>
\r
2261 <p class=MsoNormal style='page-break-after:avoid'><o:p> </o:p></p>
\r
2263 <table class=MsoTableGrid border=0 cellspacing=0 cellpadding=0
\r
2264 style='border-collapse:collapse;mso-yfti-tbllook:480;mso-padding-alt:0in 5.4pt 0in 5.4pt'>
\r
2265 <tr style='mso-yfti-irow:0'>
\r
2266 <td width=89 valign=top style='width:66.6pt;border:none;border-bottom:solid windowtext 1.0pt;
\r
2267 mso-border-bottom-alt:solid windowtext .5pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2268 <p class=MsoNormal style='page-break-after:avoid'><b><span style='font-size:
\r
2269 9.0pt;font-family:Arial'>Iteration<o:p></o:p></span></b></p>
\r
2271 <td width=461 valign=top style='width:4.8in;border:none;border-bottom:solid windowtext 1.0pt;
\r
2272 mso-border-bottom-alt:solid windowtext .5pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2273 <p class=MsoNormal style='page-break-after:avoid'><b><span style='font-size:
\r
2274 9.0pt;font-family:Arial'>Actions<o:p></o:p></span></b></p>
\r
2277 <tr style='mso-yfti-irow:1'>
\r
2278 <td width=89 valign=top style='width:66.6pt;border:none;mso-border-top-alt:
\r
2279 solid windowtext .5pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2280 <p class=MsoNormal style='page-break-after:avoid'>1</p>
\r
2282 <td width=461 valign=top style='width:4.8in;border:none;mso-border-top-alt:
\r
2283 solid windowtext .5pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2284 <p class=MsoNormal style='page-break-after:avoid'>Distance matrix by <i>k</i>-<span
\r
2285 class=SpellE>mer</span> clustering, estimate tree, progressive alignment
\r
2286 according to this tree.</p>
\r
2287 <p class=MsoNormal style='page-break-after:avoid'><o:p> </o:p></p>
\r
2290 <tr style='mso-yfti-irow:2'>
\r
2291 <td width=89 valign=top style='width:66.6pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2292 <p class=MsoNormal style='page-break-after:avoid'>2</p>
\r
2294 <td width=461 valign=top style='width:4.8in;padding:0in 5.4pt 0in 5.4pt'>
\r
2295 <p class=MsoNormal style='page-break-after:avoid'>Distance matrix by
\r
2296 pair-wise identities from current multiple alignment, estimate tree,
\r
2297 progressive alignment according to new tree, repeat until convergence or specified
\r
2298 maximum number of times.</p>
\r
2299 <p class=MsoNormal style='page-break-after:avoid'><o:p> </o:p></p>
\r
2302 <tr style='mso-yfti-irow:3;mso-yfti-lastrow:yes'>
\r
2303 <td width=89 valign=top style='width:66.6pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2304 <p class=MsoNormal style='page-break-after:avoid'>3, 4 ...</p>
\r
2306 <td width=461 valign=top style='width:4.8in;padding:0in 5.4pt 0in 5.4pt'>
\r
2307 <p class=MsoNormal style='page-break-after:avoid'>Tree-dependent refinement. <span
\r
2308 class=GramE>One iteration</span> visits every edge in the tree one time.</p>
\r
2313 <h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954784"><![if !supportLists]><span
\r
2314 style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>4.2 </span></span><![endif]>Command-line
\r
2317 <p class=MsoNormal>There are two types of command-line options: value options
\r
2318 and flag options. Value options are followed by the value of the given
\r
2319 parameter, for example
\96<i>in <filename></i>; flag options just stand for
\r
2320 themselves, such as
\96<span class=SpellE><i>msf</i></span>. All options are a
\r
2321 dash (not two dashes!) followed by a long name; there are no single-letter
\r
2322 equivalents. Value options must be separated from their values by white space
\r
2323 in the command line. Thus, <i>muscle</i> does not follow <span class=GramE>Unix</span>,
\r
2324 Linux or <span class=SpellE>Posix</span> standards, for which we apologize. The
\r
2325 order in which options are given is irrelevant unless two options contradict,
\r
2326 in which case the right-most option silently wins.<o:p></o:p></p>
\r
2328 <h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954785"><![if !supportLists]><span
\r
2329 style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>4.3 </span></span><![endif]>The
\r
2330 maxiters option</a></h2>
\r
2332 <p class=MsoNormal>You can control the number of iterations that MUSCLE does by
\r
2333 specifying the <i>
\96maxiters</i> option. If you specify 1, 2 or 3, then this is
\r
2334 exactly the number of iterations that will be performed. If the value is
\r
2335 greater than 3, then <i>muscle</i> will continue up to the maximum you specify
\r
2336 or until convergence is reached, which ever happens sooner. The default is 16.
\r
2337 If you have a large number of sequences, refinement may be rather slow.</p>
\r
2339 <h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954786"><![if !supportLists]><span
\r
2340 style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>4.4 </span></span><![endif]>The
\r
2341 </a><span class=SpellE><span style='mso-bookmark:_Toc113954786'>maxtrees</span></span><span
\r
2342 style='mso-bookmark:_Toc113954786'> option</span></h2>
\r
2344 <p class=MsoNormal>This option controls the maximum number of new trees to
\r
2345 create in iteration 2. Our experience suggests that a point of diminishing
\r
2346 returns is typically reached after the first tree, so the default value is 1.
\r
2347 If a larger value is given, the process will repeat until convergence or until
\r
2348 this number of trees has been created, which ever comes first.</p>
\r
2350 <h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954787"><![if !supportLists]><span
\r
2351 style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>4.5 </span></span><![endif]>The
\r
2352 </a><span class=SpellE><span style='mso-bookmark:_Toc113954787'>maxhours</span></span><span
\r
2353 style='mso-bookmark:_Toc113954787'> option</span></h2>
\r
2355 <p class=MsoNormal>If you have a large alignment, <i>muscle</i> may take a long
\r
2356 time to complete. It is sometimes convenient to say "I want the best
\r
2357 alignment I can get in 24 hours" rather than specifying a set of options
\r
2358 that will take an unknown length of time. This is done by using <i>
\96<span
\r
2359 class=SpellE>maxhours</span></i>, which specifies a floating-point number of
\r
2360 hours. If this time is exceeded, <i>muscle</i> will write out current alignment
\r
2361 and stop. For example,</p>
\r
2363 <p class=MsoNormal><o:p> </o:p></p>
\r
2365 <p class=Code>muscle -in huge.fa -out huge.afa -maxiters 9999 -maxhours 24.0</p>
\r
2367 <p class=MsoNormal><o:p> </o:p></p>
\r
2369 <p class=MsoNormal>Note that the actual time may exceed the specified limit by
\r
2370 a few minutes while <i>muscle</i> finishes up on a step. It is also possible
\r
2371 for no alignment to be produced if the time limit is too small.</p>
\r
2373 <h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954788"><![if !supportLists]><span
\r
2374 style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>4.6 </span></span><![endif]>The
\r
2375 </a><span class=SpellE><span style='mso-bookmark:_Toc113954788'>maxmb</span></span><span
\r
2376 style='mso-bookmark:_Toc113954788'> option</span></h2>
\r
2378 <p class=MsoNormal>If the amount of memory needed by MUSCLE exceeds available
\r
2379 physical RAM, then the operating system will probably begin paging (i.e.,
\r
2380 swapping memory to and from hard disk), causing MUSCLE to run very slowly. This
\r
2381 is especially problematic when MUSCLE is used for batch processing, where one or
\r
2382 two very large alignments can cause a batch to effectively hang. Starting in
\r
2383 version 3.52, MUSCLE attempts to limit the amount of memory used. If the limit
\r
2384 is exceeded, MUSCLE quits, saving the best alignment so far produced (if any).
