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-ol\r
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-ul\r
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--->\r
-</style>\r
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-<style>\r
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-</head>\r
-\r
-<body lang=EN-US link=blue vlink=purple style='tab-interval:.25in'>\r
-\r
-<div class=Section1>\r
-\r
-<p class=MsoNormal><o:p> </o:p></p>\r
-\r
-<p class=MsoNormal><o:p> </o:p></p>\r
-\r
-<p class=MsoNormal><o:p> </o:p></p>\r
-\r
-<p class=MsoNormal><o:p> </o:p></p>\r
-\r
-<p class=MsoNormal align=right style='text-align:right'><span style='font-size:\r
-24.0pt;font-family:"Arial Black"'>MUSCLE User Guide<o:p></o:p></span></p>\r
-\r
-<p class=MsoNormal align=right style='text-align:right'><u> <o:p></o:p></u></p>\r
-\r
-<p class=MsoNormal align=right style='text-align:right'><b><span\r
-style='font-family:Arial'><o:p> </o:p></span></b></p>\r
-\r
-<p class=MsoNormal><span style='font-family:Arial'><o:p> </o:p></span></p>\r
-\r
-<p class=MsoNormal><span style='font-family:Arial'><o:p> </o:p></span></p>\r
-\r
-<p class=MsoNormal><span style='font-family:Arial'><o:p> </o:p></span></p>\r
-\r
-<p class=MsoNormal><span style='font-family:Arial'><o:p> </o:p></span></p>\r
-\r
-<p class=MsoNormal><span style='font-family:Arial'><o:p> </o:p></span></p>\r
-\r
-<p class=MsoNormal><span style='font-family:Arial'>Multiple sequence comparison\r
-by log-expectation<o:p></o:p></span></p>\r
-\r
-<p class=MsoNormal><span class=GramE><span style='font-family:Arial'>by</span></span><span\r
-style='font-family:Arial'> Robert C. Edgar<o:p></o:p></span></p>\r
-\r
-<p class=MsoNormal><span style='font-family:Arial'><o:p> </o:p></span></p>\r
-\r
-<p class=MsoNormal><span style='font-family:Arial'>Version 3.6<o:p></o:p></span></p>\r
-\r
-<p class=MsoNormal><span style='font-family:Arial'>September 2005<o:p></o:p></span></p>\r
-\r
-<p class=MsoNormal><span style='font-family:Arial'><o:p> </o:p></span></p>\r
-\r
-<p class=MsoNormal><span style='font-family:Arial'><o:p> </o:p></span></p>\r
-\r
-<p class=MsoNormal><span style='font-family:Arial'><a\r
-href="http://www.drive5.com/muscle">http://www.drive5.com/muscle</a><o:p></o:p></span></p>\r
-\r
-<p class=MsoNormal><span class=GramE><span style='font-family:Arial'>email</span></span><span\r
-style='font-family:Arial'>: muscle (at) drive5.com<o:p></o:p></span></p>\r
-\r
-<p class=MsoNormal><span style='font-family:Arial'><o:p> </o:p></span></p>\r
-\r
-<p class=MsoNormal><span style='font-family:Arial'>MUSCLE is updated regularly.\r
-Send me an e-mail if you would like to be notified of new releases.<o:p></o:p></span></p>\r
-\r
-<p class=MsoNormal><span style='font-family:Arial'><span\r
-style='mso-spacerun:yes'>Â </span><o:p></o:p></span></p>\r
-\r
-<p class=MsoNormal><span style='font-family:Arial'><o:p> </o:p></span></p>\r
-\r
-<p class=MsoNormal><i><span style='font-family:Arial'>Citation:<o:p></o:p></span></i></p>\r
-\r
-<p class=MsoNormal><span style='font-family:Arial'><o:p> </o:p></span></p>\r
-\r
-<p class=MsoNormal><span style='font-family:Arial'><a\r
-href="http://nar.oupjournals.org/cgi/content/full/32/5/1792?ijkey=48Nmt1tta0fMg&keytype=ref">Edgar,\r
-Robert C. (2004), MUSCLE: multiple sequence alignment with high accuracy and\r
-high throughput, <i>Nucleic Acids Research</i> <b>32</b>(5), 1792-97</a>.<o:p></o:p></span></p>\r
-\r
-<p class=MsoNormal><span style='font-family:Arial'><o:p> </o:p></span></p>\r
-\r
-<p class=MsoNormal><i><span style='font-family:Arial'>For a complete\r
-description of the algorithm, see also:<o:p></o:p></span></i></p>\r
-\r
-<p class=MsoNormal><span style='font-family:Arial'><o:p> </o:p></span></p>\r
-\r
-<p class=MsoNormal><span style='font-family:Arial'><a\r
-href="http://www.biomedcentral.com/1471-2105/5/113">Edgar, Robert C (2004), <span\r
-style='mso-bidi-font-weight:bold'>MUSCLE: a multiple sequence alignment method\r
-with reduced time and <span class=GramE>space</span> complexity</span>. <i\r
-style='mso-bidi-font-style:normal'>BMC Bioinformatics</i>, <b style='mso-bidi-font-weight:\r
-normal'>5</b>(1):113</a>.<br clear=all style='page-break-before:always'>\r
-</span><b><span style='font-size:16.0pt;font-family:Arial'>Table of Contents<o:p></o:p></span></b></p>\r
-\r
-<p class=MsoToc1 style='tab-stops:right dotted 431.5pt'><!--[if supportFields]><span\r
-style='font-family:Arial'><span style='mso-element:field-begin'></span><span\r
-style='mso-spacerun:yes'>Â </span>TOC \o "1-3" \h \z \u <span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954755">1\r
-Introduction<span style='color:windowtext;display:none;mso-hide:screen;\r
-text-decoration:none;text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc113954755 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>3</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700350035000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc1 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954756">2\r
-Quick Start<span style='color:windowtext;display:none;mso-hide:screen;\r
-text-decoration:none;text-underline:none'><span style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc113954756 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>3</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700350036000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954757">2.1\r
-Installation<span style='color:windowtext;display:none;mso-hide:screen;\r
-text-decoration:none;text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc113954757 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>3</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700350037000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954758">2.2\r
-Making an alignment<span style='color:windowtext;display:none;mso-hide:screen;\r
-text-decoration:none;text-underline:none'><span style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc113954758 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>3</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700350038000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954759">2.3\r
-Large alignments<span style='color:windowtext;display:none;mso-hide:screen;\r
-text-decoration:none;text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc113954759 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>3</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700350039000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954760">2.4\r
-Faster speed<span style='color:windowtext;display:none;mso-hide:screen;\r
-text-decoration:none;text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc113954760 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>4</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700360030000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954761">2.5\r
-Huge alignments<span style='color:windowtext;display:none;mso-hide:screen;\r
-text-decoration:none;text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc113954761 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>4</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700360031000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954762">2.6\r
-Accuracy: caveat emptor<span style='color:windowtext;display:none;mso-hide:\r
-screen;text-decoration:none;text-underline:none'><span style='mso-tab-count:\r
-1 dotted'> </span></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-begin'></span></span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'> PAGEREF\r
-_Toc113954762 \h </span><span style='color:windowtext;display:none;mso-hide:\r
-screen;text-decoration:none;text-underline:none'><span style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>4</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700360032000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954763">2.7\r
-Pipelining<span style='color:windowtext;display:none;mso-hide:screen;\r
-text-decoration:none;text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc113954763 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>4</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700360033000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954764">2.8\r
-Refining an existing alignment<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc113954764 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>4</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700360034000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954765">2.9\r
-Using a pre-computed guide tree<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc113954765 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>4</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700360035000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954766">2.10\r
-Profile-profile alignment<span style='color:windowtext;display:none;mso-hide:\r
-screen;text-decoration:none;text-underline:none'><span style='mso-tab-count:\r
-1 dotted'> </span></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-begin'></span></span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'> PAGEREF\r
-_Toc113954766 \h </span><span style='color:windowtext;display:none;mso-hide:\r
-screen;text-decoration:none;text-underline:none'><span style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>5</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700360036000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954767">2.11\r
-Adding sequences to an existing alignment<span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc113954767 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>5</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700360037000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954768">2.12\r
-Sequence clustering<span style='color:windowtext;display:none;mso-hide:screen;\r
-text-decoration:none;text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc113954768 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>5</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700360038000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954769">2.13\r
-Specifying a substitution matrix<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc113954769 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>6</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700360039000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954770">2.14\r
-Refining a long alignment<span style='color:windowtext;display:none;mso-hide:\r
-screen;text-decoration:none;text-underline:none'><span style='mso-tab-count:\r
-1 dotted'> </span></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-begin'></span></span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'> PAGEREF\r
-_Toc113954770 \h </span><span style='color:windowtext;display:none;mso-hide:\r
-screen;text-decoration:none;text-underline:none'><span style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>6</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700370030000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc1 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954771">3\r
-File Formats<span style='color:windowtext;display:none;mso-hide:screen;\r
-text-decoration:none;text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc113954771 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>6</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700370031000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954772">3.1\r
-Input files<span style='color:windowtext;display:none;mso-hide:screen;\r
-text-decoration:none;text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc113954772 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>6</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700370032000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954773">3.1.1\r
-Amino acid sequences<span style='color:windowtext;display:none;mso-hide:screen;\r
-text-decoration:none;text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc113954773 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>6</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700370033000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954774">3.1.2\r
-Nucleotide sequences<span style='color:windowtext;display:none;mso-hide:screen;\r
-text-decoration:none;text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc113954774 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>6</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700370034000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954775">3.1.3\r
-Determining sequence type<span style='color:windowtext;display:none;mso-hide:\r
-screen;text-decoration:none;text-underline:none'><span style='mso-tab-count:\r
-1 dotted'>. </span></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-begin'></span></span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'> PAGEREF\r
-_Toc113954775 \h </span><span style='color:windowtext;display:none;mso-hide:\r
-screen;text-decoration:none;text-underline:none'><span style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>7</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700370035000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954776">3.2\r
-Output files<span style='color:windowtext;display:none;mso-hide:screen;\r
-text-decoration:none;text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc113954776 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>7</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700370036000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc3 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954777">3.2.1\r
-Sequence grouping<span style='color:windowtext;display:none;mso-hide:screen;\r
-text-decoration:none;text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc113954777 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>7</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700370037000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954778">3.3\r
-CLUSTALW format<span style='color:windowtext;display:none;mso-hide:screen;\r
-text-decoration:none;text-underline:none'><span style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc113954778 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>7</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700370038000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954779">3.4\r
-MSF format<span style='color:windowtext;display:none;mso-hide:screen;\r
-text-decoration:none;text-underline:none'><span style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc113954779 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>7</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700370039000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954780">3.5\r
-HTML format<span style='color:windowtext;display:none;mso-hide:screen;\r
-text-decoration:none;text-underline:none'><span style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc113954780 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>8</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700380030000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954781">3.6\r
-Phylip format<span style='color:windowtext;display:none;mso-hide:screen;\r
-text-decoration:none;text-underline:none'><span style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc113954781 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>8</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700380031000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc1 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954782">4\r
-Using MUSCLE<span style='color:windowtext;display:none;mso-hide:screen;\r
-text-decoration:none;text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc113954782 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>8</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700380032000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954783">4.1\r
-How the algorithm works<span style='color:windowtext;display:none;mso-hide:\r
-screen;text-decoration:none;text-underline:none'><span style='mso-tab-count:\r
-1 dotted'>. </span></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-begin'></span></span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'> PAGEREF\r
-_Toc113954783 \h </span><span style='color:windowtext;display:none;mso-hide:\r
-screen;text-decoration:none;text-underline:none'><span style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>8</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700380033000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954784">4.2\r
-Command-line options<span style='color:windowtext;display:none;mso-hide:screen;\r
-text-decoration:none;text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc113954784 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>9</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700380034000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954785">4.3\r
-The maxiters option<span style='color:windowtext;display:none;mso-hide:screen;\r
-text-decoration:none;text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc113954785 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>9</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700380035000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954786">4.4\r
-The maxtrees option<span style='color:windowtext;display:none;mso-hide:screen;\r
-text-decoration:none;text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc113954786 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>10</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700380036000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954787">4.5\r
-The maxhours option<span style='color:windowtext;display:none;mso-hide:screen;\r
-text-decoration:none;text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc113954787 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>10</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700380037000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954788">4.6\r
-The maxmb option<span style='color:windowtext;display:none;mso-hide:screen;\r
-text-decoration:none;text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc113954788 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>10</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700380038000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954789">4.7\r
-The profile scoring function<span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc113954789 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>10</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700380039000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954790">4.8\r
-Diagonal optimization<span style='color:windowtext;display:none;mso-hide:screen;\r
-text-decoration:none;text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc113954790 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>10</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700390030000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954791">4.9\r
-Anchor optimization<span style='color:windowtext;display:none;mso-hide:screen;\r
-text-decoration:none;text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc113954791 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>11</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700390031000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954792">4.10\r
-Log file<span style='color:windowtext;display:none;mso-hide:screen;text-decoration:\r
-none;text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc113954792 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>11</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700390032000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954793">4.11\r
-Progress messages<span style='color:windowtext;display:none;mso-hide:screen;\r
-text-decoration:none;text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc113954793 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>11</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700390033000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954794">4.12\r
-Running out of memory<span style='color:windowtext;display:none;mso-hide:screen;\r
-text-decoration:none;text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc113954794 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>12</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700390034000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954795">4.13\r
-Troubleshooting<span style='color:windowtext;display:none;mso-hide:screen;\r
-text-decoration:none;text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc113954795 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>12</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700390035000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc2 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954796">4.14\r
-Technical support<span style='color:windowtext;display:none;mso-hide:screen;\r
-text-decoration:none;text-underline:none'><span style='mso-tab-count:1 dotted'> </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc113954796 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>12</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700390036000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoToc1 style='tab-stops:right dotted 431.5pt'><span\r
-class=MsoHyperlink><span style='mso-no-proof:yes'><a href="#_Toc113954797">5\r
-Command Line Reference<span style='color:windowtext;display:none;mso-hide:screen;\r
-text-decoration:none;text-underline:none'><span style='mso-tab-count:1 dotted'>. </span></span><!--[if supportFields]><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'><span style='mso-element:field-begin'></span></span><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'> PAGEREF _Toc113954797 \h </span><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-separator'></span></span><![endif]--><span\r
-style='color:windowtext;display:none;mso-hide:screen;text-decoration:none;\r
-text-underline:none'>13</span><span style='color:windowtext;display:none;\r
-mso-hide:screen;text-decoration:none;text-underline:none'><!--[if gte mso 9]><xml>\r
- <w:data>08D0C9EA79F9BACE118C8200AA004BA90B02000000080000000E0000005F0054006F0063003100310033003900350034003700390037000000</w:data>\r
-</xml><![endif]--></span><!--[if supportFields]><span style='color:windowtext;\r
-display:none;mso-hide:screen;text-decoration:none;text-underline:none'><span\r
-style='mso-element:field-end'></span></span><![endif]--></a></span></span><span\r
-style='font-size:12.0pt;mso-bidi-font-family:Sendnya;mso-no-proof:yes'><o:p></o:p></span></p>\r
-\r
-<p class=MsoNormal><!--[if supportFields]><span style='font-family:Arial'><span\r
-style='mso-element:field-end'></span></span><![endif]--><span style='font-family:\r
-Arial'><o:p> </o:p></span></p>\r
-\r
-<b><span style='font-size:16.0pt;font-family:Arial;mso-fareast-font-family:\r
-"MS Mincho";mso-bidi-font-family:"Times New Roman";mso-font-kerning:16.0pt;\r
-mso-ansi-language:EN-US;mso-fareast-language:JA;mso-bidi-language:AR-SA'><br\r
-clear=all style='page-break-before:always'>\r
-</span></b>\r
-\r
-<h1 style='margin-left:0in;text-indent:0in'><a name="_Toc113954755"><![if !supportLists]><span\r
-style='mso-fareast-font-family:Arial;mso-bidi-font-family:Arial'><span\r
-style='mso-list:Ignore'>1 </span></span><![endif]>Introduction</a></h1>\r
-\r
-<p class=MsoNormal>MUSCLE is a program for creating multiple alignments of\r
-amino acid or nucleotide sequences. A range of options is provided that give\r
-you the choice of optimizing accuracy, speed, or some compromise between the\r
-two. Default parameters are those that give the best average accuracy in our\r
-tests. Using versions current at the time of writing, my tests show that MUSCLE\r
-can achieve both better average accuracy and better speed than CLUSTALW or T‑Coffee,\r
-depending on the chosen options. Many command line options are provided to vary\r
-the internals of the algorithm; some of these will primarily be of interest to\r
-algorithm developers who wish to better understand which features of the algorithm\r
-are important in different circumstances.</p>\r
-\r
-<h1 style='margin-left:0in;text-indent:0in'><a name="_Toc113954756"><![if !supportLists]><span\r
-style='mso-fareast-font-family:Arial;mso-bidi-font-family:Arial'><span\r
-style='mso-list:Ignore'>2 </span></span><![endif]>Quick Start</a></h1>\r
-\r
-<p class=MsoNormal>The MUSCLE algorithm is delivered as a command-line program\r
-called <i>muscle</i>. If you are running under Linux or <span class=GramE>Unix</span>\r
-you will be working at a shell prompt. If you are running under Windows, you should\r
-be in a command window (nostalgically known to us older people as a DOS prompt).\r
-If you don't know how to use command-line programs, you should get help from a\r
-local guru.</p>\r
-\r
-<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954757"><![if !supportLists]><span\r
-style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>2.1 </span></span><![endif]>Installation</a></h2>\r
-\r
-<p class=MsoNormal>Copy the <i>muscle</i> binary file to a directory that is\r
-accessible from your computer. That's it\97there are no configuration files,\r
-libraries, environment variables or other settings to worry about. If you are\r
-using Windows, then the binary file is named <i>muscle.exe</i>. From now on <i>muscle</i>\r
-should be understood to mean "<i>muscle</i> if you are using Linux or <span\r
-class=GramE>Unix</span>, <i>muscle.exe</i> if you are using Windows".<o:p></o:p></p>\r
-\r
-<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954758"><![if !supportLists]><span\r
-style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>2.2 </span></span><![endif]>Making\r
-an alignment</a></h2>\r
-\r
-<p class=MsoNormal>Make a FASTA file containing some sequences. (If you are not\r
-familiar with FASTA format, it is described in detail later in this Guide.) For\r
-now, just to make things fast, limit the number of sequence in the file to no\r
-more than 50 and the sequence length to be no more than 500. Call the input\r
-file <span class=SpellE><i>seqs.fa</i></span>. (An example file named <span\r
-class=SpellE><i>seqs.fa</i></span> is distributed with the standard MUSCLE\r
-package). Make sure the directory containing the <i>muscle</i> binary is in\r
-your path. (If it isn't, you can run it by typing the full path name, and the\r
-following example command lines must be changed accordingly). Now type:</p>\r
-\r
-<p class=MsoNormal><o:p> </o:p></p>\r
-\r
-<p class=Code>muscle -in seqs.fa -out seqs.afa</p>\r
-\r
-<p class=MsoNormal><o:p> </o:p></p>\r
-\r
-<p class=MsoNormal>You should see some progress messages. If <i>muscle</i> completes\r
-successfully, it will create a file <span class=SpellE><i>seqs.afa</i></span>\r
-containing the alignment. By default, output is created in "aligned\r
-FASTA" format (hence the <i>.<span class=SpellE>afa</span></i> extension).\r
-This is just like regular FASTA except that gaps are added in order to align\r
-the sequences. This is a nice format for computers but not very readable for\r
-people, so to look at the alignment you will want an alignment viewer such as <span\r
-class=SpellE>Belvu</span>, or a script that converts FASTA to a more readable format.\r
-You can also use the \96<span class=SpellE><i>clw</i></span> command-line option\r
-to request output in CLUSTALW format, which is easier to understand for people.\r
-If <i>muscle</i> gives an error message and you don't know how to fix it,\r
-please read the Troubleshooting section.<o:p></o:p></p>\r
-\r
-<p class=MsoNormal><o:p> </o:p></p>\r
-\r
-<p class=MsoNormal>The default settings are designed to give the best accuracy,\r
-so this may be all you need to know.</p>\r
-\r
-<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954759"><![if !supportLists]><span\r
-style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>2.3 </span></span><![endif]>Large\r
-alignments</a></h2>\r
-\r
-<p class=MsoNormal>If you have a large number of sequences (a few thousand), or\r
-they are very long, then the default settings of may be too slow for practical\r
-use. A good compromise between speed and accuracy is to run just the first two\r
-iterations of the algorithm. On average, this gives accuracy comparable to\r
-T-Coffee and speeds much faster than CLUSTALW. This is done by the option <i>\96maxiters\r
-2</i>, as in the following example.</p>\r
-\r
-<p class=MsoNormal><o:p> </o:p></p>\r
-\r
-<p class=Code>muscle -in seqs.fa -out seqs.afa -maxiters 2</p>\r
-\r
-<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954760"><![if !supportLists]><span\r
-style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>2.4 </span></span><![endif]>Faster\r
-speed</a></h2>\r
-\r
-<p class=MsoNormal>The <i>\96<span class=SpellE>diags</span></i> option enables\r
-an optimization for speed by finding common words (6-mers in a compressed amino\r
-acid alphabet) between the two sequences as seeds for diagonals. This is\r
-related to optimizations in programs such as BLAST and FASTA: you get faster speed,\r
-but sometimes lower average accuracy. For large numbers of closely related\r
-sequences, this option works very well.</p>\r
-\r
-<p class=MsoNormal><o:p> </o:p></p>\r
-\r
-<p class=MsoNormal>If you want the fastest possible speed, then the following\r
-example shows the applicable options for proteins.</p>\r
-\r
-<p class=MsoNormal><o:p> </o:p></p>\r
-\r
-<p class=Code>muscle -in seqs.fa -out seqs.afa -maxiters 1 -diags -sv\r
--distance1 kbit20_3</p>\r
-\r
-<p class=Code><o:p> </o:p></p>\r
-\r
-<p class=MsoNormal>For nucleotides, use:</p>\r
-\r
-<p class=MsoNormal><o:p> </o:p></p>\r
-\r
-<p class=Code>muscle -in seqs.fa -out seqs.afa -maxiters 1 -diags</p>\r
-\r
-<p class=MsoNormal><o:p> </o:p></p>\r
-\r
-<p class=MsoNormal>At the time of writing, <i>muscle</i> with these options is faster\r
-than any other multiple sequence alignment <span class=GramE>program</span>\r
-that I have tested. The alignments are not bad, especially when the sequences\r
-are closely related. However, as you might expect, this blazing speed comes at\r
-the cost of the lowest average accuracy of the options that <i>muscle</i>\r
-provides.</p>\r
-\r
-<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954761"><![if !supportLists]><span\r
-style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>2.5 </span></span><![endif]>Huge\r
-alignments</a></h2>\r
-\r
-<p class=MsoNormal>If you have a <i>very</i> large number of sequences (several\r
-thousand), or they are very long, then the <i>kbit20_3</i> option may cause\r
-problems because it needs a relatively large amount of memory. Better is to use\r
-the default distance measure, which is roughly 2× or 3× slower but needs less\r
-memory, like this:</p>\r
-\r
-<p class=MsoNormal><o:p> </o:p></p>\r
-\r
-<p class=Code>muscle -in seqs.fa -out seqs.afa -maxiters 1 -diags1 -sv</p>\r
-\r
-<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954762"><![if !supportLists]><span\r
-style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>2.6 </span></span><![endif]>Accuracy:\r
-caveat emptor</a></h2>\r
-\r
-<p class=MsoNormal>Why do I keep using the clumsy phrase "average\r
-accuracy" instead of just saying "accuracy"? That's because the\r
-quality of alignments produced by MUSCLE varies, as do those produced other programs\r
-such as CLUSTALW and T-Coffee. The state of the art leaves plenty of room for\r
-improvement. Sometimes the fastest speed options to <i>muscle</i> give\r
-alignments that are better than T-Coffee, though the reverse will more often be\r
-the case. With challenging sets of sequences, it is a good idea to make several\r
-different alignments using different <i>muscle</i> options and to try other programs\r
-too. Regions where different alignments agree are more believable than regions\r
-where they disagree. <o:p></o:p></p>\r
-\r
-<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954763"><![if !supportLists]><span\r
-style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>2.7 </span></span><![endif]>Pipelining</a></h2>\r
-\r
-<p class=MsoNormal>Input can be taken from standard input, and output can be\r
-written to standard output. This is the default, so our first example would\r
-also work like this:</p>\r
-\r
-<p class=MsoNormal><o:p> </o:p></p>\r
-\r
-<p class=Code>muscle < seqs.fa > seqs.afa</p>\r
-\r
-<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954764"><![if !supportLists]><span\r
-style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>2.8 </span></span><![endif]>Refining\r
-an existing alignment</a></h2>\r
-\r
-<p class=MsoNormal>You can ask <i>muscle</i> to try to improve an existing\r
-alignment by using the \96<i>refine</i> option. The input file must then be a\r
-FASTA file containing an alignment. All sequences must be of equal length, gaps\r
-can be specified using dots "." or dashes "\96". For example:</p>\r
-\r
-<p class=MsoNormal><o:p> </o:p></p>\r
-\r
-<p class=Code>muscle -in seqs.afa -out refined.afa -refine</p>\r
-\r
-<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954765"><![if !supportLists]><span\r
-style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>2.9 </span></span><![endif]>Using\r
-a pre-computed guide tree</a></h2>\r
-\r
-<p class=MsoNormal>The \96<span class=SpellE><i>usetree</i></span> option allows\r
-you to provide your own guide tree. For example,</p>\r
-\r
-<p class=MsoNormal><o:p> </o:p></p>\r
-\r
-<p class=Code>muscle -in seqs.fa -out seqs.afa -usetree mytree.phy</p>\r
-\r
-<p class=MsoNormal><o:p> </o:p></p>\r
-\r
-<p class=MsoNormal>The tree must by in <span class=SpellE>Newick</span> format,\r
-as used by the <span class=SpellE>Phylip</span> package (hence the <i>.<span\r
-class=SpellE>phy</span></i> extension). The <span class=SpellE>Newick</span>\r
-format is described here:</p>\r
-\r
-<p class=MsoNormal><o:p> </o:p></p>\r
-\r
-<p class=MsoNormal><span style='mso-tab-count:1'>Â Â Â Â Â Â Â </span><a\r
-href="http://evolution.genetics.washington.edu/phylip/newicktree.html">http://evolution.genetics.washington.edu/phylip/newicktree.html</a></p>\r
-\r
-<p class=MsoNormal><o:p> </o:p></p>\r
-\r
-<p class=MsoNormal><span class=GramE><b>WARNING</b>.</span> Do not use this\r
-option just because you believe that you have an accurate evolutionary tree for\r
-your sequences. The best guide tree for multiple <span class=GramE>alignment</span>\r