\r
2385 MUSCLE attempts to determine the amount of physical RAM by making an
\r
2386 appropriate operating system call. Under Linux and Windows, this works well. On
\r
2387 other systems, particularly other flavors of <span class=GramE>Unix</span>,
\r
2388 MUSCLE doesn't know how to query the system and assumes that there is 500 Mb of
\r
2389 RAM. To override this default, you can specify the maximum number of megabytes
\r
2390 to allocate by using the
\96<span class=SpellE><i>maxmb</i></span> option, for
\r
2391 example to set a limit of 1.5 <span class=SpellE><span class=GramE>Gb</span></span>:</p>
\r
2393 <p class=MsoNormal><o:p> </o:p></p>
\r
2395 <p class=Code>muscle -in huge.fa -out huge.afa -maxhours 1.0 -maxmb 1500</p>
\r
2397 <p class=MsoNormal><o:p> </o:p></p>
\r
2399 <p class=MsoNormal>This feature has been hacked on top of code that wasn't
\r
2400 really designed for it. So it doesn't always work perfectly, but is better than
\r
2401 nothing. The ideal solution would be to implement linear space dynamic
\r
2402 programming code (e.g., the Myers-Miller algorithm) for situations where memory
\r
2403 is tight. One day I might do this if there is sufficient interest. If you are
\r
2404 interested in contributing the code, e.g. for a class project, please let me
\r
2405 know, I'll be glad to provide support.<o:p></o:p></p>
\r
2407 <h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954789"><![if !supportLists]><span
\r
2408 style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>4.7 </span></span><![endif]>The
\r
2409 profile scoring function</a></h2>
\r
2411 <p class=MsoNormal>Three different protein profile scoring functions are
\r
2412 supported, the log-expectation score (
\96<i>le</i> option) and a sum of pairs
\r
2413 score using either the PAM200 matrix (
\96<i>sp</i>) or the VTML240 matrix (
\96<span
\r
2414 class=SpellE><i>sv</i></span>). The log-expectation score is the default as it
\r
2415 gives better results on our tests, but is typically somewhere between two or
\r
2416 three times slower than the sum-of-pairs score. For nucleotides,
\96<span
\r
2417 class=SpellE><i>spn</i></span> is currently the only option (which is of course
\r
2418 the default for nucleotide data, so you don't need to specify this option).<o:p></o:p></p>
\r
2420 <h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954790"><![if !supportLists]><span
\r
2421 style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>4.8 </span></span><![endif]>Diagonal
\r
2422 optimization</a></h2>
\r
2424 <p class=MsoNormal>Creating a pair-wise alignment by dynamic programming
\r
2425 requires computing an <i>L</i><sub>1</sub> <span style='font-family:Symbol;
\r
2426 mso-ascii-font-family:"Times New Roman";mso-hansi-font-family:"Times New Roman";
\r
2427 mso-char-type:symbol;mso-symbol-font-family:Symbol'><span style='mso-char-type:
\r
2428 symbol;mso-symbol-font-family:Symbol'>´</span></span> <i>L</i><sub>2</sub>
\r
2429 matrix, where <i>L</i><sub>1</sub> and <i>L</i><sub>2</sub> are the sequence
\r
2430 lengths. A trick used in algorithms such as BLAST is to reduce the size of this
\r
2431 matrix by using fast methods to find "diagonals", i.e. short regions
\r
2432 of high similarity between the two sequences. This speeds up the algorithm at
\r
2433 the expense of some reduction in accuracy. MUSCLE uses a technique called <i>k</i>-<span
\r
2434 class=SpellE>mer</span> extension to find diagonals. It is disabled by default
\r
2435 because of the slight reduction in average accuracy and can be turned on by
\r
2436 specifying the
\96<span class=SpellE><i>diags</i></span> option. To enable
\r
2437 diagonal optimization in the first iteration, use
\96<i>diags1</i>, to enable
\r
2438 diagonal optimization in the second iteration, use
\96<i>diags2</i>. These are
\r
2439 provided separately because it would be a reasonable strategy to enable
\r
2440 diagonals in the first iteration but not the second (because the main goal of
\r
2441 the first iteration is to construct a multiple alignment quickly in order to
\r
2442 improve the distance matrix, which is not very sensitive to alignment quality;
\r
2443 whereas the goal of the second iteration is to make the best possible
\r
2444 progressive alignment).<o:p></o:p></p>
\r
2446 <h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954791"><![if !supportLists]><span
\r
2447 style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>4.9 </span></span><![endif]>Anchor
\r
2448 optimization</a></h2>
\r
2450 <p class=MsoNormal>Tree-dependent refinement (iterations 3, 4 <span
\r
2451 class=GramE>... )</span> can be speeded up by dividing the alignment vertically
\r
2452 into blocks. Block boundaries are found by identifying high-scoring columns
\r
2453 (e.g., a perfectly conserved column of Cs or Ws would be a candidate). Each
\r
2454 vertical block is then refined independently before reassembling the complete
\r
2455 alignment, which is faster because of the <i>L</i><sup>2</sup> factor in
\r
2456 dynamic programming (e.g., suppose the alignment is split into two vertical
\r
2457 blocks, then 2 <span style='font-family:Symbol;mso-ascii-font-family:"Times New Roman";
\r
2458 mso-hansi-font-family:"Times New Roman";mso-char-type:symbol;mso-symbol-font-family:
\r
2459 Symbol'><span style='mso-char-type:symbol;mso-symbol-font-family:Symbol'>´</span></span>
\r
2460 0.5<sup>2</sup> = 0.5, so the dynamic programming time is roughly halved). The
\r
2461 \96<span class=SpellE><i>noanchors</i></span> option is used to disable this
\r
2462 feature. This option has no effect if <i>
\96maxiters 1</i> or
\96<i>maxiters 2</i>
\r
2463 is specified. On benchmark tests, enabling anchors has little or no effect on
\r
2464 accuracy, but if you want to be very conservative and are striving for the best
\r
2465 possible accuracy then
\96<span class=SpellE><i>noanchors</i></span> is a
\r
2466 reasonable choice.<o:p></o:p></p>
\r
2468 <h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954792"><![if !supportLists]><span
\r
2469 style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>4.10 </span></span><![endif]>Log
\r
2472 <p class=MsoNormal>You can specify a log file by using
\96<i>log <filename></i>
\r
2473 or
\96<span class=SpellE><i>loga</i></span><i> <filename></i>. Using
\96<i>log</i>
\r
2474 causes any existing file to be deleted,
\96<span class=SpellE><i>loga</i></span>
\r
2475 appends to any existing file. A message will be written to the log file when <i>muscle</i>
\r
2476 starts and stops. Error and warning messages will also be written to the log.
\r
2477 If
\96<i>verbose</i> is specified, then more information will be written,
\r
2478 including the command line used to invoke <i>muscle</i>, the resulting internal
\r
2479 parameter settings, and also progress messages. The content and format of
\r
2480 verbose log file output is subject to change in future versions. </p>
\r
2482 <p class=MsoNormal><o:p> </o:p></p>
\r
2484 <p class=MsoNormal>The use of a log file may seem contrary to <span
\r
2485 class=GramE>Unix</span> conventions for using standard output and standard
\r
2486 error. I like these conventions, but never found a fully satisfactory way to
\r
2487 use them. I like progress messages (see below), but they mess up a file if you
\r
2488 re-direct standard error and there are errors or warning messages too. I could
\r
2489 try to detect whether a standard file handle is a <span class=SpellE><span
\r
2490 class=GramE><i>tty</i></span></span> device or a disk file and change behavior
\r
2491 accordingly, but I regard this as too complicated and too hard for the user to
\r
2492 understand. On Windows it can be hard to re-direct standard file handles,
\r
2493 especially when working in a GUI debugger. Maybe one day I will figure out a
\r
2494 better solution (suggestions welcomed).</p>
\r
2496 <p class=MsoNormal><o:p> </o:p></p>
\r
2498 <p class=MsoNormal>I highly recommend using
\96<i>verbose </i>and
\ad\96<i>log[a]</i>,
\r
2499 especially when running <i>muscle</i> in a batch mode. This enables you to
\r
2500 verify whether a particular alignment was completed and to review any errors or
\r
2501 warnings that occurred.<o:p></o:p></p>
\r
2503 <h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954793"><![if !supportLists]><span
\r
2504 style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>4.11 </span></span><![endif]>Progress
\r
2507 <p class=MsoNormal>By default, <i>muscle</i> writes progress messages to
\r
2508 standard error periodically so that you know it's doing something and get some
\r
2509 feedback about the time and memory requirements for the alignment. Here is a
\r
2510 typical progress message.</p>
\r
2512 <p class=MsoNormal><o:p> </o:p></p>
\r
2514 <p class=Code>00:00:23<span style='mso-spacerun:yes'>Â Â Â Â </span>25 Mb (5%)<span
\r
2515 style='mso-spacerun:yes'>Â </span>Iter<span style='mso-spacerun:yes'>Â Â
\r
2516 </span>2<span style='mso-spacerun:yes'>Â </span>87.20%<span
\r
2517 style='mso-spacerun:yes'>Â </span>Build guide tree</p>
\r
2519 <p class=MsoNormal><o:p> </o:p></p>
\r
2521 <p class=MsoNormal style='page-break-after:avoid'>The fields are as follows.</p>
\r
2523 <p class=MsoNormal style='page-break-after:avoid'><o:p> </o:p></p>
\r
2525 <table class=MsoTableGrid border=0 cellspacing=0 cellpadding=0
\r
2526 style='border-collapse:collapse;mso-yfti-tbllook:480;mso-padding-alt:0in 5.4pt 0in 5.4pt'>
\r
2527 <tr style='mso-yfti-irow:0'>
\r
2528 <td width=118 valign=top style='width:88.2pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2529 <p class=Code style='page-break-after:avoid'>00:00:23</p>
\r
2531 <td width=408 valign=top style='width:306.05pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2532 <p class=MsoNormal style='page-break-after:avoid'>Elapsed time since <i>muscle</i>
\r
2533 started.<o:p></o:p></p>
\r
2536 <tr style='mso-yfti-irow:1'>
\r
2537 <td width=118 valign=top style='width:88.2pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2538 <p class=Code style='page-break-after:avoid'>25 Mb (5%)</p>
\r
2540 <td width=408 valign=top style='width:306.05pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2541 <p class=MsoNormal style='page-break-after:avoid'>Peak memory use in megabytes
\r
2542 (i.e., not the current usage, but the maximum amount of memory used since <i>muscle</i>
\r
2543 started). The number in parentheses is the fraction of physical memory (see
\96<span
\r
2544 class=SpellE><i>maxmb</i></span> option for more discussion).<o:p></o:p></p>
\r
2547 <tr style='mso-yfti-irow:2'>
\r
2548 <td width=118 valign=top style='width:88.2pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2549 <p class=Code style='page-break-after:avoid'>Iter 2</p>
\r
2551 <td width=408 valign=top style='width:306.05pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2552 <p class=MsoNormal style='page-break-after:avoid'>Iteration currently in
\r
2556 <tr style='mso-yfti-irow:3'>
\r
2557 <td width=118 valign=top style='width:88.2pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2558 <p class=Code style='page-break-after:avoid'>87.20%</p>
\r
2560 <td width=408 valign=top style='width:306.05pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2561 <p class=MsoNormal style='page-break-after:avoid'>How much of the current step
\r
2562 has been completed (percentage).</p>
\r
2565 <tr style='mso-yfti-irow:4;mso-yfti-lastrow:yes'>
\r
2566 <td width=118 valign=top style='width:88.2pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2567 <p class=Code>Build...</p>
\r
2569 <td width=408 valign=top style='width:306.05pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2570 <p class=MsoNormal>A brief description of the current step.</p>
\r
2575 <p class=MsoNormal><o:p> </o:p></p>
\r
2577 <p class=MsoNormal>The