-is <i>not</i> in general the correct evolutionary tree. This can be understood\r
-by the following argument. Alignment accuracy decreases with lower sequence\r
-identity. It follows that given a set of <span class=GramE>profiles,</span> the\r
-two that can be aligned most accurately will tend to be the pair with the\r
-highest identity, i.e. at the shortest evolutionary distance. This is exactly\r
-the pair selected by the nearest-neighbor criterion which MUSCLE uses by\r
-default. When mutation rates are variable, the <i>evolutionary </i>neighbor may\r
-not be the <i>nearest </i>neighbor. This explains why a nearest-neighbor tree\r
-may be superior to the true evolutionary tree for guiding a progressive alignment.</p>\r
-\r
-<p class=MsoNormal><o:p> </o:p></p>\r
-\r
-<p class=MsoNormal>You will get a warning if you use the \96<span class=SpellE><i>usetree</i></span>\r
-option. To disable the warning, use \ad<i>\96<span class=SpellE>usetree_nowarn</span></i>\r
-instead, </p>\r
-\r
-<p class=MsoNormal>e.g.:</p>\r
-\r
-<p class=MsoNormal><o:p> </o:p></p>\r
-\r
-<p class=Code>muscle -in seqs.fa -out seqs.afa -usetree_nowarn mytree.phy</p>\r
-\r
-<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954766"><![if !supportLists]><span\r
-style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>2.10 </span></span><![endif]>Profile-profile\r
-alignment</a></h2>\r
-\r
-<p class=MsoNormal>A fundamental step in the MUSCLE algorithm is aligning two\r
-multiple sequence alignments. This operation is sometimes called\r
-"profile-profile alignment". If you have two existing alignments of\r
-related sequences you can use the <i>\96profile</i> option of MUSCLE to align\r
-those two sequences. Typical usage is:</p>\r
-\r
-<p class=MsoNormal><o:p> </o:p></p>\r
-\r
-<p class=Code>muscle -profile -in1 one.afa -in2 two.afa -out both.afa</p>\r
-\r
-<p class=MsoNormal><o:p> </o:p></p>\r
-\r
-<p class=MsoNormal>The alignments in <span class=SpellE><i>one.afa</i></span>\r
-and <span class=SpellE><i>two.afa</i></span>, which must be in aligned FASTA\r
-format, are aligned to each other, keeping input columns intact and inserting\r
-columns of gaps where needed. Output is stored in <span class=SpellE><i>both.afa</i></span>.</p>\r
-\r
-<p class=MsoNormal><o:p> </o:p></p>\r
-\r
-<p class=MsoNormal>MUSCLE does not compute a similarity measure or measure of\r
-statistical significance (such as an E-value), so this option is not useful for\r
-discriminating homologs from unrelated sequences. For this task, I recommend <span\r
-class=SpellE>Sadreyev</span> & <span class=SpellE>Grishin's</span> COMPASS\r
-program.</p>\r
-\r
-<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954767"><![if !supportLists]><span\r
-style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>2.11 </span></span><![endif]>Adding\r
-sequences to an existing alignment</a></h2>\r
-\r
-<p class=MsoNormal>To add a sequence to an existing alignment that you wish to\r
-keep intact, use profile-profile alignment with the new sequence as a profile.\r
-For example, if you have an existing alignment <span class=SpellE><i>existing_aln.afa</i></span>\r
-and want to add a new sequence in <span class=SpellE><i>new_seq.fa</i></span>,\r
-use the following commands:</p>\r
-\r
-<p class=MsoNormal><o:p> </o:p></p>\r
-\r
-<p class=Code>muscle -profile -in1 existing_aln.afa -in2 new_seq.fa -out\r
-combined.afa<o:p></o:p></p>\r
-\r
-<p class=MsoNormal><o:p> </o:p></p>\r
-\r
-<p class=MsoNormal>If you have more than one new <span class=GramE>sequences</span>,\r
-you can align them first then add them, for example:</p>\r
-\r
-<p class=MsoNormal><o:p> </o:p></p>\r
-\r
-<p class=Code>muscle -in new_seqs.fa -out new_seqs.afa</p>\r
-\r
-<p class=Code>muscle -profile -in1 existing_aln.afa -in2 new_seqs.fa -out\r
-combined.afas</p>\r
-\r
-<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954768"><![if !supportLists]><span\r
-style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>2.12 </span></span><![endif]>Sequence\r
-clustering</a></h2>\r
-\r
-<p class=MsoNormal>The first stage in MUSCLE is a fast clustering algorithm.\r
-This may be of use in other applications. Typical usage is:</p>\r
-\r
-<p class=MsoNormal><o:p> </o:p></p>\r
-\r
-<p class=Code>muscle -cluster -in seqs.fa -tree1 tree.phy -maxiters 1</p>\r
-\r
-<p class=MsoNormal><o:p> </o:p></p>\r
-\r
-<p class=MsoNormal>The sequences will be clustered, and a tree written to <span\r
-class=SpellE><i>tree.phy</i></span>. Options \96<i>weight1</i>, \96<i>distance1</i>,\r
-\96<i>cluster1</i> and \96<i>root1</i> can be applied if desired. Note that by\r
-default, UPGMA clustering is used. You can use</p>\r
-\r
-<p class=MsoNormal><span style='mso-spacerun:yes'>Â </span><span class=GramE>\96<span\r
-class=SpellE><i>neighborjoining</i></span> if you prefer, but note that this is\r
-substantially slower than UPGMA for large numbers of sequences, and is also\r
-slightly less accurate.</span> See discussion of \96<span class=SpellE><i>usetree</i></span>\r
-above.</p>\r
-\r
-<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954769"><![if !supportLists]><span\r
-style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>2.13 </span></span><![endif]>Specifying\r
-a substitution matrix</a></h2>\r
-\r
-<p class=MsoNormal>You can specify your own substitution matrix by using the <i>-matrix</i>\r
-option. This reads a protein substitution matrix in NCBI or WU-BLAST format.\r
-The alphabet is assumed to be amino acid, and sum-of-pairs scoring is used. The\r
-\ad<i>-<span class=SpellE>gapopen</span></i>, <i>-<span class=SpellE>gapextend</span></i>\r
-and -<i>center</i> parameters should be specified; normally you will specify a\r
-zero value for the center. Note that gap penalties MUST be negative. The\r
-environment variable MUSCLE_MXPATH can be used to specify a path where the\r
-matrices are stored. For example,</p>\r
-\r
-<p class=MsoNormal><o:p> </o:p></p>\r
-\r
-<p class=Code>muscle -in seqs.fa -out seqs.afa -matrix blosum62 -gapopen -12.0</p>\r
-\r
-<p class=Code><span style='mso-tab-count:1'>Â Â </span><span\r
-style='mso-spacerun:yes'>Â </span>-gapextend -1.0 -center 0.0</p>\r
-\r
-<p class=MsoNormal><o:p> </o:p></p>\r
-\r
-<p class=MsoNormal>You can hack a nucleotide matrix by pretending that AGCT are\r
-amino acids and making a 20x20 matrix out of the original 4x4 matrix. Let me\r
-know if this isn't clear, I can help you through it.<o:p></o:p></p>\r
-\r
-<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954770"><![if !supportLists]><span\r
-style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>2.14 </span></span><![endif]>Refining\r
-a long alignment</a></h2>\r
-\r
-<p class=MsoNormal>A long alignment can be refined using the \96<span\r
-class=SpellE><i>refinew</i></span> option, which is primarily designed for\r
-refining whole-genome nucleotide alignments. Usage is:</p>\r
-\r
-<p class=MsoNormal><o:p> </o:p></p>\r
-\r
-<p class=Code>muscle -in input.afa -out output.afa</p>\r
-\r
-<p class=MsoNormal><o:p> </o:p></p>\r
-\r
-<p class=MsoNormal>MUSCLE divides the input alignment into non-overlapping\r
-windows and re-aligns each window from scratch, i.e. all gap characters are\r
-discarded. The \96<span class=SpellE><i>refinewindow</i></span> option may be\r
-used to change the window length, which <span class=GramE>is</span> 200 columns\r
-by default.<o:p></o:p></p>\r
-\r
-<h1 style='margin-left:0in;text-indent:0in'><a name="_Toc113954771"><![if !supportLists]><span\r
-style='mso-fareast-font-family:Arial;mso-bidi-font-family:Arial'><span\r
-style='mso-list:Ignore'>3 </span></span><![endif]>File Formats</a></h1>\r
-\r
-<p class=MsoNormal>MUSCLE uses FASTA format for both input and output. For\r
-output only, it also offers CLUSTALW, MSF, HTML, <span class=SpellE>Phylip</span>\r
-sequential and <span class=SpellE>Phylip</span> interleaved formats. See the\r
-following command-line options: ‑<span class=SpellE><i>clw</i></span>, ‑<span\r
-class=SpellE><i>clwstrict</i></span><i>, </i>\96<span class=SpellE><i>msf</i></span>,\r
-\96<i>html</i>, \96<i>phys</i>, \96<span class=SpellE><i>phyi</i></span><i>,</i> ‑<span\r
-class=SpellE><i>clwout</i></span>, ‑<span class=SpellE><i>clwstrictout</i></span><i>,\r
-</i>\96<span class=SpellE><i>msfout</i></span>, \96<span class=SpellE><i>htmlout</i></span>,\r
-\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
-\r
-<p class=MsoNormal><o:p> </o:p></p>\r
-\r
-<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954772"><![if !supportLists]><span\r
-style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>3.1 </span></span><![endif]>Input\r
-files</a></h2>\r
-\r
-<p class=MsoNormal>Input files must be in FASTA format. These are plain text\r
-files (word processing files such as Word documents are not understood!). <span\r
-class=GramE>Unix</span>, Windows and DOS text files are supported (end-of-line\r
-may be NL or CR NL). There is no explicit limit on the length of a sequence,\r
-however if you are running a 32-bit version of <i>muscle</i> then the maximum\r
-will be very roughly 10,000 letters due to maximum addressable size of tables\r
-required in memory. Each sequence starts with an annotation line, which is\r
-recognized by having a greater-than symbol ">" as its first\r
-character. There is no limit on the length of an annotation line (this is new\r
-as of version 3.5), and there is no requirement that the annotation be unique. The\r
-sequence itself follows on one or more subsequent lines, and is terminated\r
-either by the next annotation line or by the end of the file. </p>\r
-\r
-<h3 style='margin-left:0in;text-indent:0in'><a name="_Toc113954773"><![if !supportLists]><span\r
-style='mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:"Times New Roman"'><span\r
-style='mso-list:Ignore'>3.1.1 </span></span><![endif]>Amino acid sequences</a></h3>\r
-\r
-<p class=MsoNormal>The standard single-letter amino acid alphabet is used. Upper\r
-and lower case is allowed, the case is not significant. The special characters\r
-X, B, Z and U are understood. X means "unknown amino acid", B is D or\r
-N, Z is E or Q. U is understood to be the 21st amino acid <span class=SpellE>Selenocysteine</span>.\r
-White space (spaces, tabs and the end-of-line characters CR and NL) is allowed\r
-inside sequence data. Dots "." and dashes "\96" in sequences\r
-are allowed and are discarded unless the input is expected to be aligned (e.g.\r
-for the \96<i>refine</i> option). </p>\r
-\r
-<h3 style='margin-left:0in;text-indent:0in'><a name="_Toc113954774"><![if !supportLists]><span\r
-style='mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:"Times New Roman"'><span\r
-style='mso-list:Ignore'>3.1.2 </span></span><![endif]>Nucleotide sequences</a></h3>\r
-\r
-<p class=MsoNormal>The usual letters A, G, C, T and U stand for nucleotides.\r
-The letters T and U are equivalent as far as MUSCLE is concerned. N is the\r
-wildcard meaning "unknown nucleotide". R means A or G, Y means C or\r
-T/U. Other wildcards, such as those used by RFAM, are not understood in this\r
-version and will be replaced by Ns. If you would like support for other DNA /\r
-RNA alphabets, please let me know.</p>\r
-\r
-<h3 style='margin-left:0in;text-indent:0in'><a name="_Toc113954775"><![if !supportLists]><span\r
-style='mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:"Times New Roman"'><span\r
-style='mso-list:Ignore'>3.1.3 </span></span><![endif]>Determining sequence type</a></h3>\r
-\r
-<p class=MsoNormal>By default, MUSCLE looks at the first 100 letters in the\r
-input sequence data (excluding gaps). If 95% or more of those letters are valid\r
-nucleotides (AGCTUN), then the file is treated as nucleotides, otherwise as\r
-amino acids. This method almost always guesses correctly, but you can make sure\r
-by specifying the sequence type on the command line. This is done using the \96<span\r
-class=SpellE><i>seqtype</i></span> option, which can take the following values:</p>\r
-\r
-<p class=MsoNormal><o:p> </o:p></p>\r
-\r
-<p class=MsoNormal><span style='mso-tab-count:1'>Â Â Â Â Â Â Â </span>\96\ad<span\r
-class=SpellE><i>seqtype</i></span><i> protein</i><span style='mso-tab-count:\r
-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
-\r
-<p class=MsoNormal><span style='mso-tab-count:1'>Â Â Â Â Â Â Â </span>\96<span\r
-class=SpellE>s<i>eqtype</i></span><i> <span class=SpellE>nucleo</span></i><span\r
-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
-\r
-<p class=MsoNormal><span style='mso-tab-count:1'>Â Â Â Â Â Â Â </span><span\r
-class=GramE>\96<span class=SpellE><i>seqtype</i></span><i> auto</i><span\r
-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
-detection (default).</span><o:p></o:p></p>\r
-\r
-<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954776"><![if !supportLists]><span\r
-style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>3.2 </span></span><![endif]>Output\r
-files</a></h2>\r
-\r
-<p class=MsoNormal>By default, output is also written in FASTA format. All\r
-letters are upper-case and gaps are represented by dashes "\96". Output\r
-is written to the following destination(s):</p>\r
-\r
-<p class=MsoNormal><o:p> </o:p></p>\r
-\r
-<p class=MsoNormal><span style='mso-tab-count:1'>Â Â Â Â Â Â Â </span>If no other\r
-output option is given, then standard output.</p>\r
-\r
-<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
-is given, to the specified file.</p>\r
-\r
-<p class=MsoNormal><span style='mso-tab-count:1'>Â Â Â Â Â Â Â </span><span\r
-class=GramE>For all of the <i>-<span class=SpellE>xxxout</span></i> options\r
-(e.g. -<span class=SpellE><i>fastaout</i></span>, -<span class=SpellE><i>clwout</i></span>),\r
-to the specified files.</span><o:p></o:p></p>\r
-\r
-<h3 style='margin-left:0in;text-indent:0in'><a name="_Toc113954777"><![if !supportLists]><span\r
-style='mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:"Times New Roman"'><span\r
-style='mso-list:Ignore'>3.2.1 </span></span><![endif]>Sequence grouping</a></h3>\r
-\r
-<p class=MsoNormal>By default, MUSCLE re-arranges sequences so that similar\r
-sequences are adjacent in the output file. (This is done by ordering sequences\r
-according to a prefix traversal of the guide tree). This makes the alignment\r
-easier to evaluate by eye. If you want to the sequences to be output in the\r
-same order as the input file, you can use the \96<i>stable</i> option.</p>\r
-\r
-<h3 style='margin-left:0in;text-indent:0in'><![if !supportLists]><span\r
-style='mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:"Times New Roman"'><span\r
-style='mso-list:Ignore'>3.2.2 </span></span><![endif]>Output to multiple file\r
-formats</h3>\r
-\r
-<p class=MsoNormal>You can request output to more than one file format by using\r
-the -<span class=SpellE><i>xxxout</i></span> options. For example, to get both\r
-FASTA and CLUSTALW formats:</p>\r
-\r
-<p class=MsoNormal><o:p> </o:p></p>\r
-\r
-<p class=Code>muscle -in seqs.fa -fastaout seqs.afa -clwout seqs.aln<o:p></o:p></p>\r
-\r
-<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954778"><![if !supportLists]><span\r
-style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>3.3 </span></span><![endif]>CLUSTALW\r
-format</a></h2>\r
-\r
-<p class=MsoNormal>You can request CLUSTALW output by using the \96<span\r
-class=SpellE><i>clw</i></span> option. This should be compatible with CLUSTALW,\r
-with the exception of the program name in the file header. You can ask MUSCLE\r
-to impersonate CLUSTALW by writing "CLUSTAL W (1.81)" as the program\r
-name by using \96<span class=SpellE><i>clwstrict</i></span> or <i>‑<span\r
-class=SpellE>clwstrictout</span></i>. Note that MUSCLE allows duplicate\r
-sequence labels, while CLUSTALW forbids duplicates. If you use the \96<i>stable</i>\r
-option of <i>muscle</i>, then the order of the input sequences is preserved and\r
-sequences can be unambiguously identified even if the labels differ. If you\r
-have problems parsing MUSCLE output with scripts designed for CLUSTALW, please\r
-let me know and I'll do my best to provide a fix.<o:p></o:p></p>\r
-\r
-<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954779"><![if !supportLists]><span\r
-style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>3.4 </span></span><![endif]>MSF\r
-format</a></h2>\r
-\r
-<p class=MsoNormal>MSF format, as used in the GCG package, is requested by\r
-using the \96<span class=SpellE><i>msf</i></span> option. As with CLUSTALW\r
-format, this is easier for people to read than FASTA. As of MUSCLE 3.52, the\r
-MSF format has been tweaked to be more compatible with GCG. The following\r
-differences remain.</p>\r
-\r
-<p class=MsoNormal><o:p> </o:p></p>\r
-\r
-<p class=MsoNormal>(a) MUSCLE truncates at the first white space or after 63\r
-characters, which ever comes first. The GCG package apparently truncates after\r
-10 characters. If this is a problem for you, please let me know and I'll add an\r
-option to truncate after 10 in a future version.</p>\r
-\r
-<p class=MsoNormal><o:p> </o:p></p>\r
-\r
-<p class=MsoNormal>(b) MUSCLE allows duplicate sequence labels, while GCG\r
-forbids duplicates. If you use the \96<i>stable</i> option of <i>muscle</i>, then\r
-the order of the input sequences is preserved and sequences can be\r
-unambiguously identified even if the labels differ.</p>\r
-\r
-<p class=MsoNormal><o:p> </o:p></p>\r
-\r
-<p class=MsoNormal>Thanks to Eric Martel for help with improving GCG\r
-compatibility.<o:p></o:p></p>\r
-\r
-<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954780"><![if !supportLists]><span\r
-style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>3.5 </span></span><![endif]>HTML\r
-format</a></h2>\r
-\r
-<p class=MsoNormal>I've added an experimental feature starting in version 3.4. To\r
-get a Web page as output, use the \96<i>html</i> option. The alignment is colored\r
-using a color scheme from Eric <span class=SpellE>Sonnhammer's</span> <span\r
-class=SpellE>Belvu</span> editor, which is my personal favorite. A drawback of\r
-this option is that the Web page typically contains a very large number of HTML\r
-tags, which can be slow to display in the Internet Explorer browser. The\r
-Netscape browser works much better. If you have any ideas about good ways to\r
-make Web pages, please let me know.</p>\r
-\r
-<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954781"><![if !supportLists]><span\r
-style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>3.6 </span></span><![endif]></a><span\r
-class=SpellE><span style='mso-bookmark:_Toc113954781'>Phylip</span></span><span\r
-style='mso-bookmark:_Toc113954781'> format</span></h2>\r
-\r
-<p class=MsoNormal>The <span class=SpellE>Phylip</span> package supports two\r
-different multiple sequence alignment file formats, called sequential and\r
-interleaved respectively.<o:p></o:p></p>\r
-\r
-<h1 style='margin-left:0in;text-indent:0in'><a name="_Toc113954782"><![if !supportLists]><span\r
-style='mso-fareast-font-family:Arial;mso-bidi-font-family:Arial'><span\r
-style='mso-list:Ignore'>4 </span></span><![endif]>Using MUSCLE</a></h1>\r
-\r
-<p class=MsoNormal>In this section we give more details of the MUSCLE algorithm\r
-and the more important options offered by the <i>muscle</i> implementation.<o:p></o:p></p>\r
-\r
-<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954783"><![if !supportLists]><span\r
-style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>4.1 </span></span><![endif]>How\r
-the algorithm works</a></h2>\r
-\r
-<p class=MsoNormal>I won't give a complete description of the MUSCLE algorithm\r
-here\97for that, you will have to read the papers. (See citations on title page\r
-above). But hopefully a summary will help explain what some of the command-line\r
-options do and how they might be useful in your work.</p>\r
-\r
-<p class=MsoNormal><o:p> </o:p></p>\r
-\r
-<p class=MsoNormal>The first step is to calculate a tree. In CLUSTALW, this is\r
-done as follows. Each pair of input sequences is aligned, and used to compute\r
-the pair-wise identity of the pair. Identities are converted to a measure of\r
-distance. Finally, the distance matrix is converted to a tree using a\r
-clustering method (CLUSTALW uses neighbor-joining). If you have 1,000\r
-sequences, there are (1,000 <span style='font-family:Symbol;mso-ascii-font-family:\r
-"Times New Roman";mso-hansi-font-family:"Times New Roman";mso-char-type:symbol;\r
-mso-symbol-font-family:Symbol'><span style='mso-char-type:symbol;mso-symbol-font-family:\r
-Symbol'>´</span></span> 999)/2 = 499,500 pairs, so aligning every pair can take\r
-a while. MUSCLE uses a much faster, but somewhat more approximate, method to\r
-compute distances: it counts the number of short sub-sequences (known as <i>k</i>-<span\r
-class=SpellE>mers</span>, <i>k</i>-<span class=SpellE>tuples</span> or words)\r
-that two sequences have in common, without constructing an alignment. This is\r
-typically around 3,000 times faster that <span class=SpellE>CLUSTALW's</span>\r
-method, but the trees will generally be less accurate. We call this step "<i>k</i>-<span\r
-class=SpellE>mer</span> clustering".<o:p></o:p></p>\r
-\r
-<p class=MsoNormal><o:p> </o:p></p>\r
-\r
-<p class=MsoNormal>The second step is to use the tree to construct what is\r
-known as a progressive alignment. At each node of the binary tree, a pair-wise\r
-alignment is constructed, progressing from the leaves towards the root. The\r
-first alignment will be made from two sequences. Later alignments will be one\r
-of the three following types: sequence-sequence, profile-sequence or\r
-profile-profile, where "profile" means the multiple <span\r
-class=GramE>alignment</span> of the sequences under a given internal node of\r
-the tree. This is very similar to what CLUSTALW does once it has built a tree.</p>\r
-\r
-<p class=MsoNormal><o:p> </o:p></p>\r
-\r
-<p class=MsoNormal style='page-break-after:avoid'>Now we have a multiple\r
-alignment, which has been built very quickly compared with conventional\r
-methods, mainly because of the distance calculation using <i>k</i>-<span\r
-class=SpellE>mers</span> rather than alignments. The quality of this alignment\r
-is typically pretty good\97it will often tie or beat a T-Coffee alignment on our\r
-tests. However, on average, we find that it can be improved by proceeding\r
-through the following steps.</p>\r
-\r
-<p class=MsoNormal style='page-break-after:avoid'><o:p> </o:p></p>\r
-\r
-<p class=MsoNormal style='page-break-after:avoid'>From the multiple <span\r
-class=GramE>alignment</span>, we can now compute the pair-wise identities of\r
-each pair of sequences. This gives us a new distance matrix, from which we\r
-estimate a new tree. We compare the old and new trees, and re-align subgroups\r
-where needed to produce a progressive multiple alignment from the new tree. If\r
-the two trees are identical, there is nothing to do; if there are no subtrees\r
-that agree (very unusual), then the whole progressive alignment procedure must\r
-be repeated from scratch. Typically we find that the tree is pretty stable near\r
-the leaves, but some re-alignments are needed closer the root. This procedure\r
-(compute pair-wise identities, estimate new tree, compare trees, re-align) is\r
-iterated until the tree stabilizes or until a specified maximum number of\r
-iterations has been done. We call this process "tree refinement",\r
-although it also tends to improve the alignment.</p>\r
-\r
-<p class=MsoNormal style='page-break-after:avoid'><o:p> </o:p></p>\r
-\r
-<p class=MsoNormal style='page-break-after:avoid'>We now keep the tree fixed\r
-and move to a new procedure which is designed to improve the multiple\r
-alignment. The set of sequences is divided into two subsets (i.e., we make a\r
-bipartition on the set of sequences). A profile is constructed for each of the\r
-two subsets based on the current multiple <span class=GramE>alignment</span>.\r
-These two profiles are then re-aligned to each other using the same pair-wise\r
-alignment algorithm as used in the progressive stage. If this improves an\r
-"objective score" that measures the quality of the alignment, then\r
-the new multiple <span class=GramE>alignment</span> is kept, otherwise it is\r
-discarded. By default, the objective score is the classic sum-of-pairs score\r
-that takes the (sequence weighted) average of the pair-wise alignment score of\r
-every pair of sequences in the alignment. Bipartitions are chosen by deleting\r
-an edge in the guide tree, each of the two resulting subtrees defines a subset\r
-of sequences. This procedure is called "tree dependent refinement". <span\r
-class=GramE>One iteration</span> of tree dependent refinement tries\r
-bipartitions produced by deleting every edge of the tree in depth order moving\r
-from the leaves towards the center of the tree. Iterations continue until\r
-convergence or up to a specified maximum.</p>\r
-\r
-<p class=MsoNormal style='page-break-after:avoid'><o:p> </o:p></p>\r
-\r
-<p class=MsoNormal style='page-break-after:avoid'>For convenience, the major\r
-steps in MUSCLE are described as "iterations", though the first three\r
-iterations all do quite different things and may take very different lengths of\r
-time to complete. The tree-dependent refinement iterations 3, 4 ... are true\r
-iterations and will take similar lengths of time. </p>\r
-\r
-<p class=MsoNormal style='page-break-after:avoid'><o:p> </o:p></p>\r
-\r
-<table class=MsoTableGrid border=0 cellspacing=0 cellpadding=0\r
- style='border-collapse:collapse;mso-yfti-tbllook:480;mso-padding-alt:0in 5.4pt 0in 5.4pt'>\r
- <tr style='mso-yfti-irow:0'>\r
- <td width=89 valign=top style='width:66.6pt;border:none;border-bottom:solid windowtext 1.0pt;\r
- mso-border-bottom-alt:solid windowtext .5pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'><b><span style='font-size:\r
- 9.0pt;font-family:Arial'>Iteration<o:p></o:p></span></b></p>\r
- </td>\r
- <td width=461 valign=top style='width:4.8in;border:none;border-bottom:solid windowtext 1.0pt;\r
- mso-border-bottom-alt:solid windowtext .5pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'><b><span style='font-size:\r
- 9.0pt;font-family:Arial'>Actions<o:p></o:p></span></b></p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:1'>\r
- <td width=89 valign=top style='width:66.6pt;border:none;mso-border-top-alt:\r
- solid windowtext .5pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'>1</p>\r
- </td>\r
- <td width=461 valign=top style='width:4.8in;border:none;mso-border-top-alt:\r
- solid windowtext .5pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'>Distance matrix by <i>k</i>-<span\r
- class=SpellE>mer</span> clustering, estimate tree, progressive alignment\r
- according to this tree.</p>\r
- <p class=MsoNormal style='page-break-after:avoid'><o:p> </o:p></p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:2'>\r
- <td width=89 valign=top style='width:66.6pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'>2</p>\r
- </td>\r
- <td width=461 valign=top style='width:4.8in;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'>Distance matrix by\r
- pair-wise identities from current multiple alignment, estimate tree,\r
- progressive alignment according to new tree, repeat until convergence or specified\r
- maximum number of times.</p>\r
- <p class=MsoNormal style='page-break-after:avoid'><o:p> </o:p></p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:3;mso-yfti-lastrow:yes'>\r
- <td width=89 valign=top style='width:66.6pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'>3, 4 ...</p>\r
- </td>\r
- <td width=461 valign=top style='width:4.8in;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'>Tree-dependent refinement. <span\r
- class=GramE>One iteration</span> visits every edge in the tree one time.</p>\r
- </td>\r
- </tr>\r
-</table>\r
-\r
-<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954784"><![if !supportLists]><span\r
-style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>4.2 </span></span><![endif]>Command-line\r
-options</a></h2>\r
-\r
-<p class=MsoNormal>There are two types of command-line options: value options\r
-and flag options. Value options are followed by the value of the given\r
-parameter, for example \96<i>in <filename></i>; flag options just stand for\r
-themselves, such as \96<span class=SpellE><i>msf</i></span>. All options are a\r
-dash (not two dashes!) followed by a long name; there are no single-letter\r
-equivalents. Value options must be separated from their values by white space\r
-in the command line. Thus, <i>muscle</i> does not follow <span class=GramE>Unix</span>,\r
-Linux or <span class=SpellE>Posix</span> standards, for which we apologize. The\r
-order in which options are given is irrelevant unless two options contradict,\r
-in which case the right-most option silently wins.<o:p></o:p></p>\r
-\r
-<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954785"><![if !supportLists]><span\r
-style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>4.3 </span></span><![endif]>The\r
-maxiters option</a></h2>\r
-\r
-<p class=MsoNormal>You can control the number of iterations that MUSCLE does by\r
-specifying the <i>\96maxiters</i> option. If you specify 1, 2 or 3, then this is\r
-exactly the number of iterations that will be performed. If the value is\r
-greater than 3, then <i>muscle</i> will continue up to the maximum you specify\r
-or until convergence is reached, which ever happens sooner. The default is 16.\r
-If you have a large number of sequences, refinement may be rather slow.</p>\r
-\r
-<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954786"><![if !supportLists]><span\r
-style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>4.4 </span></span><![endif]>The\r
-</a><span class=SpellE><span style='mso-bookmark:_Toc113954786'>maxtrees</span></span><span\r
-style='mso-bookmark:_Toc113954786'> option</span></h2>\r
-\r
-<p class=MsoNormal>This option controls the maximum number of new trees to\r
-create in iteration 2. Our experience suggests that a point of diminishing\r
-returns is typically reached after the first tree, so the default value is 1.\r
-If a larger value is given, the process will repeat until convergence or until\r
-this number of trees has been created, which ever comes first.</p>\r
-\r
-<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954787"><![if !supportLists]><span\r
-style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>4.5 </span></span><![endif]>The\r
-</a><span class=SpellE><span style='mso-bookmark:_Toc113954787'>maxhours</span></span><span\r
-style='mso-bookmark:_Toc113954787'> option</span></h2>\r
-\r
-<p class=MsoNormal>If you have a large alignment, <i>muscle</i> may take a long\r
-time to complete. It is sometimes convenient to say "I want the best\r
-alignment I can get in 24 hours" rather than specifying a set of options\r
-that will take an unknown length of time. This is done by using <i>\96<span\r
-class=SpellE>maxhours</span></i>, which specifies a floating-point number of\r
-hours. If this time is exceeded, <i>muscle</i> will write out current alignment\r
-and stop. For example,</p>\r
-\r
-<p class=MsoNormal><o:p> </o:p></p>\r
-\r
-<p class=Code>muscle -in huge.fa -out huge.afa -maxiters 9999 -maxhours 24.0</p>\r
-\r
-<p class=MsoNormal><o:p> </o:p></p>\r
-\r
-<p class=MsoNormal>Note that the actual time may exceed the specified limit by\r
-a few minutes while <i>muscle</i> finishes up on a step. It is also possible\r
-for no alignment to be produced if the time limit is too small.</p>\r
-\r
-<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954788"><![if !supportLists]><span\r
-style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>4.6 </span></span><![endif]>The\r
-</a><span class=SpellE><span style='mso-bookmark:_Toc113954788'>maxmb</span></span><span\r
-style='mso-bookmark:_Toc113954788'> option</span></h2>\r
-\r
-<p class=MsoNormal>If the amount of memory needed by MUSCLE exceeds available\r
-physical RAM, then the operating system will probably begin paging (i.e.,\r
-swapping memory to and from hard disk), causing MUSCLE to run very slowly. This\r
-is especially problematic when MUSCLE is used for batch processing, where one or\r
-two very large alignments can cause a batch to effectively hang. Starting in\r
-version 3.52, MUSCLE attempts to limit the amount of memory used. If the limit\r
-is exceeded, MUSCLE quits, saving the best alignment so far produced (if any).\r
-MUSCLE attempts to determine the amount of physical RAM by making an\r
-appropriate operating system call. Under Linux and Windows, this works well. On\r
-other systems, particularly other flavors of <span class=GramE>Unix</span>,\r
-MUSCLE doesn't know how to query the system and assumes that there is 500 Mb of\r
-RAM. To override this default, you can specify the maximum number of megabytes\r
-to allocate by using the \96<span class=SpellE><i>maxmb</i></span> option, for\r
-example to set a limit of 1.5 <span class=SpellE><span class=GramE>Gb</span></span>:</p>\r
-\r
-<p class=MsoNormal><o:p> </o:p></p>\r
-\r
-<p class=Code>muscle -in huge.fa -out huge.afa -maxhours 1.0 -maxmb 1500</p>\r
-\r
-<p class=MsoNormal><o:p> </o:p></p>\r
-\r
-<p class=MsoNormal>This feature has been hacked on top of code that wasn't\r
-really designed for it. So it doesn't always work perfectly, but is better than\r
-nothing. The ideal solution would be to implement linear space dynamic\r
-programming code (e.g., the Myers-Miller algorithm) for situations where memory\r
-is tight. One day I might do this if there is sufficient interest. If you are\r
-interested in contributing the code, e.g. for a class project, please let me\r
-know, I'll be glad to provide support.<o:p></o:p></p>\r
-\r
-<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954789"><![if !supportLists]><span\r
-style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>4.7 </span></span><![endif]>The\r
-profile scoring function</a></h2>\r
-\r
-<p class=MsoNormal>Three different protein profile scoring functions are\r
-supported, the log-expectation score (\96<i>le</i> option) and a sum of pairs\r
-score using either the PAM200 matrix (\96<i>sp</i>) or the VTML240 matrix (\96<span\r
-class=SpellE><i>sv</i></span>). The log-expectation score is the default as it\r
-gives better results on our tests, but is typically somewhere between two or\r