\96<i>quiet</i> command-line option disables writing
\r
2578 progress messages to standard error. If the
\96<i>verbose</i> command-line option
\r
2579 is specified, a progress message will be written to the log file when <span
\r
2580 class=GramE>each iteration</span> completes. So
\96<i>quiet</i> and
\96<i>verbose</i>
\r
2581 are not contradictory.</p>
\r
2583 <h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954794"><![if !supportLists]><span
\r
2584 style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>4.12 </span></span><![endif]>Running
\r
2585 out of memory</a></h2>
\r
2587 <p class=MsoNormal>The <i>muscle</i> code tries to deal gracefully with
\r
2588 low-memory conditions by using the following technique. A block of "emergency
\r
2589 reserve" memory is allocated when <i>muscle</i> starts. If a later request
\r
2590 to allocate memory fails, this reserve block is made available, and <i>muscle</i>
\r
2591 attempts to save the current alignment. With luck, the reserved memory will be
\r
2592 enough to allow <i>muscle</i> to save the alignment and exit gracefully with an
\r
2593 informative error message. See also the
\96<span class=SpellE><i>maxmb</i></span>
\r
2594 option.<o:p></o:p></p>
\r
2596 <h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954795"><![if !supportLists]><span
\r
2597 style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>4.13 </span></span><![endif]>Troubleshooting</a></h2>
\r
2599 <p class=MsoNormal>Here is some general advice on what to do if <i>muscle</i>
\r
2600 fails and you don't understand what happened. The code is designed to fail
\r
2601 gracefully with an informative error message when something goes wrong, but
\r
2602 there will no doubt be situations I haven't anticipated (not to mention bugs).</p>
\r
2604 <p class=MsoNormal><o:p> </o:p></p>
\r
2606 <p class=MsoNormal>Check the MUSCLE web site for updates, bug reports and other
\r
2607 relevant information.</p>
\r
2609 <p class=MsoNormal><o:p> </o:p></p>
\r
2611 <p class=MsoNormal style='page-break-after:avoid'><span style='mso-tab-count:
\r
2612 1'>Â Â Â Â Â Â Â </span><a href="http://www.drive5.com/muscle">http://www.drive5.com/muscle</a><i><o:p></o:p></i></p>
\r
2614 <p class=MsoNormal><o:p> </o:p></p>
\r
2616 <p class=MsoNormal>Check the input file to make sure it is in valid FASTA
\r
2617 format. Try giving it to another sequence analysis program that can accept
\r
2618 large FASTA files (e.g., the NCBI <span class=SpellE><i>formatdb</i></span>
\r
2619 utility) to see if you get an informative error message. Try dividing the file
\r
2620 into two halves and using each half individually as input. If one half fails
\r
2621 and the other <span class=GramE>does</span> not, repeat until the problem is
\r
2622 localized as far as possible.</p>
\r
2624 <p class=MsoNormal><o:p> </o:p></p>
\r
2626 <p class=MsoNormal>Use
\96<i>log</i> or
\96<span class=SpellE><i>loga</i></span>
\r
2627 and
\96\ad<i>verbose</i> and check the log file to see if there are any messages
\r
2628 that give you a hint about the problem. Look at the peak memory requirements
\r
2629 (reported in progress messages) to see if you may be exceeding the physical or
\r
2630 virtual memory capacity of your computer.</p>
\r
2632 <p class=MsoNormal><o:p> </o:p></p>
\r
2634 <p class=MsoNormal>If <i>muscle</i> crashes without giving an error message, or
\r
2635 hangs, then you may need to refer to the source code or use a debugger. A
\r
2636 "debug" version, <i>muscled</i>, may be provided. This is built from
\r
2637 the same source code but with the DEBUG macro defined and without compiler
\r
2638 optimizations. This version runs much more slowly (perhaps by a factor of three
\r
2639 or more), but does a lot more internal checking and may be able to catch
\r
2640 something that is going wrong in the code. The
\96\ad<i>core</i> option specifies
\r
2641 that <i>muscle</i> should not catch exceptions. When
\96<i>core</i> is specified,
\r
2642 an exception may result in a debugger trap or a core dump, depending on the
\r
2643 execution environment. The
\96<span class=SpellE><i>nocore</i></span> option has
\r
2644 the opposite effect. In <i>muscle</i>,
\96<span class=SpellE><i>nocore</i></span>
\r
2645 is the default,
\96\ad<i>core</i> is the default in <i>muscled</i>.</p>
\r
2647 <h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954796"><![if !supportLists]><span
\r
2648 style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>4.14 </span></span><![endif]>Technical
\r
2651 <p class=MsoNormal>I am happy to provide support. But I am busy, and am
\r
2652 offering this program at no charge, so I ask you to make a reasonable effort to
\r
2653 figure things out for yourself before contacting me.</p>
\r
2655 <h1 style='margin-left:0in;text-indent:0in'><a name="_Toc113954797"><![if !supportLists]><span
\r
2656 style='mso-fareast-font-family:Arial;mso-bidi-font-family:Arial'><span
\r
2657 style='mso-list:Ignore'>5 </span></span><![endif]>Command Line Reference</a></h1>
\r
2659 <p class=MsoNormal style='page-break-after:avoid'><o:p> </o:p></p>
\r
2661 <table class=MsoTableGrid border=0 cellspacing=0 cellpadding=0
\r
2662 style='border-collapse:collapse;mso-yfti-tbllook:480;mso-padding-alt:0in 5.4pt 0in 5.4pt'>
\r
2664 <tr style='mso-yfti-irow:0'>
\r
2665 <td width=110 valign=top style='width:82.85pt;border:none;border-bottom:
\r
2666 solid windowtext 1.0pt;mso-border-bottom-alt:solid windowtext .5pt;
\r
2667 padding:0in 5.4pt 0in 5.4pt'>
\r
2668 <p class=MsoNormal style='page-break-after:avoid'><b><span style='font-size:
\r
2669 9.0pt;font-family:Arial'>Value option<o:p></o:p></span></b></p>
\r
2671 <td width=113 valign=top style='width:84.8pt;border:none;border-bottom:solid windowtext 1.0pt;
\r
2672 mso-border-bottom-alt:solid windowtext .5pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2673 <p class=MsoNormal style='page-break-after:avoid'><b><span style='font-size:
\r
2674 9.0pt;font-family:Arial'>Legal values<o:p></o:p></span></b></p>
\r
2676 <td width=103 valign=top style='width:77.35pt;border:none;border-bottom:
\r
2677 solid windowtext 1.0pt;mso-border-bottom-alt:solid windowtext .5pt;
\r
2678 padding:0in 5.4pt 0in 5.4pt'>
\r
2679 <p class=MsoNormal style='page-break-after:avoid'><b><span style='font-size:
\r
2680 9.0pt;font-family:Arial'>Default<o:p></o:p></span></b></p>
\r
2682 <td width=264 valign=top style='width:197.8pt;border:none;border-bottom:
\r
2683 solid windowtext 1.0pt;mso-border-bottom-alt:solid windowtext .5pt;
\r
2684 padding:0in 5.4pt 0in 5.4pt'>
\r
2685 <p class=MsoNormal style='page-break-after:avoid'><b><span style='font-size:
\r
2686 9.0pt;font-family:Arial'>Description<o:p></o:p></span></b></p>
\r
2690 <tr style='mso-yfti-irow:1'>
\r
2691 <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2692 <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span
\r
2693 style='font-size:8.0pt;font-family:"Courier New"'>anchorspacing</span></span><span
\r
2694 style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>
\r
2696 <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2697 <p class=MsoNormal style='page-break-after:avoid'>Integer</p>
\r
2699 <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2700 <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
\r
2701 8.0pt;font-family:"Courier New"'>32<o:p></o:p></span></p>
\r
2703 <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2704 <p class=MsoNormal style='page-break-after:avoid'>Minimum spacing between
\r
2705 anchor columns.</p>
\r
2706 <p class=MsoNormal style='page-break-after:avoid'><o:p> </o:p></p>
\r
2709 <tr style='mso-yfti-irow:2'>
\r
2710 <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2711 <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
\r
2712 8.0pt;font-family:"Courier New"'>center<o:p></o:p></span></p>
\r
2714 <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2715 <p class=MsoNormal style='page-break-after:avoid'>Floating point</p>
\r
2717 <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2718 <p class=MsoNormal style='page-break-after:avoid'>[1]<o:p></o:p></p>
\r
2720 <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2721 <p class=MsoNormal style='page-break-after:avoid'>Center parameter. Should be
\r
2723 <p class=MsoNormal style='page-break-after:avoid'><o:p> </o:p></p>
\r
2726 <tr style='mso-yfti-irow:3'>
\r
2727 <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2728 <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
\r
2729 8.0pt;font-family:"Courier New"'>cluster1<o:p></o:p></span></p>
\r
2730 <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
\r
2731 8.0pt;font-family:"Courier New"'>cluster2<o:p></o:p></span></p>
\r
2733 <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2734 <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span
\r
2735 style='font-size:8.0pt;font-family:"Courier New"'>upgma</span></span><span
\r
2736 style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>
\r
2737 <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span
\r
2738 style='font-size:8.0pt;font-family:"Courier New"'>upgmb</span></span><span
\r
2739 style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>
\r
2740 <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span
\r
2741 style='font-size:8.0pt;font-family:"Courier New"'>neighborjoining</span></span><span
\r
2742 style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>
\r
2744 <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2745 <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span
\r
2746 style='font-size:8.0pt;font-family:"Courier New"'>upgmb</span></span><span
\r
2747 style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>
\r
2749 <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2750 <p class=MsoNormal style='page-break-after:avoid'>Clustering method. <span
\r
2751 class=GramE>cluster1</span> is used in iteration 1 and 2, cluster2 in later
\r
2753 <p class=MsoNormal style='page-break-after:avoid'><o:p> </o:p></p>
\r
2756 <tr style='mso-yfti-irow:4'>
\r
2757 <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2758 <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span
\r
2759 style='font-size:8.0pt;font-family:"Courier New"'>clwout</span></span><span
\r
2760 style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>
\r
2762 <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2763 <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
\r
2764 8.0pt;font-family:"Courier New"'>File name<o:p></o:p></span></p>
\r
2766 <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2767 <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
\r
2768 8.0pt;font-family:"Courier New"'>None<o:p></o:p></span></p>
\r
2770 <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2771 <p class=MsoNormal style='page-break-after:avoid'>Write output in CLUSTALW
\r
2772 format to given file name.</p>
\r
2775 <tr style='mso-yfti-irow:5'>
\r
2776 <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2777 <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span
\r
2778 style='font-size:8.0pt;font-family:"Courier New"'>clwout</span></span><span
\r
2779 style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>
\r
2781 <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2782 <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
\r
2783 8.0pt;font-family:"Courier New"'>File name<o:p></o:p></span></p>
\r
2785 <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2786 <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
\r
2787 8.0pt;font-family:"Courier New"'>None<o:p></o:p></span></p>
\r
2789 <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2790 <p class=MsoNormal style='page-break-after:avoid'>As <i>-<span class=SpellE>clwout</span></i>,
\r
2791 except that header is strictly compatible with CLUSTALW 1.81.</p>
\r