-three times slower than the sum-of-pairs score. For nucleotides, \96<span\r
-class=SpellE><i>spn</i></span> is currently the only option (which is of course\r
-the default for nucleotide data, so you don't need to specify this option).<o:p></o:p></p>\r
-\r
-<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954790"><![if !supportLists]><span\r
-style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>4.8 </span></span><![endif]>Diagonal\r
-optimization</a></h2>\r
-\r
-<p class=MsoNormal>Creating a pair-wise alignment by dynamic programming\r
-requires computing an <i>L</i><sub>1</sub> <span style='font-family:Symbol;\r
-mso-ascii-font-family:"Times New Roman";mso-hansi-font-family:"Times New Roman";\r
-mso-char-type:symbol;mso-symbol-font-family:Symbol'><span style='mso-char-type:\r
-symbol;mso-symbol-font-family:Symbol'>´</span></span> <i>L</i><sub>2</sub>\r
-matrix, where <i>L</i><sub>1</sub> and <i>L</i><sub>2</sub> are the sequence\r
-lengths. A trick used in algorithms such as BLAST is to reduce the size of this\r
-matrix by using fast methods to find "diagonals", i.e. short regions\r
-of high similarity between the two sequences. This speeds up the algorithm at\r
-the expense of some reduction in accuracy. MUSCLE uses a technique called <i>k</i>-<span\r
-class=SpellE>mer</span> extension to find diagonals. It is disabled by default\r
-because of the slight reduction in average accuracy and can be turned on by\r
-specifying the \96<span class=SpellE><i>diags</i></span> option. To enable\r
-diagonal optimization in the first iteration, use \96<i>diags1</i>, to enable\r
-diagonal optimization in the second iteration, use \96<i>diags2</i>. These are\r
-provided separately because it would be a reasonable strategy to enable\r
-diagonals in the first iteration but not the second (because the main goal of\r
-the first iteration is to construct a multiple alignment quickly in order to\r
-improve the distance matrix, which is not very sensitive to alignment quality;\r
-whereas the goal of the second iteration is to make the best possible\r
-progressive alignment).<o:p></o:p></p>\r
-\r
-<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954791"><![if !supportLists]><span\r
-style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>4.9 </span></span><![endif]>Anchor\r
-optimization</a></h2>\r
-\r
-<p class=MsoNormal>Tree-dependent refinement (iterations 3, 4 <span\r
-class=GramE>... )</span> can be speeded up by dividing the alignment vertically\r
-into blocks. Block boundaries are found by identifying high-scoring columns\r
-(e.g., a perfectly conserved column of Cs or Ws would be a candidate). Each\r
-vertical block is then refined independently before reassembling the complete\r
-alignment, which is faster because of the <i>L</i><sup>2</sup> factor in\r
-dynamic programming (e.g., suppose the alignment is split into two vertical\r
-blocks, then 2 <span style='font-family:Symbol;mso-ascii-font-family:"Times New Roman";\r
-mso-hansi-font-family:"Times New Roman";mso-char-type:symbol;mso-symbol-font-family:\r
-Symbol'><span style='mso-char-type:symbol;mso-symbol-font-family:Symbol'>´</span></span>\r
-0.5<sup>2</sup> = 0.5, so the dynamic programming time is roughly halved). The\r
-\96<span class=SpellE><i>noanchors</i></span> option is used to disable this\r
-feature. This option has no effect if <i>\96maxiters 1</i> or \96<i>maxiters 2</i>\r
-is specified. On benchmark tests, enabling anchors has little or no effect on\r
-accuracy, but if you want to be very conservative and are striving for the best\r
-possible accuracy then \96<span class=SpellE><i>noanchors</i></span> is a\r
-reasonable choice.<o:p></o:p></p>\r
-\r
-<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954792"><![if !supportLists]><span\r
-style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>4.10 </span></span><![endif]>Log\r
-file</a></h2>\r
-\r
-<p class=MsoNormal>You can specify a log file by using \96<i>log <filename></i>\r
-or \96<span class=SpellE><i>loga</i></span><i> <filename></i>. Using \96<i>log</i>\r
-causes any existing file to be deleted, \96<span class=SpellE><i>loga</i></span>\r
-appends to any existing file. A message will be written to the log file when <i>muscle</i>\r
-starts and stops. Error and warning messages will also be written to the log.\r
-If \96<i>verbose</i> is specified, then more information will be written,\r
-including the command line used to invoke <i>muscle</i>, the resulting internal\r
-parameter settings, and also progress messages. The content and format of\r
-verbose log file output is subject to change in future versions. </p>\r
-\r
-<p class=MsoNormal><o:p> </o:p></p>\r
-\r
-<p class=MsoNormal>The use of a log file may seem contrary to <span\r
-class=GramE>Unix</span> conventions for using standard output and standard\r
-error. I like these conventions, but never found a fully satisfactory way to\r
-use them. I like progress messages (see below), but they mess up a file if you\r
-re-direct standard error and there are errors or warning messages too. I could\r
-try to detect whether a standard file handle is a <span class=SpellE><span\r
-class=GramE><i>tty</i></span></span> device or a disk file and change behavior\r
-accordingly, but I regard this as too complicated and too hard for the user to\r
-understand. On Windows it can be hard to re-direct standard file handles,\r
-especially when working in a GUI debugger. Maybe one day I will figure out a\r
-better solution (suggestions welcomed).</p>\r
-\r
-<p class=MsoNormal><o:p> </o:p></p>\r
-\r
-<p class=MsoNormal>I highly recommend using \96<i>verbose </i>and \ad\96<i>log[a]</i>,\r
-especially when running <i>muscle</i> in a batch mode. This enables you to\r
-verify whether a particular alignment was completed and to review any errors or\r
-warnings that occurred.<o:p></o:p></p>\r
-\r
-<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954793"><![if !supportLists]><span\r
-style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>4.11 </span></span><![endif]>Progress\r
-messages</a></h2>\r
-\r
-<p class=MsoNormal>By default, <i>muscle</i> writes progress messages to\r
-standard error periodically so that you know it's doing something and get some\r
-feedback about the time and memory requirements for the alignment. Here is a\r
-typical progress message.</p>\r
-\r
-<p class=MsoNormal><o:p> </o:p></p>\r
-\r
-<p class=Code>00:00:23<span style='mso-spacerun:yes'>Â Â Â Â </span>25 Mb (5%)<span\r
-style='mso-spacerun:yes'>Â </span>Iter<span style='mso-spacerun:yes'>Â Â \r
-</span>2<span style='mso-spacerun:yes'>Â </span>87.20%<span\r
-style='mso-spacerun:yes'>Â </span>Build guide tree</p>\r
-\r
-<p class=MsoNormal><o:p> </o:p></p>\r
-\r
-<p class=MsoNormal style='page-break-after:avoid'>The fields are as follows.</p>\r
-\r
-<p class=MsoNormal style='page-break-after:avoid'><o:p> </o:p></p>\r
-\r
-<table class=MsoTableGrid border=0 cellspacing=0 cellpadding=0\r
- style='border-collapse:collapse;mso-yfti-tbllook:480;mso-padding-alt:0in 5.4pt 0in 5.4pt'>\r
- <tr style='mso-yfti-irow:0'>\r
- <td width=118 valign=top style='width:88.2pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=Code style='page-break-after:avoid'>00:00:23</p>\r
- </td>\r
- <td width=408 valign=top style='width:306.05pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'>Elapsed time since <i>muscle</i>\r
- started.<o:p></o:p></p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:1'>\r
- <td width=118 valign=top style='width:88.2pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=Code style='page-break-after:avoid'>25 Mb (5%)</p>\r
- </td>\r
- <td width=408 valign=top style='width:306.05pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'>Peak memory use in megabytes\r
- (i.e., not the current usage, but the maximum amount of memory used since <i>muscle</i>\r
- started). The number in parentheses is the fraction of physical memory (see \96<span\r
- class=SpellE><i>maxmb</i></span> option for more discussion).<o:p></o:p></p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:2'>\r
- <td width=118 valign=top style='width:88.2pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=Code style='page-break-after:avoid'>Iter 2</p>\r
- </td>\r
- <td width=408 valign=top style='width:306.05pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'>Iteration currently in\r
- progress.</p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:3'>\r
- <td width=118 valign=top style='width:88.2pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=Code style='page-break-after:avoid'>87.20%</p>\r
- </td>\r
- <td width=408 valign=top style='width:306.05pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'>How much of the current step\r
- has been completed (percentage).</p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:4;mso-yfti-lastrow:yes'>\r
- <td width=118 valign=top style='width:88.2pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=Code>Build...</p>\r
- </td>\r
- <td width=408 valign=top style='width:306.05pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal>A brief description of the current step.</p>\r
- </td>\r
- </tr>\r
-</table>\r
-\r
-<p class=MsoNormal><o:p> </o:p></p>\r
-\r
-<p class=MsoNormal>The \96<i>quiet</i> command-line option disables writing\r
-progress messages to standard error. If the \96<i>verbose</i> command-line option\r
-is specified, a progress message will be written to the log file when <span\r
-class=GramE>each iteration</span> completes. So \96<i>quiet</i> and \96<i>verbose</i>\r
-are not contradictory.</p>\r
-\r
-<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954794"><![if !supportLists]><span\r
-style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>4.12 </span></span><![endif]>Running\r
-out of memory</a></h2>\r
-\r
-<p class=MsoNormal>The <i>muscle</i> code tries to deal gracefully with\r
-low-memory conditions by using the following technique. A block of "emergency\r
-reserve" memory is allocated when <i>muscle</i> starts. If a later request\r
-to allocate memory fails, this reserve block is made available, and <i>muscle</i>\r
-attempts to save the current alignment. With luck, the reserved memory will be\r
-enough to allow <i>muscle</i> to save the alignment and exit gracefully with an\r
-informative error message. See also the \96<span class=SpellE><i>maxmb</i></span>\r
-option.<o:p></o:p></p>\r
-\r
-<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954795"><![if !supportLists]><span\r
-style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>4.13 </span></span><![endif]>Troubleshooting</a></h2>\r
-\r
-<p class=MsoNormal>Here is some general advice on what to do if <i>muscle</i>\r
-fails and you don't understand what happened. The code is designed to fail\r
-gracefully with an informative error message when something goes wrong, but\r
-there will no doubt be situations I haven't anticipated (not to mention bugs).</p>\r
-\r
-<p class=MsoNormal><o:p> </o:p></p>\r
-\r
-<p class=MsoNormal>Check the MUSCLE web site for updates, bug reports and other\r
-relevant information.</p>\r
-\r
-<p class=MsoNormal><o:p> </o:p></p>\r
-\r
-<p class=MsoNormal style='page-break-after:avoid'><span style='mso-tab-count:\r
-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
-\r
-<p class=MsoNormal><o:p> </o:p></p>\r
-\r
-<p class=MsoNormal>Check the input file to make sure it is in valid FASTA\r
-format. Try giving it to another sequence analysis program that can accept\r
-large FASTA files (e.g., the NCBI <span class=SpellE><i>formatdb</i></span>\r
-utility) to see if you get an informative error message. Try dividing the file\r
-into two halves and using each half individually as input. If one half fails\r
-and the other <span class=GramE>does</span> not, repeat until the problem is\r
-localized as far as possible.</p>\r
-\r
-<p class=MsoNormal><o:p> </o:p></p>\r
-\r
-<p class=MsoNormal>Use \96<i>log</i> or \96<span class=SpellE><i>loga</i></span>\r
-and \96\ad<i>verbose</i> and check the log file to see if there are any messages\r
-that give you a hint about the problem. Look at the peak memory requirements\r
-(reported in progress messages) to see if you may be exceeding the physical or\r
-virtual memory capacity of your computer.</p>\r
-\r
-<p class=MsoNormal><o:p> </o:p></p>\r
-\r
-<p class=MsoNormal>If <i>muscle</i> crashes without giving an error message, or\r
-hangs, then you may need to refer to the source code or use a debugger. A\r
-"debug" version, <i>muscled</i>, may be provided. This is built from\r
-the same source code but with the DEBUG macro defined and without compiler\r
-optimizations. This version runs much more slowly (perhaps by a factor of three\r
-or more), but does a lot more internal checking and may be able to catch\r
-something that is going wrong in the code. The \96\ad<i>core</i> option specifies\r
-that <i>muscle</i> should not catch exceptions. When \96<i>core</i> is specified,\r
-an exception may result in a debugger trap or a core dump, depending on the\r
-execution environment. The \96<span class=SpellE><i>nocore</i></span> option has\r
-the opposite effect. In <i>muscle</i>, \96<span class=SpellE><i>nocore</i></span>\r
-is the default, \96\ad<i>core</i> is the default in <i>muscled</i>.</p>\r
-\r
-<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc113954796"><![if !supportLists]><span\r
-style='mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>4.14 </span></span><![endif]>Technical\r
-support</a></h2>\r
-\r
-<p class=MsoNormal>I am happy to provide support. But I am busy, and am\r
-offering this program at no charge, so I ask you to make a reasonable effort to\r
-figure things out for yourself before contacting me.</p>\r
-\r
-<h1 style='margin-left:0in;text-indent:0in'><a name="_Toc113954797"><![if !supportLists]><span\r
-style='mso-fareast-font-family:Arial;mso-bidi-font-family:Arial'><span\r
-style='mso-list:Ignore'>5 </span></span><![endif]>Command Line Reference</a></h1>\r
-\r
-<p class=MsoNormal style='page-break-after:avoid'><o:p> </o:p></p>\r
-\r
-<table class=MsoTableGrid border=0 cellspacing=0 cellpadding=0\r
- style='border-collapse:collapse;mso-yfti-tbllook:480;mso-padding-alt:0in 5.4pt 0in 5.4pt'>\r
- <thead>\r
- <tr style='mso-yfti-irow:0'>\r
- <td width=110 valign=top style='width:82.85pt;border:none;border-bottom:\r
- solid windowtext 1.0pt;mso-border-bottom-alt:solid windowtext .5pt;\r
- padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'><b><span style='font-size:\r
- 9.0pt;font-family:Arial'>Value option<o:p></o:p></span></b></p>\r
- </td>\r
- <td width=113 valign=top style='width:84.8pt;border:none;border-bottom:solid windowtext 1.0pt;\r
- mso-border-bottom-alt:solid windowtext .5pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'><b><span style='font-size:\r
- 9.0pt;font-family:Arial'>Legal values<o:p></o:p></span></b></p>\r
- </td>\r
- <td width=103 valign=top style='width:77.35pt;border:none;border-bottom:\r
- solid windowtext 1.0pt;mso-border-bottom-alt:solid windowtext .5pt;\r
- padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'><b><span style='font-size:\r
- 9.0pt;font-family:Arial'>Default<o:p></o:p></span></b></p>\r
- </td>\r
- <td width=264 valign=top style='width:197.8pt;border:none;border-bottom:\r
- solid windowtext 1.0pt;mso-border-bottom-alt:solid windowtext .5pt;\r
- padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'><b><span style='font-size:\r
- 9.0pt;font-family:Arial'>Description<o:p></o:p></span></b></p>\r
- </td>\r
- </tr>\r
- </thead>\r
- <tr style='mso-yfti-irow:1'>\r
- <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span\r
- style='font-size:8.0pt;font-family:"Courier New"'>anchorspacing</span></span><span\r
- style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>\r
- </td>\r
- <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'>Integer</p>\r
- </td>\r
- <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:\r
- 8.0pt;font-family:"Courier New"'>32<o:p></o:p></span></p>\r
- </td>\r
- <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'>Minimum spacing between\r
- anchor columns.</p>\r
- <p class=MsoNormal style='page-break-after:avoid'><o:p> </o:p></p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:2'>\r
- <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:\r
- 8.0pt;font-family:"Courier New"'>center<o:p></o:p></span></p>\r
- </td>\r
- <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'>Floating point</p>\r
- </td>\r
- <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'>[1]<o:p></o:p></p>\r
- </td>\r
- <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'>Center parameter. Should be\r
- negative.</p>\r
- <p class=MsoNormal style='page-break-after:avoid'><o:p> </o:p></p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:3'>\r
- <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:\r
- 8.0pt;font-family:"Courier New"'>cluster1<o:p></o:p></span></p>\r
- <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:\r
- 8.0pt;font-family:"Courier New"'>cluster2<o:p></o:p></span></p>\r
- </td>\r
- <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span\r
- style='font-size:8.0pt;font-family:"Courier New"'>upgma</span></span><span\r
- style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>\r
- <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span\r
- style='font-size:8.0pt;font-family:"Courier New"'>upgmb</span></span><span\r
- style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>\r
- <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span\r
- style='font-size:8.0pt;font-family:"Courier New"'>neighborjoining</span></span><span\r
- style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>\r
- </td>\r
- <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span\r
- style='font-size:8.0pt;font-family:"Courier New"'>upgmb</span></span><span\r
- style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>\r
- </td>\r
- <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'>Clustering method. <span\r
- class=GramE>cluster1</span> is used in iteration 1 and 2, cluster2 in later\r
- iterations.</p>\r
- <p class=MsoNormal style='page-break-after:avoid'><o:p> </o:p></p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:4'>\r
- <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span\r
- style='font-size:8.0pt;font-family:"Courier New"'>clwout</span></span><span\r
- style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>\r
- </td>\r
- <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:\r
- 8.0pt;font-family:"Courier New"'>File name<o:p></o:p></span></p>\r
- </td>\r
- <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:\r
- 8.0pt;font-family:"Courier New"'>None<o:p></o:p></span></p>\r
- </td>\r
- <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'>Write output in CLUSTALW\r
- format to given file name.</p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:5'>\r
- <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span\r
- style='font-size:8.0pt;font-family:"Courier New"'>clwout</span></span><span\r
- style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>\r
- </td>\r
- <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:\r
- 8.0pt;font-family:"Courier New"'>File name<o:p></o:p></span></p>\r
- </td>\r
- <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:\r
- 8.0pt;font-family:"Courier New"'>None<o:p></o:p></span></p>\r
- </td>\r
- <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'>As <i>-<span class=SpellE>clwout</span></i>,\r
- except that header is strictly compatible with CLUSTALW 1.81.</p>\r
- <p class=MsoNormal style='page-break-after:avoid'><o:p> </o:p></p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:6'>\r
- <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
- font-family:"Courier New"'>diagbreak</span></span><span style='font-size:\r
- 8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>\r
- </td>\r
- <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal>Integer<o:p></o:p></p>\r
- </td>\r
- <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal>1</p>\r
- </td>\r
- <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal>Maximum distance between two diagonals that allows them to\r
- merge into one diagonal.</p>\r
- <p class=MsoNormal><o:p> </o:p></p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:7'>\r
- <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span\r
- style='font-size:8.0pt;font-family:"Courier New"'>diaglength</span></span><span\r
- style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>\r
- </td>\r
- <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'>Integer<o:p></o:p></p>\r
- </td>\r
- <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:\r
- 8.0pt;font-family:"Courier New"'>24<o:p></o:p></span></p>\r
- </td>\r
- <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'>Minimum length of diagonal.</p>\r
- <p class=MsoNormal style='page-break-after:avoid'><o:p> </o:p></p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:8'>\r
- <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span\r
- style='font-size:8.0pt;font-family:"Courier New"'>diagmargin</span></span><span\r
- style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>\r
- </td>\r
- <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'>Integer<o:p></o:p></p>\r
- </td>\r
- <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:\r
- 8.0pt;font-family:"Courier New"'>5<o:p></o:p></span></p>\r
- </td>\r
- <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'>Discard this many positions\r
- at ends of diagonal.</p>\r
- <p class=MsoNormal style='page-break-after:avoid'><o:p> </o:p></p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:9'>\r
- <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>distance1<o:p></o:p></span></p>\r
- <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><o:p> </o:p></span></p>\r
- </td>\r
- <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>kmer6_6<o:p></o:p></span></p>\r
- <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>kmer20_3<o:p></o:p></span></p>\r
- <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>kmer20_4<o:p></o:p></span></p>\r
- <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>kbit20_3<o:p></o:p></span></p>\r
- <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>kmer4_6<o:p></o:p></span></p>\r
- <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><o:p> </o:p></span></p>\r
- </td>\r
- <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>Kmer6_6\r
- (amino) or Kmer4_6 (<span class=SpellE>nucleo</span>)</span></p>\r
- </td>\r
- <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal>Distance measure for iteration 1.</p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:10'>\r
- <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>distance2<o:p></o:p></span></p>\r
- <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><o:p> </o:p></span></p>\r
- </td>\r
- <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>kmer6_6<o:p></o:p></span></p>\r
- <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>kmer20_3<o:p></o:p></span></p>\r
- <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>kmer20_4<o:p></o:p></span></p>\r
- <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>kbit20_3<o:p></o:p></span></p>\r
- <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
- font-family:"Courier New"'>pctid_kimura</span></span><span style='font-size:\r
- 8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>\r
- <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
- font-family:"Courier New"'>pctid_log</span></span><span style='font-size:\r
- 8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>\r
- <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><o:p> </o:p></span></p>\r
- </td>\r
- <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
- font-family:"Courier New"'>pctid_kimura</span></span></p>\r
- </td>\r
- <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal>Distance measure for iterations 2, 3 ...</p>\r
- <p class=MsoNormal><o:p> </o:p></p>\r
- <p class=MsoNormal><o:p> </o:p></p>\r
- <p class=MsoNormal><o:p> </o:p></p>\r
- <p class=MsoNormal><o:p> </o:p></p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:11'>\r
- <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
- font-family:"Courier New"'>fastaout</span></span><span style='font-size:8.0pt;\r
- font-family:"Courier New"'><o:p></o:p></span></p>\r
- </td>\r
- <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>File\r
- name<o:p></o:p></span></p>\r
- </td>\r
- <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>None<o:p></o:p></span></p>\r
- </td>\r
- <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal>Write output in FASTA format to the given file.</p>\r
- <p class=MsoNormal><o:p> </o:p></p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:12'>\r
- <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
- font-family:"Courier New"'>gapopen</span></span><span style='font-size:8.0pt;\r
- font-family:"Courier New"'><o:p></o:p></span></p>\r
- </td>\r
- <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal>Floating point</p>\r
- </td>\r
- <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal>[1]<o:p></o:p></p>\r
- </td>\r
- <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal>The <span class=GramE>gap open</span> score. Must be\r
- negative.</p>\r
- <p class=MsoNormal><o:p> </o:p></p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:13'>\r
- <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>hydro<o:p></o:p></span></p>\r
- </td>\r
- <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal>Integer<o:p></o:p></p>\r
- </td>\r
- <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>5</span><o:p></o:p></p>\r
- </td>\r
- <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal>Window size for determining whether a region is\r
- hydrophobic.</p>\r
- <p class=MsoNormal><o:p> </o:p></p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:14'>\r
- <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
- font-family:"Courier New"'>hydrofactor</span></span><span style='font-size:\r
- 8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>\r
- </td>\r
- <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal>Floating point</p>\r
- </td>\r
- <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>1.2<o:p></o:p></span></p>\r
- </td>\r
- <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal>Multiplier for gap open/close penalties in hydrophobic\r
- regions.</p>\r
- <p class=MsoNormal><o:p> </o:p></p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:15'>\r
- <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>in<o:p></o:p></span></p>\r
- </td>\r
- <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal>Any file name</p>\r
- </td>\r
- <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal>standard input</p>\r
- </td>\r
- <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal>Where to find the input sequences.</p>\r
- <p class=MsoNormal><o:p> </o:p></p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:16'>\r
- <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>in1<o:p></o:p></span></p>\r
- </td>\r
- <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal>Any file name</p>\r
- </td>\r
- <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal>None</p>\r
- </td>\r
- <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal>Where to find an input alignment.</p>\r
- <p class=MsoNormal><o:p> </o:p></p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:17'>\r
- <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>in2<o:p></o:p></span></p>\r
- </td>\r
- <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal>Any file name</p>\r
- </td>\r
- <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal>None</p>\r
- </td>\r
- <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal>Where to find an input alignment.</p>\r
- <p class=MsoNormal><o:p> </o:p></p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:18'>\r
- <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>log<o:p></o:p></span></p>\r
- </td>\r
- <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal>File name<o:p></o:p></p>\r
- </td>\r
- <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal>None.<o:p></o:p></p>\r
- </td>\r
- <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal>Log file name (delete existing file).</p>\r
- <p class=MsoNormal><o:p> </o:p></p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:19'>\r
- <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
- font-family:"Courier New"'>loga</span></span><span style='font-size:8.0pt;\r
- font-family:"Courier New"'><o:p></o:p></span></p>\r
- </td>\r
- <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal>File name</p>\r
- </td>\r
- <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal>None.</p>\r
- </td>\r
- <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal>Log file name (append to existing file).</p>\r
- <p class=MsoNormal><o:p> </o:p></p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:20'>\r
- <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>matrix<o:p></o:p></span></p>\r
- </td>\r
- <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal>File name</p>\r
- </td>\r
- <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal>None</p>\r
- </td>\r
- <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal>File name for substitution matrix in NCBI or WU-BLAST\r
- format. If you specify your own matrix, you should also specify:</p>\r
- <p class=MsoNormal><o:p> </o:p></p>\r
- <p class=MsoNormal>-<span class=SpellE>gapopen</span> <g>, -<span\r
- class=SpellE>gapextend</span> <e> -center 0.0</p>\r
- <p class=MsoNormal><o:p> </o:p></p>\r
- <p class=MsoNormal>Note that <g> and <e> MUST be negative.</p>\r
- <p class=MsoNormal><o:p> </o:p></p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:21'>\r
- <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
- font-family:"Courier New"'>maxhours</span></span><span style='font-size:8.0pt;\r
- font-family:"Courier New"'><o:p></o:p></span></p>\r
- </td>\r
- <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal>Floating point</p>\r
- </td>\r
- <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal>None.</p>\r
- </td>\r
- <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal>Maximum time to run in hours. The actual time may exceed\r
- the requested limit by a few minutes. Decimals are allowed, so 1.5 means one hour\r
- and 30 minutes.</p>\r
- <p class=MsoNormal><o:p> </o:p></p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:22'>\r
- <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
- font-family:"Courier New"'>maxiters</span></span><span style='font-size:8.0pt;\r
- font-family:"Courier New"'><o:p></o:p></span></p>\r
- </td>\r
- <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal>Integer 1, 2 ...</p>\r
- </td>\r
- <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>16<o:p></o:p></span></p>\r
- </td>\r
- <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal>Maximum number of iterations.</p>\r
- <p class=MsoNormal><o:p> </o:p></p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:23'>\r
- <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
- font-family:"Courier New"'>maxmb</span></span><span style='font-size:8.0pt;\r
- font-family:"Courier New"'><o:p></o:p></span></p>\r
- </td>\r
- <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal>Integer</p>\r
- </td>\r
- <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>80%\r
- of Physical RAM, or 500 Mb if not known.<o:p></o:p></span></p>\r
- <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><o:p> </o:p></span></p>\r
- </td>\r
- <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal>Maximum memory to allocate in Mb.</p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:24'>\r
- <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
- font-family:"Courier New"'>maxtrees</span></span><span style='font-size:8.0pt;\r
- font-family:"Courier New"'><o:p></o:p></span></p>\r
- </td>\r
- <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal>Integer</p>\r
- </td>\r
- <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>1<o:p></o:p></span></p>\r
- </td>\r
- <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal>Maximum number of new trees to build in iteration 2.</p>\r
- <p class=MsoNormal><o:p> </o:p></p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:25'>\r
- <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span\r
- style='font-size:8.0pt;font-family:"Courier New"'>minbestcolscore</span></span><span\r
- style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>\r
- </td>\r
- <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'>Floating point </p>\r
- </td>\r
- <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'>[1]</p>\r
- </td>\r
- <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'>Minimum score a column must\r
- have to be an anchor.</p>\r
- <p class=MsoNormal style='page-break-after:avoid'><o:p> </o:p></p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:26'>\r
- <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span\r
- style='font-size:8.0pt;font-family:"Courier New"'>minsmoothscore</span></span><span\r
- style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>\r
- </td>\r
- <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'>Floating point</p>\r
- </td>\r
- <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'>[1]</p>\r
- </td>\r
- <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'>Minimum smoothed score a\r
- column must have to be an anchor.</p>\r
- <p class=MsoNormal style='page-break-after:avoid'><o:p> </o:p></p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:27'>\r
- <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span\r
- style='font-size:8.0pt;font-family:"Courier New"'>msaout</span></span><span\r
- style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>\r
- </td>\r
- <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'>File name</p>\r
- </td>\r
- <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'>None</p>\r
- </td>\r
- <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'>Write output to given file\r
- name in MSF format.</p>\r
- <p class=MsoNormal style='page-break-after:avoid'><o:p> </o:p></p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:28'>\r
- <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
- font-family:"Courier New"'>objscore</span></span><span style='font-size:8.0pt;\r
- font-family:"Courier New"'><o:p></o:p></span></p>\r
- </td>\r