2792 <p class=MsoNormal style='page-break-after:avoid'><o:p> </o:p></p>
\r
2795 <tr style='mso-yfti-irow:6'>
\r
2796 <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2797 <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;
\r
2798 font-family:"Courier New"'>diagbreak</span></span><span style='font-size:
\r
2799 8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>
\r
2801 <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2802 <p class=MsoNormal>Integer<o:p></o:p></p>
\r
2804 <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2805 <p class=MsoNormal>1</p>
\r
2807 <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2808 <p class=MsoNormal>Maximum distance between two diagonals that allows them to
\r
2809 merge into one diagonal.</p>
\r
2810 <p class=MsoNormal><o:p> </o:p></p>
\r
2813 <tr style='mso-yfti-irow:7'>
\r
2814 <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2815 <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span
\r
2816 style='font-size:8.0pt;font-family:"Courier New"'>diaglength</span></span><span
\r
2817 style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>
\r
2819 <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2820 <p class=MsoNormal style='page-break-after:avoid'>Integer<o:p></o:p></p>
\r
2822 <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2823 <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
\r
2824 8.0pt;font-family:"Courier New"'>24<o:p></o:p></span></p>
\r
2826 <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2827 <p class=MsoNormal style='page-break-after:avoid'>Minimum length of diagonal.</p>
\r
2828 <p class=MsoNormal style='page-break-after:avoid'><o:p> </o:p></p>
\r
2831 <tr style='mso-yfti-irow:8'>
\r
2832 <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2833 <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span
\r
2834 style='font-size:8.0pt;font-family:"Courier New"'>diagmargin</span></span><span
\r
2835 style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>
\r
2837 <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2838 <p class=MsoNormal style='page-break-after:avoid'>Integer<o:p></o:p></p>
\r
2840 <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2841 <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
\r
2842 8.0pt;font-family:"Courier New"'>5<o:p></o:p></span></p>
\r
2844 <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2845 <p class=MsoNormal style='page-break-after:avoid'>Discard this many positions
\r
2846 at ends of diagonal.</p>
\r
2847 <p class=MsoNormal style='page-break-after:avoid'><o:p> </o:p></p>
\r
2850 <tr style='mso-yfti-irow:9'>
\r
2851 <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2852 <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>distance1<o:p></o:p></span></p>
\r
2853 <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><o:p> </o:p></span></p>
\r
2855 <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2856 <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>kmer6_6<o:p></o:p></span></p>
\r
2857 <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>kmer20_3<o:p></o:p></span></p>
\r
2858 <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>kmer20_4<o:p></o:p></span></p>
\r
2859 <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>kbit20_3<o:p></o:p></span></p>
\r
2860 <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>kmer4_6<o:p></o:p></span></p>
\r
2861 <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><o:p> </o:p></span></p>
\r
2863 <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2864 <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>Kmer6_6
\r
2865 (amino) or Kmer4_6 (<span class=SpellE>nucleo</span>)</span></p>
\r
2867 <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2868 <p class=MsoNormal>Distance measure for iteration 1.</p>
\r
2871 <tr style='mso-yfti-irow:10'>
\r
2872 <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2873 <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>distance2<o:p></o:p></span></p>
\r
2874 <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><o:p> </o:p></span></p>
\r
2876 <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2877 <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>kmer6_6<o:p></o:p></span></p>
\r
2878 <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>kmer20_3<o:p></o:p></span></p>
\r
2879 <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>kmer20_4<o:p></o:p></span></p>
\r
2880 <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>kbit20_3<o:p></o:p></span></p>
\r
2881 <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;
\r
2882 font-family:"Courier New"'>pctid_kimura</span></span><span style='font-size:
\r
2883 8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>
\r
2884 <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;
\r
2885 font-family:"Courier New"'>pctid_log</span></span><span style='font-size:
\r
2886 8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>
\r
2887 <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><o:p> </o:p></span></p>
\r
2889 <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2890 <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;
\r
2891 font-family:"Courier New"'>pctid_kimura</span></span></p>
\r
2893 <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2894 <p class=MsoNormal>Distance measure for iterations 2, 3 ...</p>
\r
2895 <p class=MsoNormal><o:p> </o:p></p>
\r
2896 <p class=MsoNormal><o:p> </o:p></p>
\r
2897 <p class=MsoNormal><o:p> </o:p></p>
\r
2898 <p class=MsoNormal><o:p> </o:p></p>
\r
2901 <tr style='mso-yfti-irow:11'>
\r
2902 <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2903 <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;
\r
2904 font-family:"Courier New"'>fastaout</span></span><span style='font-size:8.0pt;
\r
2905 font-family:"Courier New"'><o:p></o:p></span></p>
\r
2907 <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2908 <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>File
\r
2909 name<o:p></o:p></span></p>
\r
2911 <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2912 <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>None<o:p></o:p></span></p>
\r
2914 <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2915 <p class=MsoNormal>Write output in FASTA format to the given file.</p>
\r
2916 <p class=MsoNormal><o:p> </o:p></p>
\r
2919 <tr style='mso-yfti-irow:12'>
\r
2920 <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2921 <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;
\r
2922 font-family:"Courier New"'>gapopen</span></span><span style='font-size:8.0pt;
\r
2923 font-family:"Courier New"'><o:p></o:p></span></p>
\r
2925 <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2926 <p class=MsoNormal>Floating point</p>
\r
2928 <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2929 <p class=MsoNormal>[1]<o:p></o:p></p>
\r
2931 <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2932 <p class=MsoNormal>The <span class=GramE>gap open</span> score. Must be
\r
2934 <p class=MsoNormal><o:p> </o:p></p>
\r
2937 <tr style='mso-yfti-irow:13'>
\r
2938 <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2939 <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>hydro<o:p></o:p></span></p>
\r
2941 <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2942 <p class=MsoNormal>Integer<o:p></o:p></p>
\r
2944 <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2945 <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>5</span><o:p></o:p></p>
\r
2947 <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2948 <p class=MsoNormal>Window size for determining whether a region is
\r
2950 <p class=MsoNormal><o:p> </o:p></p>
\r
2953 <tr style='mso-yfti-irow:14'>
\r
2954 <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2955 <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;
\r
2956 font-family:"Courier New"'>hydrofactor</span></span><span style='font-size:
\r
2957 8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>
\r
2959 <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2960 <p class=MsoNormal>Floating point</p>
\r
2962 <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2963 <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>1.2<o:p></o:p></span></p>
\r
2965 <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2966 <p class=MsoNormal>Multiplier for gap open/close penalties in hydrophobic
\r
2968 <p class=MsoNormal><o:p> </o:p></p>
\r
2971 <tr style='mso-yfti-irow:15'>
\r
2972 <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2973 <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>in<o:p></o:p></span></p>
\r
2975 <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2976 <p class=MsoNormal>Any file name</p>
\r
2978 <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2979 <p class=MsoNormal>standard input</p>
\r
2981 <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2982 <p class=MsoNormal>Where to find the input sequences.</p>
\r
2983 <p class=MsoNormal><o:p> </o:p></p>
\r
2986 <tr style='mso-yfti-irow:16'>
\r
2987 <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2988 <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>in1<o:p></o:p></span></p>
\r
2990 <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2991 <p class=MsoNormal>Any file name</p>
\r
2993 <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2994 <p class=MsoNormal>None</p>
\r
2996 <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
2997 <p class=MsoNormal>Where to find an input alignment.</p>
\r
2998 <p class=MsoNormal><o:p> </o:p></p>
\r
3001 <tr style='mso-yfti-irow:17'>
\r
3002 <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3003 <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>in2<o:p></o:p></span></p>
\r
3005 <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3006 <p class=MsoNormal>Any file name</p>
\r
3008 <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3009 <p class=MsoNormal>None</p>
\r
3011 <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3012 <p class=MsoNormal>Where to find an input alignment.</p>
\r
3013 <p class=MsoNormal><o:p> </o:p></p>
\r
3016 <tr style='mso-yfti-irow:18'>
\r
3017 <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3018 <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>log<o:p></o:p></span></p>
\r
3020 <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3021 <p class=MsoNormal>File name<o:p></o:p></p>
\r
3023 <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3024 <p class=MsoNormal>None.<o:p></o:p></p>
\r
3026 <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3027 <p class=MsoNormal>Log file name (delete existing file).</p>
\r
3028 <p class=MsoNormal><o:p> </o:p></p>
\r
3031 <tr style='mso-yfti-irow:19'>
\r
3032 <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3033 <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;
\r
3034 font-family:"Courier New"'>loga</span></span><span style='font-size:8.0pt;
\r
3035 font-family:"Courier New"'><o:p></o:p></span></p>
\r
3037 <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3038 <p class=MsoNormal>File name</p>
\r
3040 <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3041 <p class=MsoNormal>None.</p>
\r
3043 <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3044 <p class=MsoNormal>Log file name (append to existing file).</p>
\r
3045 <p class=MsoNormal><o:p> </o:p></p>
\r
3048 <tr style='mso-yfti-irow:20'>
\r
3049 <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3050 <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>matrix<o:p></o:p></span></p>
\r
3052 <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3053 <p class=MsoNormal>File name</p>
\r
3055 <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3056 <p class=MsoNormal>None</p>
\r
3058 <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3059 <p class=MsoNormal>File name for substitution matrix in NCBI or WU-BLAST