- <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>sp<o:p></o:p></span></p>\r
- <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
- font-family:"Courier New"'>ps</span></span><span style='font-size:8.0pt;\r
- font-family:"Courier New"'><o:p></o:p></span></p>\r
- <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
- font-family:"Courier New"'>dp</span></span><span style='font-size:8.0pt;\r
- font-family:"Courier New"'><o:p></o:p></span></p>\r
- <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
- font-family:"Courier New"'>xp</span></span><span style='font-size:8.0pt;\r
- font-family:"Courier New"'><o:p></o:p></span></p>\r
- <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
- font-family:"Courier New"'>spf</span></span><span style='font-size:8.0pt;\r
- font-family:"Courier New"'><o:p></o:p></span></p>\r
- <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
- font-family:"Courier New"'>spm</span></span><span style='font-size:8.0pt;\r
- font-family:"Courier New"'><o:p></o:p></span></p>\r
- </td>\r
- <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
- font-family:"Courier New"'>spm</span></span><span style='font-size:8.0pt;\r
- font-family:"Courier New"'><o:p></o:p></span></p>\r
- </td>\r
- <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal>Objective score used by tree dependent refinement.</p>\r
- <p class=MsoNormal><span class=GramE>sp=</span>sum-of-pairs score.</p>\r
- <p class=MsoNormal><span class=SpellE>spf</span>=sum-of-pairs score (dimer\r
- approximation)</p>\r
- <p class=MsoNormal><span class=SpellE>spm</span>=sp for < 100 <span\r
- class=SpellE>seqs</span>, otherwise <span class=SpellE>spf</span></p>\r
- <p class=MsoNormal><span class=SpellE><span class=GramE>dp</span></span><span\r
- class=GramE>=</span>dynamic programming score.</p>\r
- <p class=MsoNormal><span class=SpellE><span class=GramE>ps</span></span><span\r
- class=GramE>=</span>average profile-sequence score.</p>\r
- <p class=MsoNormal><span class=SpellE><span class=GramE>xp</span></span><span\r
- class=GramE>=</span>cross profile score.</p>\r
- <p class=MsoNormal><o:p> </o:p></p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:29'>\r
- <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>out<o:p></o:p></span></p>\r
- </td>\r
- <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal>File name</p>\r
- </td>\r
- <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal>standard output</p>\r
- </td>\r
- <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal>Where to write the alignment.</p>\r
- <p class=MsoNormal><o:p> </o:p></p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:30'>\r
- <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
- font-family:"Courier New"'>phyiout</span></span><span style='font-size:8.0pt;\r
- font-family:"Courier New"'><o:p></o:p></span></p>\r
- </td>\r
- <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal>File name</p>\r
- </td>\r
- <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal>None</p>\r
- </td>\r
- <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal>Write output in <span class=SpellE>Phylip</span>\r
- interleaved format to given file name.</p>\r
- <p class=MsoNormal><o:p> </o:p></p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:31'>\r
- <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
- font-family:"Courier New"'>physout</span></span><span style='font-size:8.0pt;\r
- font-family:"Courier New"'><o:p></o:p></span></p>\r
- </td>\r
- <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal>File name</p>\r
- </td>\r
- <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal>None</p>\r
- </td>\r
- <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal>Write output in <span class=SpellE>Phylip</span>\r
- sequential format to given file name.</p>\r
- <p class=MsoNormal><o:p> </o:p></p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:32'>\r
- <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
- font-family:"Courier New"'>refinewindow</span></span><span style='font-size:\r
- 8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>\r
- </td>\r
- <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal>Integer</p>\r
- </td>\r
- <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal>200</p>\r
- </td>\r
- <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal>Length of window for <i>-<span class=SpellE>refinew</span></i>.</p>\r
- <p class=MsoNormal><o:p> </o:p></p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:33'>\r
- <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>root1<o:p></o:p></span></p>\r
- <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>root2<o:p></o:p></span></p>\r
- </td>\r
- <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>pseudo<o:p></o:p></span></p>\r
- <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
- font-family:"Courier New"'>midlongestspan</span></span><span\r
- style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>\r
- <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
- font-family:"Courier New"'>minavgleafdist</span></span><span\r
- style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>\r
- </td>\r
- <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
- font-family:"Courier New"'>psuedo</span></span><span style='font-size:8.0pt;\r
- font-family:"Courier New"'><o:p></o:p></span></p>\r
- </td>\r
- <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal>Method used to root tree; root1 is used in iteration 1 and\r
- 2, root2 in later iterations.</p>\r
- <p class=MsoNormal><o:p> </o:p></p>\r
- <p class=MsoNormal><o:p> </o:p></p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:34'>\r
- <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
- font-family:"Courier New"'>scorefile</span></span><span style='font-size:\r
- 8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>\r
- </td>\r
- <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>File\r
- name<o:p></o:p></span></p>\r
- </td>\r
- <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>None<o:p></o:p></span></p>\r
- </td>\r
- <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal>File name where to write a score file. This contains one\r
- line for each column in the alignment. The line contains the letters in the\r
- column followed by the average BLOSUM62 score over pairs of letters in the column.</p>\r
- <p class=MsoNormal><o:p> </o:p></p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:35'>\r
- <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
- font-family:"Courier New"'>seqtype</span></span><span style='font-size:8.0pt;\r
- font-family:"Courier New"'><o:p></o:p></span></p>\r
- </td>\r
- <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>protein<o:p></o:p></span></p>\r
- <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
- font-family:"Courier New"'>nucleo</span></span><span style='font-size:8.0pt;\r
- font-family:"Courier New"'><o:p></o:p></span></p>\r
- <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>auto<o:p></o:p></span></p>\r
- <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><o:p> </o:p></span></p>\r
- </td>\r
- <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>auto<o:p></o:p></span></p>\r
- </td>\r
- <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal>Sequence type.</p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:36'>\r
- <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
- font-family:"Courier New"'>smoothscoreceil</span></span><span\r
- style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>\r
- </td>\r
- <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal>Floating point</p>\r
- </td>\r
- <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal>[1]</p>\r
- </td>\r
- <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal>Maximum <span class=GramE>value of column score</span> for\r
- smoothing purposes.</p>\r
- <p class=MsoNormal><o:p> </o:p></p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:37'>\r
- <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
- font-family:"Courier New"'>smoothwindow</span></span><span style='font-size:\r
- 8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>\r
- </td>\r
- <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal>Integer<o:p></o:p></p>\r
- </td>\r
- <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>7<o:p></o:p></span></p>\r
- </td>\r
- <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal>Window used for anchor column smoothing.</p>\r
- <p class=MsoNormal><o:p> </o:p></p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:38'>\r
- <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
- font-family:"Courier New"'>spscore</span></span><span style='font-size:8.0pt;\r
- font-family:"Courier New"'><o:p></o:p></span></p>\r
- </td>\r
- <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal>File name<o:p></o:p></p>\r
- </td>\r
- <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><o:p> </o:p></span></p>\r
- </td>\r
- <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal>Compute SP objective score of multiple <span class=GramE>alignment</span>.</p>\r
- <p class=MsoNormal><o:p> </o:p></p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:39'>\r
- <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>SUEFF<o:p></o:p></span></p>\r
- </td>\r
- <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal>Floating point value between 0 and 1.</p>\r
- <p class=MsoNormal><o:p> </o:p></p>\r
- </td>\r
- <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>0.1<o:p></o:p></span></p>\r
- </td>\r
- <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal>Constant used in UPGMB clustering. Determines the relative\r
- fraction of average linkage (SUEFF) vs. nearest-neighbor linkage (1 \96 SUEFF).<br\r
- style='mso-special-character:line-break'>\r
- <![if !supportLineBreakNewLine]><br style='mso-special-character:line-break'>\r
- <![endif]></p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:40'>\r
- <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>tree1<o:p></o:p></span></p>\r
- <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>tree2<o:p></o:p></span></p>\r
- </td>\r
- <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal>File name</p>\r
- </td>\r
- <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal>None<o:p></o:p></p>\r
- </td>\r
- <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal>Save tree produced in first or second iteration to given\r
- file in <span class=SpellE>Newick</span> (<span class=SpellE>Phylip</span>-compatible)\r
- format.</p>\r
- <p class=MsoNormal><o:p> </o:p></p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:41'>\r
- <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
- font-family:"Courier New"'>usetree</span></span><span style='font-size:8.0pt;\r
- font-family:"Courier New"'><o:p></o:p></span></p>\r
- </td>\r
- <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal>File name</p>\r
- </td>\r
- <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal>None<o:p></o:p></p>\r
- </td>\r
- <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal>Use given tree as guide tree. Must by in <span\r
- class=SpellE>Newick</span> (<span class=SpellE>Phyip</span>-compatible)\r
- format.</p>\r
- <p class=MsoNormal><o:p> </o:p></p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:42;mso-yfti-lastrow:yes'>\r
- <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:\r
- 8.0pt;font-family:"Courier New"'>weight1<o:p></o:p></span></p>\r
- <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:\r
- 8.0pt;font-family:"Courier New"'>weight2<o:p></o:p></span></p>\r
- </td>\r
- <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:\r
- 8.0pt;font-family:"Courier New"'>none<o:p></o:p></span></p>\r
- <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span\r
- style='font-size:8.0pt;font-family:"Courier New"'>henikoff</span></span><span\r
- style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>\r
- <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span\r
- style='font-size:8.0pt;font-family:"Courier New"'>henikoffpb</span></span><span\r
- style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>\r
- <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span\r
- style='font-size:8.0pt;font-family:"Courier New"'>gsc</span></span><span\r
- style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>\r
- <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span\r
- style='font-size:8.0pt;font-family:"Courier New"'>clustalw</span></span><span\r
- style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>\r
- <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span\r
- style='font-size:8.0pt;font-family:"Courier New"'>threeway</span></span></p>\r
- </td>\r
- <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span\r
- style='font-size:8.0pt;font-family:"Courier New"'>clustalw</span></span><span\r
- style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>\r
- <p class=MsoNormal style='page-break-after:avoid'><o:p> </o:p></p>\r
- </td>\r
- <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'>Sequence weighting scheme.</p>\r
- <p class=MsoNormal style='page-break-after:avoid'><span class=GramE>weight1</span>\r
- is used in iterations 1 and 2.</p>\r
- <p class=MsoNormal style='page-break-after:avoid'><span class=GramE>weight2</span>\r
- is used for tree-dependent refinement.</p>\r
- <p class=MsoNormal style='page-break-after:avoid'><span class=GramE>none=</span>all\r
- sequences have equal weight.</p>\r
- <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span\r
- class=GramE>henikoff</span></span><span class=GramE>=</span>Henikoff &\r
- Henikoff weighting scheme.</p>\r
- <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span\r
- class=GramE>henikoffpb</span></span><span class=GramE>=</span>Modified\r
- Henikoff scheme as used in PSI-BLAST.</p>\r
- <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span\r
- class=GramE>clustalw</span></span><span class=GramE>=</span>CLUSTALW method.</p>\r
- <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span\r
- class=GramE>threeway</span></span><span class=GramE>=</span>Gotoh three-way\r
- method.</p>\r
- <p class=MsoNormal style='page-break-after:avoid'><o:p> </o:p></p>\r
- </td>\r
- </tr>\r
-</table>\r
-\r
-<p class=MsoNormal><o:p> </o:p></p>\r
-\r
-<table class=MsoTableGrid border=0 cellspacing=0 cellpadding=0\r
- style='border-collapse:collapse;mso-yfti-tbllook:480;mso-padding-alt:0in 5.4pt 0in 5.4pt'>\r
- <thead>\r
- <tr style='mso-yfti-irow:0'>\r
- <td width=137 valign=top style='width:102.6pt;border:none;border-bottom:\r
- solid windowtext 1.0pt;mso-border-bottom-alt:solid windowtext .5pt;\r
- padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'><b><span style='font-size:\r
- 9.0pt;font-family:Arial'>Flag option<o:p></o:p></span></b></p>\r
- </td>\r
- <td width=106 valign=top style='width:1.1in;border:none;border-bottom:solid windowtext 1.0pt;\r
- mso-border-bottom-alt:solid windowtext .5pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'><b><span style='font-size:\r
- 9.0pt;font-family:Arial'>Set by default?<o:p></o:p></span></b></p>\r
- </td>\r
- <td width=348 valign=top style='width:261.0pt;border:none;border-bottom:\r
- solid windowtext 1.0pt;mso-border-bottom-alt:solid windowtext .5pt;\r
- padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'><b><span style='font-size:\r
- 9.0pt;font-family:Arial'>Description<o:p></o:p></span></b></p>\r
- </td>\r
- </tr>\r
- </thead>\r
- <tr style='mso-yfti-irow:1;height:6.25pt'>\r
- <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:\r
- 8.0pt;font-family:"Courier New"'>anchors<o:p></o:p></span></p>\r
- </td>\r
- <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'>yes<o:p></o:p></p>\r
- </td>\r
- <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'>Use anchor optimization in\r
- tree dependent refinement iterations.</p>\r
- <p class=MsoNormal style='page-break-after:avoid'><o:p> </o:p></p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:2;height:6.25pt'>\r
- <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span\r
- style='font-size:8.0pt;font-family:"Courier New"'>brenner</span></span><span\r
- style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>\r
- </td>\r
- <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'>no</p>\r
- </td>\r
- <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'>Use Steven Brenner's method\r
- for computing the root alignment.</p>\r
- <p class=MsoNormal style='page-break-after:avoid'><o:p> </o:p></p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:3;height:6.25pt'>\r
- <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:\r
- 8.0pt;font-family:"Courier New"'>cluster<o:p></o:p></span></p>\r
- </td>\r
- <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'>no</p>\r
- </td>\r
- <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'>Perform fast clustering of\r
- input sequences. Use the \96<i>tree1</i> option to save the tree.</p>\r
- <p class=MsoNormal style='page-break-after:avoid'><o:p> </o:p></p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:4;height:6.25pt'>\r
- <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:\r
- 8.0pt;font-family:"Courier New"'>dimer<o:p></o:p></span></p>\r
- </td>\r
- <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'>no</p>\r
- </td>\r
- <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'>Use dimer approximation for\r
- the SP score (faster, slightly less accurate).</p>\r
- <p class=MsoNormal style='page-break-after:avoid'><o:p> </o:p></p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:5;height:6.25pt'>\r
- <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span\r
- style='font-size:8.0pt;font-family:"Courier New"'>clw</span></span><span\r
- style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>\r
- </td>\r
- <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'>no<o:p></o:p></p>\r
- </td>\r
- <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'>Write output in CLUSTALW\r
- format (default is FASTA).</p>\r
- <p class=MsoNormal style='page-break-after:avoid'><o:p> </o:p></p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:6;height:6.25pt'>\r
- <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span\r
- style='font-size:8.0pt;font-family:"Courier New"'>clwstrict</span></span><span\r
- style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>\r
- </td>\r
- <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'>no</p>\r
- </td>\r
- <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'>Write output in CLUSTALW\r
- format with the "CLUSTAL W (1.81)" header rather than the MUSCLE\r
- version. This is useful when a post-processing step is picky about the file\r
- header.</p>\r
- <p class=MsoNormal style='page-break-after:avoid'><o:p> </o:p></p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:7;height:6.25pt'>\r
- <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:\r
- 8.0pt;font-family:"Courier New"'>core<o:p></o:p></span></p>\r
- </td>\r
- <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'>yes in muscle,</p>\r
- <p class=MsoNormal style='page-break-after:avoid'><span class=GramE>no</span>\r
- in muscled.<o:p></o:p></p>\r
- </td>\r
- <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'>Do not catch exceptions.</p>\r
- <p class=MsoNormal style='page-break-after:avoid'><o:p> </o:p></p>\r
- <p class=MsoNormal style='page-break-after:avoid'><o:p> </o:p></p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:8;height:6.25pt'>\r
- <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span\r
- style='font-size:8.0pt;font-family:"Courier New"'>diags</span></span><span\r
- style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>\r
- </td>\r
- <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'>no<o:p></o:p></p>\r
- </td>\r
- <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'>Use diagonal optimizations.\r
- Faster, especially for closely related sequences, but may be less accurate.</p>\r
- <p class=MsoNormal style='page-break-after:avoid'><o:p> </o:p></p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:9;height:6.25pt'>\r
- <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:\r
- 8.0pt;font-family:"Courier New"'>diags1<o:p></o:p></span></p>\r
- </td>\r
- <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'>no</p>\r
- </td>\r
- <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'>Use diagonal optimizations\r
- in first iteration.</p>\r
- <p class=MsoNormal style='page-break-after:avoid'><o:p> </o:p></p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:10;height:6.25pt'>\r
- <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:\r
- 8.0pt;font-family:"Courier New"'>diags2<o:p></o:p></span></p>\r
- </td>\r
- <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'>no</p>\r
- </td>\r
- <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'>Use diagonal optimizations\r
- in second iteration.</p>\r
- <p class=MsoNormal style='page-break-after:avoid'><o:p> </o:p></p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:11;height:6.25pt'>\r
- <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span\r
- style='font-size:8.0pt;font-family:"Courier New"'>fasta</span></span><span\r
- style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>\r
- </td>\r
- <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'>yes<o:p></o:p></p>\r
- </td>\r
- <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'>Write output in FASTA\r
- format.</p>\r
- <p class=MsoNormal style='page-break-after:avoid'><o:p> </o:p></p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:12;height:6.25pt'>\r
- <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:\r
- 8.0pt;font-family:"Courier New"'>group<o:p></o:p></span></p>\r
- </td>\r
- <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'>yes<o:p></o:p></p>\r
- </td>\r
- <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'>Group similar sequences\r
- together in the output. This is the default. See also \96<i>stable</i>.</p>\r
- <p class=MsoNormal style='page-break-after:avoid'><o:p> </o:p></p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:13;height:6.25pt'>\r
- <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:\r
- 8.0pt;font-family:"Courier New"'>html<o:p></o:p></span></p>\r
- </td>\r
- <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'>no<o:p></o:p></p>\r
- </td>\r
- <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'>Write output in HTML format\r
- (default is FASTA).</p>\r
- <p class=MsoNormal style='page-break-after:avoid'><o:p> </o:p></p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:14'>\r
- <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:\r
- 8.0pt;font-family:"Courier New"'>le</span></p>\r
- </td>\r
- <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal>maybe<o:p></o:p></p>\r
- </td>\r
- <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt'>\r
- <p class=MsoNormal>Use log-expectation profile score (VTML240). Alternatives\r
- are to use \96<i>sp</i> or <i>\96<span class=SpellE>sv</span></i>. This is the\r
- default for amino acid sequences.<o:p></o:p></p>\r
- <p class=MsoNormal><o:p> </o:p></p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:15;height:6.25pt'>\r
- <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
- font-family:"Courier New"'>msf</span></span><span style='font-size:8.0pt;\r
- font-family:"Courier New"'><o:p></o:p></span></p>\r
- </td>\r
- <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal>no<o:p></o:p></p>\r
- </td>\r
- <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal>Write output in MSF format (default is FASTA). Designed to\r
- be compatible with the GCG package.</p>\r
- <p class=MsoNormal><o:p> </o:p></p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:16;height:6.25pt'>\r
- <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
- font-family:"Courier New"'>noanchors</span></span><span style='font-size:\r
- 8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>\r
- </td>\r
- <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal>no<o:p></o:p></p>\r
- </td>\r
- <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal>Disable anchor optimization. Default is \96<i>anchors</i>.<o:p></o:p></p>\r
- <p class=MsoNormal><o:p> </o:p></p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:17;height:6.25pt'>\r
- <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
- font-family:"Courier New"'>nocore</span></span><span style='font-size:8.0pt;\r
- font-family:"Courier New"'><o:p></o:p></span></p>\r
- </td>\r
- <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal>no in muscle,</p>\r
- <p class=MsoNormal><span class=GramE>yes</span> in muscled.<o:p></o:p></p>\r
- </td>\r
- <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal>Catch exceptions and give an error message if possible.</p>\r
- <p class=MsoNormal><o:p> </o:p></p>\r
- <p class=MsoNormal><o:p> </o:p></p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:18;height:6.25pt'>\r
- <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
- font-family:"Courier New"'>phyi</span></span><span style='font-size:8.0pt;\r
- font-family:"Courier New"'><o:p></o:p></span></p>\r
- </td>\r
- <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal>no<o:p></o:p></p>\r
- </td>\r
- <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal>Write output in <span class=SpellE>Phylip</span>\r
- interleaved format.</p>\r
- <p class=MsoNormal><o:p> </o:p></p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:19;height:6.25pt'>\r
- <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>phys<o:p></o:p></span></p>\r
- </td>\r
- <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal>no</p>\r
- </td>\r
- <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal>Write output in <span class=SpellE>Phylip</span>\r
- sequential format.</p>\r
- <p class=MsoNormal><o:p> </o:p></p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:20;height:6.25pt'>\r
- <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>profile<o:p></o:p></span></p>\r
- </td>\r
- <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal>no<o:p></o:p></p>\r
- </td>\r
- <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal>Compute profile-profile alignment. Input alignments must\r
- be given using \96<i>in1</i> and \96<i>in2</i> options.</p>\r
- <p class=MsoNormal><o:p> </o:p></p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:21;height:6.25pt'>\r
- <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>quiet<o:p></o:p></span></p>\r
- </td>\r
- <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal>no<o:p></o:p></p>\r
- </td>\r
- <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal>Do not display progress messages.</p>\r
- <p class=MsoNormal><o:p> </o:p></p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:22;height:6.25pt'>\r
- <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>refine<o:p></o:p></span></p>\r
- </td>\r
- <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal>no<o:p></o:p></p>\r
- </td>\r
- <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal>Input file is already aligned, skip first two iterations\r
- and begin tree dependent refinement.</p>\r
- <p class=MsoNormal><o:p> </o:p></p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:23;height:6.25pt'>\r
- <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
- font-family:"Courier New"'>refinew</span></span><span style='font-size:8.0pt;\r
- font-family:"Courier New"'><o:p></o:p></span></p>\r
- </td>\r
- <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal>no<o:p></o:p></p>\r
- </td>\r
- <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal>Refine an alignment by dividing it into non-overlapping\r
- windows and re-aligning each window. Typically used for whole-genome\r
- nucleotide alignments.</p>\r
- <p class=MsoNormal><o:p> </o:p></p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:24;height:6.25pt'>\r
- <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:\r
- 8.0pt;font-family:"Courier New"'>sp<o:p></o:p></span></p>\r
- </td>\r
- <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal>no<o:p></o:p></p>\r
- </td>\r
- <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal>Use sum-of-pairs protein profile score (PAM200). Default\r
- is \96<i>le.<o:p></o:p></i></p>\r
- <p class=MsoNormal><o:p> </o:p></p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:25;height:6.25pt'>\r
- <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span\r
- style='font-size:8.0pt;font-family:"Courier New"'>spscore</span></span><span\r
- style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>\r
- </td>\r
- <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal>no</p>\r
- </td>\r
- <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal>Compute alignment score of profile-profile alignment.\r
- Input alignments must be given using \96<i>in1</i> and \96<i>in2</i> options.\r
- These must be pre-aligned with gapped columns as needed, i.e. must be of the\r
- same length (have same number of columns).</p>\r
- <p class=MsoNormal><o:p> </o:p></p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:26;height:6.25pt'>\r
- <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'><span class=SpellE><span\r
- style='font-size:8.0pt;font-family:"Courier New"'>spn</span></span><span\r
- style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>\r
- </td>\r
- <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal>maybe</p>\r
- <p class=MsoNormal><o:p> </o:p></p>\r
- </td>\r
- <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal>Use sum-of-pairs nucleotide profile score. This is the\r
- only option for nucleotides, and is therefore the default. The substitution\r
- scores and gap penalty scores are "borrowed" from BLASTZ.</p>\r
- <p class=MsoNormal><o:p> </o:p></p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:27;height:6.25pt'>\r
- <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:\r
- 8.0pt;font-family:"Courier New"'>stable<o:p></o:p></span></p>\r
- </td>\r
- <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal>no<o:p></o:p></p>\r
- </td>\r
- <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal>Preserve input order of sequences in output file. Default\r
- is to group sequences by similarity (\96<i>group</i>).</p>\r
- <p class=MsoNormal><o:p> </o:p></p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:28;height:6.25pt'>\r
- <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
- font-family:"Courier New"'>sv</span></span><span style='font-size:8.0pt;\r
- font-family:"Courier New"'><o:p></o:p></span></p>\r
- </td>\r
- <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal>no<o:p></o:p></p>\r
- </td>\r
- <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal>Use sum-of-pairs profile score (VTML240). Default is \96<i>le.</i></p>\r
- <p class=MsoNormal><o:p> </o:p></p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:29;height:6.25pt'>\r
- <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>termgaps4<o:p></o:p></span></p>\r
- </td>\r
- <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal>yes<o:p></o:p></p>\r
- </td>\r
- <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal>Use 4-way test for treatment of terminal gaps. (Cannot be\r
- disabled in this version).</p>\r
- <p class=MsoNormal><o:p> </o:p></p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:30;height:6.25pt'>\r
- <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
- font-family:"Courier New"'>termgapsfull</span></span><span style='font-size:\r
- 8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>\r
- </td>\r
- <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal>no<o:p></o:p></p>\r
- </td>\r
- <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal>Terminal gaps penalized with full penalty.</p>\r
- <p class=MsoNormal>[1] Not fully supported in this version.</p>\r
- <p class=MsoNormal><o:p> </o:p></p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:31;height:6.25pt'>\r
- <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
- font-family:"Courier New"'>termgapshalf</span></span><span style='font-size:\r
- 8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>\r
- </td>\r
- <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal>yes<o:p></o:p></p>\r
- </td>\r
- <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal>Terminal gaps penalized with half penalty.</p>\r
- <p class=MsoNormal>[1] Not fully supported in this version.</p>\r
- <p class=MsoNormal><o:p> </o:p></p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:32;height:6.25pt'>\r
- <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal><span class=SpellE><span style='font-size:8.0pt;\r
- font-family:"Courier New"'>termgapshalflonger</span></span><span\r
- style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>\r
- </td>\r
- <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal>no<o:p></o:p></p>\r
- </td>\r
- <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal>Terminal gaps penalized with half penalty if gap relative\r
- to </p>\r
- <p class=MsoNormal><span class=GramE>longer</span> sequence, otherwise with\r
- full penalty.</p>\r
- <p class=MsoNormal>[1] Not fully supported in this version.</p>\r
- <p class=MsoNormal><o:p> </o:p></p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:33;height:6.25pt'>\r
- <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>verbose<o:p></o:p></span></p>\r
- </td>\r
- <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal>no<o:p></o:p></p>\r
- </td>\r
- <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal>Write parameter settings and progress messages to log\r
- file.</p>\r
- <p class=MsoNormal><o:p> </o:p></p>\r
- </td>\r
- </tr>\r
- <tr style='mso-yfti-irow:34;mso-yfti-lastrow:yes;height:6.25pt'>\r
- <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>version<o:p></o:p></span></p>\r
- </td>\r
- <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal>no<o:p></o:p></p>\r
- </td>\r
- <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;\r
- height:6.25pt'>\r
- <p class=MsoNormal>Write version string to <span class=SpellE>stdout</span>\r
- and exit.</p>\r
- </td>\r
- </tr>\r
-</table>\r
-\r
-<p class=MsoNormal><i><o:p> </o:p></i></p>\r
-\r
-<p class=MsoNormal><i>Notes<o:p></o:p></i></p>\r
-\r
-<p class=MsoNormal>[1] Default depends on the profile scoring function. To\r
-determine the default, use \96<i>verbose \96log</i> and check the log file.</p>\r
-\r
-<p class=MsoNormal><u><o:p><span style='text-decoration:none'> </span></o:p></u></p>\r
-\r
-</div>\r
-\r
-</body>\r
-\r
-</html>\r
git://source.jalview.org / jabaws.git / blobdiff