\r
3060 format. If you specify your own matrix, you should also specify:</p>
\r
3061 <p class=MsoNormal><o:p> </o:p></p>
\r
3062 <p class=MsoNormal>-<span class=SpellE>gapopen</span> <g>, -<span
\r
3063 class=SpellE>gapextend</span> <e> -center 0.0</p>
\r
3064 <p class=MsoNormal><o:p> </o:p></p>
\r
3065 <p class=MsoNormal>Note that <g> and <e> MUST be negative.</p>
\r
3066 <p class=MsoNormal><o:p> </o:p></p>
\r
3069 <tr style='mso-yfti-irow:21'>
\r
3070 <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3071 <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;
\r
3072 font-family:"Courier New"'>maxhours</span></span><span style='font-size:8.0pt;
\r
3073 font-family:"Courier New"'><o:p></o:p></span></p>
\r
3075 <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3076 <p class=MsoNormal>Floating point</p>
\r
3078 <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3079 <p class=MsoNormal>None.</p>
\r
3081 <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3082 <p class=MsoNormal>Maximum time to run in hours. The actual time may exceed
\r
3083 the requested limit by a few minutes. Decimals are allowed, so 1.5 means one hour
\r
3084 and 30 minutes.</p>
\r
3085 <p class=MsoNormal><o:p> </o:p></p>
\r
3088 <tr style='mso-yfti-irow:22'>
\r
3089 <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3090 <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;
\r
3091 font-family:"Courier New"'>maxiters</span></span><span style='font-size:8.0pt;
\r
3092 font-family:"Courier New"'><o:p></o:p></span></p>
\r
3094 <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3095 <p class=MsoNormal>Integer 1, 2 ...</p>
\r
3097 <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3098 <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>16<o:p></o:p></span></p>
\r
3100 <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3101 <p class=MsoNormal>Maximum number of iterations.</p>
\r
3102 <p class=MsoNormal><o:p> </o:p></p>
\r
3105 <tr style='mso-yfti-irow:23'>
\r
3106 <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3107 <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;
\r
3108 font-family:"Courier New"'>maxmb</span></span><span style='font-size:8.0pt;
\r
3109 font-family:"Courier New"'><o:p></o:p></span></p>
\r
3111 <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3112 <p class=MsoNormal>Integer</p>
\r
3114 <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3115 <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>80%
\r
3116 of Physical RAM, or 500 Mb if not known.<o:p></o:p></span></p>
\r
3117 <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><o:p> </o:p></span></p>
\r
3119 <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3120 <p class=MsoNormal>Maximum memory to allocate in Mb.</p>
\r
3123 <tr style='mso-yfti-irow:24'>
\r
3124 <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3125 <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;
\r
3126 font-family:"Courier New"'>maxtrees</span></span><span style='font-size:8.0pt;
\r
3127 font-family:"Courier New"'><o:p></o:p></span></p>
\r
3129 <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3130 <p class=MsoNormal>Integer</p>
\r
3132 <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3133 <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>1<o:p></o:p></span></p>
\r
3135 <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3136 <p class=MsoNormal>Maximum number of new trees to build in iteration 2.</p>
\r
3137 <p class=MsoNormal><o:p> </o:p></p>
\r
3140 <tr style='mso-yfti-irow:25'>
\r
3141 <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3142 <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span
\r
3143 style='font-size:8.0pt;font-family:"Courier New"'>minbestcolscore</span></span><span
\r
3144 style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>
\r
3146 <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3147 <p class=MsoNormal style='page-break-after:avoid'>Floating point </p>
\r
3149 <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3150 <p class=MsoNormal style='page-break-after:avoid'>[1]</p>
\r
3152 <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3153 <p class=MsoNormal style='page-break-after:avoid'>Minimum score a column must
\r
3154 have to be an anchor.</p>
\r
3155 <p class=MsoNormal style='page-break-after:avoid'><o:p> </o:p></p>
\r
3158 <tr style='mso-yfti-irow:26'>
\r
3159 <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3160 <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span
\r
3161 style='font-size:8.0pt;font-family:"Courier New"'>minsmoothscore</span></span><span
\r
3162 style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>
\r
3164 <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3165 <p class=MsoNormal style='page-break-after:avoid'>Floating point</p>
\r
3167 <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3168 <p class=MsoNormal style='page-break-after:avoid'>[1]</p>
\r
3170 <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3171 <p class=MsoNormal style='page-break-after:avoid'>Minimum smoothed score a
\r
3172 column must have to be an anchor.</p>
\r
3173 <p class=MsoNormal style='page-break-after:avoid'><o:p> </o:p></p>
\r
3176 <tr style='mso-yfti-irow:27'>
\r
3177 <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3178 <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span
\r
3179 style='font-size:8.0pt;font-family:"Courier New"'>msaout</span></span><span
\r
3180 style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>
\r
3182 <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3183 <p class=MsoNormal style='page-break-after:avoid'>File name</p>
\r
3185 <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3186 <p class=MsoNormal style='page-break-after:avoid'>None</p>
\r
3188 <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3189 <p class=MsoNormal style='page-break-after:avoid'>Write output to given file
\r
3190 name in MSF format.</p>
\r
3191 <p class=MsoNormal style='page-break-after:avoid'><o:p> </o:p></p>
\r
3194 <tr style='mso-yfti-irow:28'>
\r
3195 <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3196 <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;
\r
3197 font-family:"Courier New"'>objscore</span></span><span style='font-size:8.0pt;
\r
3198 font-family:"Courier New"'><o:p></o:p></span></p>
\r
3200 <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3201 <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>sp<o:p></o:p></span></p>
\r
3202 <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;
\r
3203 font-family:"Courier New"'>ps</span></span><span style='font-size:8.0pt;
\r
3204 font-family:"Courier New"'><o:p></o:p></span></p>
\r
3205 <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;
\r
3206 font-family:"Courier New"'>dp</span></span><span style='font-size:8.0pt;
\r
3207 font-family:"Courier New"'><o:p></o:p></span></p>
\r
3208 <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;
\r
3209 font-family:"Courier New"'>xp</span></span><span style='font-size:8.0pt;
\r
3210 font-family:"Courier New"'><o:p></o:p></span></p>
\r
3211 <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;
\r
3212 font-family:"Courier New"'>spf</span></span><span style='font-size:8.0pt;
\r
3213 font-family:"Courier New"'><o:p></o:p></span></p>
\r
3214 <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;
\r
3215 font-family:"Courier New"'>spm</span></span><span style='font-size:8.0pt;
\r
3216 font-family:"Courier New"'><o:p></o:p></span></p>
\r
3218 <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3219 <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;
\r
3220 font-family:"Courier New"'>spm</span></span><span style='font-size:8.0pt;
\r
3221 font-family:"Courier New"'><o:p></o:p></span></p>
\r
3223 <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3224 <p class=MsoNormal>Objective score used by tree dependent refinement.</p>
\r
3225 <p class=MsoNormal><span class=GramE>sp=</span>sum-of-pairs score.</p>
\r
3226 <p class=MsoNormal><span class=SpellE>spf</span>=sum-of-pairs score (dimer
\r
3227 approximation)</p>
\r
3228 <p class=MsoNormal><span class=SpellE>spm</span>=sp for < 100 <span
\r
3229 class=SpellE>seqs</span>, otherwise <span class=SpellE>spf</span></p>
\r
3230 <p class=MsoNormal><span class=SpellE><span class=GramE>dp</span></span><span
\r
3231 class=GramE>=</span>dynamic programming score.</p>
\r
3232 <p class=MsoNormal><span class=SpellE><span class=GramE>ps</span></span><span
\r
3233 class=GramE>=</span>average profile-sequence score.</p>
\r
3234 <p class=MsoNormal><span class=SpellE><span class=GramE>xp</span></span><span
\r
3235 class=GramE>=</span>cross profile score.</p>
\r
3236 <p class=MsoNormal><o:p> </o:p></p>
\r
3239 <tr style='mso-yfti-irow:29'>
\r
3240 <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3241 <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>out<o:p></o:p></span></p>
\r
3243 <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3244 <p class=MsoNormal>File name</p>
\r
3246 <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3247 <p class=MsoNormal>standard output</p>
\r
3249 <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3250 <p class=MsoNormal>Where to write the alignment.</p>
\r
3251 <p class=MsoNormal><o:p> </o:p></p>
\r
3254 <tr style='mso-yfti-irow:30'>
\r
3255 <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3256 <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;
\r
3257 font-family:"Courier New"'>phyiout</span></span><span style='font-size:8.0pt;
\r
3258 font-family:"Courier New"'><o:p></o:p></span></p>
\r
3260 <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3261 <p class=MsoNormal>File name</p>
\r
3263 <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3264 <p class=MsoNormal>None</p>
\r
3266 <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3267 <p class=MsoNormal>Write output in <span class=SpellE>Phylip</span>
\r
3268 interleaved format to given file name.</p>
\r
3269 <p class=MsoNormal><o:p> </o:p></p>
\r
3272 <tr style='mso-yfti-irow:31'>
\r
3273 <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3274 <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;
\r
3275 font-family:"Courier New"'>physout</span></span><span style='font-size:8.0pt;
\r
3276 font-family:"Courier New"'><o:p></o:p></span></p>
\r
3278 <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3279 <p class=MsoNormal>File name</p>
\r
3281 <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3282 <p class=MsoNormal>None</p>
\r
3284 <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3285 <p class=MsoNormal>Write output in <span class=SpellE>Phylip</span>
\r
3286 sequential format to given file name.</p>
\r
3287 <p class=MsoNormal><o:p> </o:p></p>
\r
3290 <tr style='mso-yfti-irow:32'>
\r
3291 <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3292 <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;
\r
3293 font-family:"Courier New"'>refinewindow</span></span><span style='font-size:
\r
3294 8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>
\r
3296 <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3297 <p class=MsoNormal>Integer</p>
\r
3299 <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3300 <p class=MsoNormal>200</p>
\r
3302 <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3303 <p class=MsoNormal>Length of window for <i>-<span class=SpellE>refinew</span></i>.</p>
\r
3304 <p class=MsoNormal><o:p> </o:p></p>
\r
3307 <tr style='mso-yfti-irow:33'>
\r
3308 <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3309 <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>root1<o:p></o:p></span></p>
\r
3310 <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>root2<o:p></o:p></span></p>
\r
3312 <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3313 <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>pseudo<o:p></o:p></span></p>
\r
3314 <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;
\r
3315 font-family:"Courier New"'>midlongestspan</span></span><span
\r
3316 style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>
\r
3317 <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;
\r
3318 font-family:"Courier New"'>minavgleafdist</span></span><span
\r
3319 style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>
\r
3321 <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3322 <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;
\r
3323 font-family:"Courier New"'>psuedo</span></span><span style='font-size:8.0pt;
\r
3324 font-family:"Courier New"'><o:p></o:p></span></p>
\r
3326 <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3327 <p class=MsoNormal>Method used to root tree; root1 is used in iteration 1 and
\r
3328 2, root2 in later iterations.</p>
\r
3329 <p class=MsoNormal><o:p> </o:p></p>
\r
3330 <p class=MsoNormal><o:p> </o:p></p>
\r
3333 <tr style='mso-yfti-irow:34'>
\r
3334 <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3335 <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;
\r
3336 font-family:"Courier New"'>scorefile</span></span><span style='font-size:
\r
3337 8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>
\r
3339 <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3340 <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>File
\r
3341 name<o:p></o:p></span></p>
\r
3343 <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3344 <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>None<o:p></o:p></span></p>
\r
3346 <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3347 <p class=MsoNormal>File name where to write a score file. This contains one
\r
3348 line for each column in the alignment. The line contains the letters in the
\r
3349 column followed by the average BLOSUM62 score over pairs of letters in the column.</p>
\r
3350 <p class=MsoNormal><o:p> </o:p></p>
\r
3353 <tr style='mso-yfti-irow:35'>
\r
3354 <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3355 <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;
\r
3356 font-family:"Courier New"'>seqtype</span></span><span style='font-size:8.0pt;
\r
3357 font-family:"Courier New"'><o:p></o:p></span></p>
\r
3359 <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3360 <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>protein<o:p></o:p></span></p>
\r
3361 <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;
\r
3362 font-family:"Courier New"'>nucleo</span></span><span style='font-size:8.0pt;
\r
3363 font-family:"Courier New"'><o:p></o:p></span></p>
\r
3364 <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>auto<o:p></o:p></span></p>
\r
3365 <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><o:p> </o:p></span></p>
\r
3367 <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3368 <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>auto<o:p></o:p></span></p>
\r
3370 <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3371 <p class=MsoNormal>Sequence type.</p>
\r
3374 <tr style='mso-yfti-irow:36'>
\r
3375 <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3376 <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;
\r
3377 font-family:"Courier New"'>smoothscoreceil</span></span><span
\r
3378 style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>
\r
3380 <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3381 <p class=MsoNormal>Floating point</p>
\r
3383 <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3384 <p class=MsoNormal>[1]</p>
\r
3386 <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3387 <p class=MsoNormal>Maximum <span class=GramE>value of column score</span> for
\r
3388 smoothing purposes.</p>
\r
3389 <p class=MsoNormal><o:p> </o:p></p>
\r
3392 <tr style='mso-yfti-irow:37'>
\r
3393 <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3394 <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;
\r
3395 font-family:"Courier New"'>smoothwindow</span></span><span style='font-size:
\r
3396 8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>
\r
3398 <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3399 <p class=MsoNormal>Integer<o:p></o:p></p>
\r
3401 <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3402 <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>7<o:p></o:p></span></p>
\r
3404 <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3405 <p class=MsoNormal>Window used for anchor column smoothing.</p>
\r
3406 <p class=MsoNormal><o:p> </o:p></p>
\r
3409 <tr style='mso-yfti-irow:38'>
\r
3410 <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3411 <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;
\r
3412 font-family:"Courier New"'>spscore</span></span><span style='font-size:8.0pt;
\r
3413 font-family:"Courier New"'><o:p></o:p></span></p>
\r
3415 <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3416 <p class=MsoNormal>File name<o:p></o:p></p>
\r
3418 <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3419 <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><o:p> </o:p></span></p>
\r
3421 <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3422 <p class=MsoNormal>Compute SP objective score of multiple <span class=GramE>alignment</span>.</p>
\r
3423 <p class=MsoNormal><o:p> </o:p></p>
\r
3426 <tr style='mso-yfti-irow:39'>
\r
3427 <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3428 <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>SUEFF<o:p></o:p></span></p>
\r
3430 <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3431 <p class=MsoNormal>Floating point value between 0 and 1.</p>
\r
3432 <p class=MsoNormal><o:p> </o:p></p>
\r
3434 <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3435 <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>0.1<o:p></o:p></span></p>
\r
3437 <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3438 <p class=MsoNormal>Constant used in UPGMB clustering. Determines the relative
\r
3439 fraction of average linkage (SUEFF) vs. nearest-neighbor linkage (1
\96 SUEFF).<br
\r
3440 style='mso-special-character:line-break'>
\r
3441 <![if !supportLineBreakNewLine]><br style='mso-special-character:line-break'>
\r
3445 <tr style='mso-yfti-irow:40'>
\r
3446 <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3447 <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>tree1<o:p></o:p></span></p>
\r
3448 <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>tree2<o:p></o:p></span></p>
\r
3450 <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3451 <p class=MsoNormal>File name</p>
\r
3453 <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3454 <p class=MsoNormal>None<o:p></o:p></p>
\r
3456 <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3457 <p class=MsoNormal>Save tree produced in first or second iteration to given
\r
3458 file in <span class=SpellE>Newick</span> (<span class=SpellE>Phylip</span>-compatible)
\r
3460 <p class=MsoNormal><o:p> </o:p></p>
\r
3463 <tr style='mso-yfti-irow:41'>
\r
3464 <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3465 <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;
\r
3466 font-family:"Courier New"'>usetree</span></span><span style='font-size:8.0pt;
\r
3467 font-family:"Courier New"'><o:p></o:p></span></p>
\r
3469 <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3470 <p class=MsoNormal>File name</p>
\r
3472 <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3473 <p class=MsoNormal>None<o:p></o:p></p>
\r
3475 <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3476 <p class=MsoNormal>Use given tree as guide tree. Must by in <span
\r
3477 class=SpellE>Newick</span> (<span class=SpellE>Phyip</span>-compatible)
\r
3479 <p class=MsoNormal><o:p> </o:p></p>
\r
3482 <tr style='mso-yfti-irow:42;mso-yfti-lastrow:yes'>
\r
3483 <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3484 <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
\r
3485 8.0pt;font-family:"Courier New"'>weight1<o:p></o:p></span></p>
\r
3486 <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
\r
3487 8.0pt;font-family:"Courier New"'>weight2<o:p></o:p></span></p>
\r
3489 <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3490 <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
\r
3491 8.0pt;font-family:"Courier New"'>none<o:p></o:p></span></p>
\r
3492 <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span
\r
3493 style='font-size:8.0pt;font-family:"Courier New"'>henikoff</span></span><span
\r
3494 style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>
\r
3495 <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span
\r
3496 style='font-size:8.0pt;font-family:"Courier New"'>henikoffpb</span></span><span
\r
3497 style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>
\r
3498 <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span
\r
3499 style='font-size:8.0pt;font-family:"Courier New"'>gsc</span></span><span
\r
3500 style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>
\r
3501 <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span
\r
3502 style='font-size:8.0pt;font-family:"Courier New"'>clustalw</span></span><span
\r
3503 style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>
\r
3504 <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span
\r
3505 style='font-size:8.0pt;font-family:"Courier New"'>threeway</span></span></p>
\r
3507 <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3508 <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span
\r
3509 style='font-size:8.0pt;font-family:"Courier New"'>clustalw</span></span><span
\r
3510 style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>
\r
3511 <p class=MsoNormal style='page-break-after:avoid'><o:p> </o:p></p>
\r
3513 <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3514 <p class=MsoNormal style='page-break-after:avoid'>Sequence weighting scheme.</p>
\r
3515 <p class=MsoNormal style='page-break-after:avoid'><span class=GramE>weight1</span>
\r
3516 is used in iterations 1 and 2.</p>
\r
3517 <p class=MsoNormal style='page-break-after:avoid'><span class=GramE>weight2</span>
\r
3518 is used for tree-dependent refinement.</p>
\r
3519 <p class=MsoNormal style='page-break-after:avoid'><span class=GramE>none=</span>all
\r
3520 sequences have equal weight.</p>
\r
3521 <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span
\r
3522 class=GramE>henikoff</span></span><span class=GramE>=</span>Henikoff &
\r
3523 Henikoff weighting scheme.</p>
\r
3524 <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span
\r
3525 class=GramE>henikoffpb</span></span><span class=GramE>=</span>Modified
\r
3526 Henikoff scheme as used in PSI-BLAST.</p>
\r
3527 <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span
\r
3528 class=GramE>clustalw</span></span><span class=GramE>=</span>CLUSTALW method.</p>
\r
3529 <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span
\r
3530 class=GramE>threeway</span></span><span class=GramE>=</span>Gotoh three-way
\r
3532 <p class=MsoNormal style='page-break-after:avoid'><o:p> </o:p></p>
\r
3537 <p class=MsoNormal><o:p> </o:p></p>
\r
3539 <table class=MsoTableGrid border=0 cellspacing=0 cellpadding=0
\r
3540 style='border-collapse:collapse;mso-yfti-tbllook:480;mso-padding-alt:0in 5.4pt 0in 5.4pt'>
\r
3542 <tr style='mso-yfti-irow:0'>
\r
3543 <td width=137 valign=top style='width:102.6pt;border:none;border-bottom:
\r
3544 solid windowtext 1.0pt;mso-border-bottom-alt:solid windowtext .5pt;
\r
3545 padding:0in 5.4pt 0in 5.4pt'>
\r
3546 <p class=MsoNormal style='page-break-after:avoid'><b><span style='font-size:
\r
3547 9.0pt;font-family:Arial'>Flag option<o:p></o:p></span></b></p>
\r
3549 <td width=106 valign=top style='width:1.1in;border:none;border-bottom:solid windowtext 1.0pt;
\r
3550 mso-border-bottom-alt:solid windowtext .5pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3551 <p class=MsoNormal style='page-break-after:avoid'><b><span style='font-size:
\r
3552 9.0pt;font-family:Arial'>Set by default?<o:p></o:p></span></b></p>
\r
3554 <td width=348 valign=top style='width:261.0pt;border:none;border-bottom:
\r
3555 solid windowtext 1.0pt;mso-border-bottom-alt:solid windowtext .5pt;
\r
3556 padding:0in 5.4pt 0in 5.4pt'>
\r
3557 <p class=MsoNormal style='page-break-after:avoid'><b><span style='font-size:
\r
3558 9.0pt;font-family:Arial'>Description<o:p></o:p></span></b></p>
\r
3562 <tr style='mso-yfti-irow:1;height:6.25pt'>
\r
3563 <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;
\r
3565 <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
\r
3566 8.0pt;font-family:"Courier New"'>anchors<o:p></o:p></span></p>
\r
3568 <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;
\r
3570 <p class=MsoNormal style='page-break-after:avoid'>yes<o:p></o:p></p>
\r
3572 <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;
\r
3574 <p class=MsoNormal style='page-break-after:avoid'>Use anchor optimization in
\r
3575 tree dependent refinement iterations.</p>
\r
3576 <p class=MsoNormal style='page-break-after:avoid'><o:p> </o:p></p>
\r
3579 <tr style='mso-yfti-irow:2;height:6.25pt'>
\r
3580 <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;
\r
3582 <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span
\r
3583 style='font-size:8.0pt;font-family:"Courier New"'>brenner</span></span><span
\r
3584 style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>
\r
3586 <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;
\r
3588 <p class=MsoNormal style='page-break-after:avoid'>no</p>
\r
3590 <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;
\r
3592 <p class=MsoNormal style='page-break-after:avoid'>Use Steven Brenner's method
\r
3593 for computing the root alignment.</p>
\r
3594 <p class=MsoNormal style='page-break-after:avoid'><o:p> </o:p></p>
\r
3597 <tr style='mso-yfti-irow:3;height:6.25pt'>
\r
3598 <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;
\r
3600 <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
\r
3601 8.0pt;font-family:"Courier New"'>cluster<o:p></o:p></span></p>
\r
3603 <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;
\r
3605 <p class=MsoNormal style='page-break-after:avoid'>no</p>
\r
3607 <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;
\r
3609 <p class=MsoNormal style='page-break-after:avoid'>Perform fast clustering of
\r
3610 input sequences. Use the
\96<i>tree1</i> option to save the tree.</p>
\r
3611 <p class=MsoNormal style='page-break-after:avoid'><o:p> </o:p></p>
\r
3614 <tr style='mso-yfti-irow:4;height:6.25pt'>
\r
3615 <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;
\r
3617 <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
\r
3618 8.0pt;font-family:"Courier New"'>dimer<o:p></o:p></span></p>
\r
3620 <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;
\r
3622 <p class=MsoNormal style='page-break-after:avoid'>no</p>
\r
3624 <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;
\r
3626 <p class=MsoNormal style='page-break-after:avoid'>Use dimer approximation for
\r
3627 the SP score (faster, slightly less accurate).</p>
\r
3628 <p class=MsoNormal style='page-break-after:avoid'><o:p> </o:p></p>
\r
3631 <tr style='mso-yfti-irow:5;height:6.25pt'>
\r
3632 <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;
\r
3634 <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span
\r
3635 style='font-size:8.0pt;font-family:"Courier New"'>clw</span></span><span
\r
3636 style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>
\r
3638 <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;
\r
3640 <p class=MsoNormal style='page-break-after:avoid'>no<o:p></o:p></p>
\r
3642 <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;
\r
3644 <p class=MsoNormal style='page-break-after:avoid'>Write output in CLUSTALW
\r
3645 format (default is FASTA).</p>
\r
3646 <p class=MsoNormal style='page-break-after:avoid'><o:p> </o:p></p>
\r
3649 <tr style='mso-yfti-irow:6;height:6.25pt'>
\r
3650 <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;
\r
3652 <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span
\r
3653 style='font-size:8.0pt;font-family:"Courier New"'>clwstrict</span></span><span
\r
3654 style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>
\r
3656 <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;
\r
3658 <p class=MsoNormal style='page-break-after:avoid'>no</p>
\r
3660 <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;
\r
3662 <p class=MsoNormal style='page-break-after:avoid'>Write output in CLUSTALW
\r
3663 format with the "CLUSTAL W (1.81)" header rather than the MUSCLE
\r
3664 version. This is useful when a post-processing step is picky about the file
\r
3666 <p class=MsoNormal style='page-break-after:avoid'><o:p> </o:p></p>
\r
3669 <tr style='mso-yfti-irow:7;height:6.25pt'>
\r
3670 <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;
\r
3672 <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
\r
3673 8.0pt;font-family:"Courier New"'>core<o:p></o:p></span></p>
\r
3675 <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;
\r
3677 <p class=MsoNormal style='page-break-after:avoid'>yes in muscle,</p>
\r
3678 <p class=MsoNormal style='page-break-after:avoid'><span class=GramE>no</span>
\r
3679 in muscled.<o:p></o:p></p>
\r
3681 <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;
\r
3683 <p class=MsoNormal style='page-break-after:avoid'>Do not catch exceptions.</p>
\r
3684 <p class=MsoNormal style='page-break-after:avoid'><o:p> </o:p></p>
\r
3685 <p class=MsoNormal style='page-break-after:avoid'><o:p> </o:p></p>
\r
3688 <tr style='mso-yfti-irow:8;height:6.25pt'>
\r
3689 <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;
\r
3691 <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span
\r
3692 style='font-size:8.0pt;font-family:"Courier New"'>diags</span></span><span
\r
3693 style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>
\r
3695 <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;
\r
3697 <p class=MsoNormal style='page-break-after:avoid'>no<o:p></o:p></p>
\r
3699 <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;
\r
3701 <p class=MsoNormal style='page-break-after:avoid'>Use diagonal optimizations.
\r
3702 Faster, especially for closely related sequences, but may be less accurate.</p>
\r
3703 <p class=MsoNormal style='page-break-after:avoid'><o:p> </o:p></p>
\r
3706 <tr style='mso-yfti-irow:9;height:6.25pt'>
\r
3707 <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;
\r
3709 <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
\r
3710 8.0pt;font-family:"Courier New"'>diags1<o:p></o:p></span></p>
\r
3712 <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;
\r
3714 <p class=MsoNormal style='page-break-after:avoid'>no</p>
\r
3716 <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;
\r
3718 <p class=MsoNormal style='page-break-after:avoid'>Use diagonal optimizations
\r
3719 in first iteration.</p>
\r
3720 <p class=MsoNormal style='page-break-after:avoid'><o:p> </o:p></p>
\r
3723 <tr style='mso-yfti-irow:10;height:6.25pt'>
\r
3724 <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;
\r
3726 <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
\r
3727 8.0pt;font-family:"Courier New"'>diags2<o:p></o:p></span></p>
\r
3729 <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;
\r
3731 <p class=MsoNormal style='page-break-after:avoid'>no</p>
\r
3733 <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;
\r
3735 <p class=MsoNormal style='page-break-after:avoid'>Use diagonal optimizations
\r
3736 in second iteration.</p>
\r
3737 <p class=MsoNormal style='page-break-after:avoid'><o:p> </o:p></p>
\r
3740 <tr style='mso-yfti-irow:11;height:6.25pt'>
\r
3741 <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;
\r
3743 <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span
\r
3744 style='font-size:8.0pt;font-family:"Courier New"'>fasta</span></span><span
\r
3745 style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>
\r
3747 <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;
\r
3749 <p class=MsoNormal style='page-break-after:avoid'>yes<o:p></o:p></p>
\r
3751 <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;
\r
3753 <p class=MsoNormal style='page-break-after:avoid'>Write output in FASTA
\r
3755 <p class=MsoNormal style='page-break-after:avoid'><o:p> </o:p></p>
\r
3758 <tr style='mso-yfti-irow:12;height:6.25pt'>
\r
3759 <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;
\r
3761 <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
\r
3762 8.0pt;font-family:"Courier New"'>group<o:p></o:p></span></p>
\r
3764 <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;
\r
3766 <p class=MsoNormal style='page-break-after:avoid'>yes<o:p></o:p></p>
\r
3768 <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;
\r
3770 <p class=MsoNormal style='page-break-after:avoid'>Group similar sequences
\r
3771 together in the output. This is the default. See also
\96<i>stable</i>.</p>
\r
3772 <p class=MsoNormal style='page-break-after:avoid'><o:p> </o:p></p>
\r
3775 <tr style='mso-yfti-irow:13;height:6.25pt'>
\r
3776 <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;
\r
3778 <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
\r
3779 8.0pt;font-family:"Courier New"'>html<o:p></o:p></span></p>
\r
3781 <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;
\r
3783 <p class=MsoNormal style='page-break-after:avoid'>no<o:p></o:p></p>
\r
3785 <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;
\r
3787 <p class=MsoNormal style='page-break-after:avoid'>Write output in HTML format
\r
3788 (default is FASTA).</p>
\r
3789 <p class=MsoNormal style='page-break-after:avoid'><o:p> </o:p></p>
\r
3792 <tr style='mso-yfti-irow:14'>
\r
3793 <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3794 <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
\r
3795 8.0pt;font-family:"Courier New"'>le</span></p>
\r
3797 <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt'>
\r
3798 <p class=MsoNormal>maybe<o:p></o:p></p>
\r
3800 <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt'>
\r
3801 <p class=MsoNormal>Use log-expectation profile score (VTML240). Alternatives
\r
3802 are to use
\96<i>sp</i> or <i>
\96<span class=SpellE>sv</span></i>. This is the
\r
3803 default for amino acid sequences.<o:p></o:p></p>
\r
3804 <p class=MsoNormal><o:p> </o:p></p>
\r
3807 <tr style='mso-yfti-irow:15;height:6.25pt'>
\r
3808 <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;
\r
3810 <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;
\r
3811 font-family:"Courier New"'>msf</span></span><span style='font-size:8.0pt;
\r
3812 font-family:"Courier New"'><o:p></o:p></span></p>
\r
3814 <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;
\r
3816 <p class=MsoNormal>no<o:p></o:p></p>
\r
3818 <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;
\r
3820 <p class=MsoNormal>Write output in MSF format (default is FASTA). Designed to
\r
3821 be compatible with the GCG package.</p>
\r
3822 <p class=MsoNormal><o:p> </o:p></p>
\r
3825 <tr style='mso-yfti-irow:16;height:6.25pt'>
\r
3826 <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;
\r
3828 <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;
\r
3829 font-family:"Courier New"'>noanchors</span></span><span style='font-size:
\r
3830 8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>
\r
3832 <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;
\r
3834 <p class=MsoNormal>no<o:p></o:p></p>
\r
3836 <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;
\r
3838 <p class=MsoNormal>Disable anchor optimization. Default is
\96<i>anchors</i>.<o:p></o:p></p>
\r
3839 <p class=MsoNormal><o:p> </o:p></p>
\r
3842 <tr style='mso-yfti-irow:17;height:6.25pt'>
\r
3843 <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;
\r
3845 <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;
\r
3846 font-family:"Courier New"'>nocore</span></span><span style='font-size:8.0pt;
\r
3847 font-family:"Courier New"'><o:p></o:p></span></p>
\r
3849 <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;
\r
3851 <p class=MsoNormal>no in muscle,</p>
\r
3852 <p class=MsoNormal><span class=GramE>yes</span> in muscled.<o:p></o:p></p>
\r
3854 <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;
\r
3856 <p class=MsoNormal>Catch exceptions and give an error message if possible.</p>
\r
3857 <p class=MsoNormal><o:p> </o:p></p>
\r
3858 <p class=MsoNormal><o:p> </o:p></p>
\r
3861 <tr style='mso-yfti-irow:18;height:6.25pt'>
\r
3862 <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;
\r
3864 <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;
\r
3865 font-family:"Courier New"'>phyi</span></span><span style='font-size:8.0pt;
\r
3866 font-family:"Courier New"'><o:p></o:p></span></p>
\r
3868 <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;
\r
3870 <p class=MsoNormal>no<o:p></o:p></p>
\r
3872 <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;
\r
3874 <p class=MsoNormal>Write output in <span class=SpellE>Phylip</span>
\r
3875 interleaved format.</p>
\r
3876 <p class=MsoNormal><o:p> </o:p></p>
\r
3879 <tr style='mso-yfti-irow:19;height:6.25pt'>
\r
3880 <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;
\r
3882 <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>phys<o:p></o:p></span></p>
\r
3884 <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;
\r
3886 <p class=MsoNormal>no</p>
\r
3888 <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;
\r
3890 <p class=MsoNormal>Write output in <span class=SpellE>Phylip</span>
\r
3891 sequential format.</p>
\r
3892 <p class=MsoNormal><o:p> </o:p></p>
\r
3895 <tr style='mso-yfti-irow:20;height:6.25pt'>
\r
3896 <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;
\r
3898 <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>profile<o:p></o:p></span></p>
\r
3900 <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;
\r
3902 <p class=MsoNormal>no<o:p></o:p></p>
\r
3904 <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;
\r
3906 <p class=MsoNormal>Compute profile-profile alignment. Input alignments must
\r
3907 be given using
\96<i>in1</i> and
\96<i>in2</i> options.</p>
\r
3908 <p class=MsoNormal><o:p> </o:p></p>
\r
3911 <tr style='mso-yfti-irow:21;height:6.25pt'>
\r
3912 <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;
\r
3914 <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>quiet<o:p></o:p></span></p>
\r
3916 <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;
\r
3918 <p class=MsoNormal>no<o:p></o:p></p>
\r
3920 <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;
\r
3922 <p class=MsoNormal>Do not display progress messages.</p>
\r
3923 <p class=MsoNormal><o:p> </o:p></p>
\r
3926 <tr style='mso-yfti-irow:22;height:6.25pt'>
\r
3927 <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;
\r
3929 <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>refine<o:p></o:p></span></p>
\r
3931 <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;
\r
3933 <p class=MsoNormal>no<o:p></o:p></p>
\r
3935 <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;
\r
3937 <p class=MsoNormal>Input file is already aligned, skip first two iterations
\r
3938 and begin tree dependent refinement.</p>
\r
3939 <p class=MsoNormal><o:p> </o:p></p>
\r
3942 <tr style='mso-yfti-irow:23;height:6.25pt'>
\r
3943 <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;
\r
3945 <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;
\r
3946 font-family:"Courier New"'>refinew</span></span><span style='font-size:8.0pt;
\r
3947 font-family:"Courier New"'><o:p></o:p></span></p>
\r
3949 <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;
\r
3951 <p class=MsoNormal>no<o:p></o:p></p>
\r
3953 <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;
\r
3955 <p class=MsoNormal>Refine an alignment by dividing it into non-overlapping
\r
3956 windows and re-aligning each window. Typically used for whole-genome
\r
3957 nucleotide alignments.</p>
\r
3958 <p class=MsoNormal><o:p> </o:p></p>
\r
3961 <tr style='mso-yfti-irow:24;height:6.25pt'>
\r
3962 <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;
\r
3964 <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
\r
3965 8.0pt;font-family:"Courier New"'>sp<o:p></o:p></span></p>
\r
3967 <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;
\r
3969 <p class=MsoNormal>no<o:p></o:p></p>
\r
3971 <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;
\r
3973 <p class=MsoNormal>Use sum-of-pairs protein profile score (PAM200). Default
\r
3974 is
\96<i>le.<o:p></o:p></i></p>
\r
3975 <p class=MsoNormal><o:p> </o:p></p>
\r
3978 <tr style='mso-yfti-irow:25;height:6.25pt'>
\r
3979 <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;
\r
3981 <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span
\r
3982 style='font-size:8.0pt;font-family:"Courier New"'>spscore</span></span><span
\r
3983 style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>
\r
3985 <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;
\r
3987 <p class=MsoNormal>no</p>
\r
3989 <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;
\r
3991 <p class=MsoNormal>Compute alignment score of profile-profile alignment.
\r
3992 Input alignments must be given using
\96<i>in1</i> and
\96<i>in2</i> options.
\r
3993 These must be pre-aligned with gapped columns as needed, i.e. must be of the
\r
3994 same length (have same number of columns).</p>
\r
3995 <p class=MsoNormal><o:p> </o:p></p>
\r
3998 <tr style='mso-yfti-irow:26;height:6.25pt'>
\r
3999 <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;
\r
4001 <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span
\r
4002 style='font-size:8.0pt;font-family:"Courier New"'>spn</span></span><span
\r
4003 style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>
\r
4005 <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;
\r
4007 <p class=MsoNormal>maybe</p>
\r
4008 <p class=MsoNormal><o:p> </o:p></p>
\r
4010 <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;
\r
4012 <p class=MsoNormal>Use sum-of-pairs nucleotide profile score. This is the
\r
4013 only option for nucleotides, and is therefore the default. The substitution
\r
4014 scores and gap penalty scores are "borrowed" from BLASTZ.</p>
\r
4015 <p class=MsoNormal><o:p> </o:p></p>
\r
4018 <tr style='mso-yfti-irow:27;height:6.25pt'>
\r
4019 <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;
\r
4021 <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
\r
4022 8.0pt;font-family:"Courier New"'>stable<o:p></o:p></span></p>
\r
4024 <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;
\r
4026 <p class=MsoNormal>no<o:p></o:p></p>
\r
4028 <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;
\r
4030 <p class=MsoNormal>Preserve input order of sequences in output file. Default
\r
4031 is to group sequences by similarity (
\96<i>group</i>).</p>
\r
4032 <p class=MsoNormal><o:p> </o:p></p>
\r
4035 <tr style='mso-yfti-irow:28;height:6.25pt'>
\r
4036 <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;
\r
4038 <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;
\r
4039 font-family:"Courier New"'>sv</span></span><span style='font-size:8.0pt;
\r
4040 font-family:"Courier New"'><o:p></o:p></span></p>
\r
4042 <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;
\r
4044 <p class=MsoNormal>no<o:p></o:p></p>
\r
4046 <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;
\r
4048 <p class=MsoNormal>Use sum-of-pairs profile score (VTML240). Default is
\96<i>le.</i></p>
\r
4049 <p class=MsoNormal><o:p> </o:p></p>
\r
4052 <tr style='mso-yfti-irow:29;height:6.25pt'>
\r
4053 <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;
\r
4055 <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>termgaps4<o:p></o:p></span></p>
\r
4057 <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;
\r
4059 <p class=MsoNormal>yes<o:p></o:p></p>
\r
4061 <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;
\r
4063 <p class=MsoNormal>Use 4-way test for treatment of terminal gaps. (Cannot be
\r
4064 disabled in this version).</p>
\r
4065 <p class=MsoNormal><o:p> </o:p></p>
\r
4068 <tr style='mso-yfti-irow:30;height:6.25pt'>
\r
4069 <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;
\r
4071 <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;
\r
4072 font-family:"Courier New"'>termgapsfull</span></span><span style='font-size:
\r
4073 8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>
\r
4075 <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;
\r
4077 <p class=MsoNormal>no<o:p></o:p></p>
\r
4079 <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;
\r
4081 <p class=MsoNormal>Terminal gaps penalized with full penalty.</p>
\r
4082 <p class=MsoNormal>[1] Not fully supported in this version.</p>
\r
4083 <p class=MsoNormal><o:p> </o:p></p>
\r
4086 <tr style='mso-yfti-irow:31;height:6.25pt'>
\r
4087 <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;
\r
4089 <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;
\r
4090 font-family:"Courier New"'>termgapshalf</span></span><span style='font-size:
\r
4091 8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>
\r
4093 <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;
\r
4095 <p class=MsoNormal>yes<o:p></o:p></p>
\r
4097 <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;
\r
4099 <p class=MsoNormal>Terminal gaps penalized with half penalty.</p>
\r
4100 <p class=MsoNormal>[1] Not fully supported in this version.</p>
\r
4101 <p class=MsoNormal><o:p> </o:p></p>
\r
4104 <tr style='mso-yfti-irow:32;height:6.25pt'>
\r
4105 <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;
\r
4107 <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;
\r
4108 font-family:"Courier New"'>termgapshalflonger</span></span><span
\r
4109 style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>
\r
4111 <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;
\r
4113 <p class=MsoNormal>no<o:p></o:p></p>
\r
4115 <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;
\r
4117 <p class=MsoNormal>Terminal gaps penalized with half penalty if gap relative
\r
4119 <p class=MsoNormal><span class=GramE>longer</span> sequence, otherwise with
\r
4121 <p class=MsoNormal>[1] Not fully supported in this version.</p>
\r
4122 <p class=MsoNormal><o:p> </o:p></p>
\r
4125 <tr style='mso-yfti-irow:33;height:6.25pt'>
\r
4126 <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;
\r
4128 <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>verbose<o:p></o:p></span></p>
\r
4130 <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;
\r
4132 <p class=MsoNormal>no<o:p></o:p></p>
\r
4134 <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;
\r
4136 <p class=MsoNormal>Write parameter settings and progress messages to log
\r
4138 <p class=MsoNormal><o:p> </o:p></p>
\r
4141 <tr style='mso-yfti-irow:34;mso-yfti-lastrow:yes;height:6.25pt'>
\r
4142 <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;
\r
4144 <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>version<o:p></o:p></span></p>
\r
4146 <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;
\r
4148 <p class=MsoNormal>no<o:p></o:p></p>
\r
4150 <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;
\r
4152 <p class=MsoNormal>Write version string to <span class=SpellE>stdout</span>
\r
4158 <p class=MsoNormal><i><o:p> </o:p></i></p>
\r
4160 <p class=MsoNormal><i>Notes<o:p></o:p></i></p>
\r
4162 <p class=MsoNormal>[1] Default depends on the profile scoring function. To
\r
4163 determine the default, use
\96<i>verbose
\96log</i> and check the log file.</p>
\r
4165 <p class=MsoNormal><u><o:p><span style='text-decoration:none'> </span></o:p></u></p>
\r
git://source.jalview.org / jabaws.git / blob