muscle (1:3.8.31-1) debian-dir only changes

Summary

 debian/README.Debian   |   23 
 debian/README.source   |    3 
 debian/changelog       |  101 ++
 debian/compat          |    1 
 debian/control         |   26 
 debian/copyright       |   24 
 debian/dirs            |    1 
 debian/muscle.1        |  135 +++
 debian/muscle.1.xml    |  270 ++++++
 debian/muscle.doc-base |   15 
 debian/muscle.docs     |    1 
 debian/muscle.html     | 2042 +++++++++++++++++++++++++++++++++++++++++++++++++
 debian/muscle.install  |    1 
 debian/muscle.manpages |    1 
 debian/rules           |   35 
 debian/watch           |    2 
 16 files changed, 2681 insertions(+)

    
download this patch

Patch contents

--- muscle-3.8.31.orig/debian/muscle.manpages
+++ muscle-3.8.31/debian/muscle.manpages
@@ -0,0 +1 @@
+debian/muscle.1
--- muscle-3.8.31.orig/debian/muscle.install
+++ muscle-3.8.31/debian/muscle.install
@@ -0,0 +1 @@
+muscle	/usr/bin
--- muscle-3.8.31.orig/debian/dirs
+++ muscle-3.8.31/debian/dirs
@@ -0,0 +1 @@
+usr/bin
--- muscle-3.8.31.orig/debian/watch
+++ muscle-3.8.31/debian/watch
@@ -0,0 +1,2 @@
+version=3
+http://www.drive5.com/muscle/downloads.htm http://www.drive5.com/muscle/downloads.+?/muscle(.*)_src\.tar\.gz
--- muscle-3.8.31.orig/debian/README.source
+++ muscle-3.8.31/debian/README.source
@@ -0,0 +1,3 @@
+The original upstream archive have been repacked to remove the muscle21
+program, for which it was unsure if source was provided.  To simplify building,
+the contents of the src directory were moved to the root.
--- muscle-3.8.31.orig/debian/muscle.docs
+++ muscle-3.8.31/debian/muscle.docs
@@ -0,0 +1 @@
+debian/muscle.html
--- muscle-3.8.31.orig/debian/control
+++ muscle-3.8.31/debian/control
@@ -0,0 +1,26 @@
+Source: muscle
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Steffen Moeller <moeller@debian.org>,
+ Charles Plessy <plessy@debian.org>
+Build-Depends: debhelper (>= 8), cdbs
+Standards-Version: 3.9.2
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/muscle
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/muscle/trunk/
+Homepage: http://www.drive5.com/muscle/
+
+Package: muscle
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Conflicts: muscle-doc
+Replaces: muscle-doc
+Provides: muscle-doc
+Enhances: seaview, t-coffee
+Description: Multiple alignment program of protein sequences
+ MUSCLE is a multiple alignment program for protein sequences. MUSCLE
+ stands for multiple sequence comparison by log-expectation. In the
+ authors tests, MUSCLE achieved the highest scores of all tested
+ programs on several alignment accuracy benchmarks, and is also one of
+ the fastest programs out there.
--- muscle-3.8.31.orig/debian/changelog
+++ muscle-3.8.31/debian/changelog
@@ -0,0 +1,101 @@
+muscle (1:3.8.31-1) unstable; urgency=low
+
+  [ Charles Plessy ]
+  * New upstream release (Closes: #643443).
+  * debian/control: Enhances: t-coffee.
+  * Changed the doc-base section according to the new policy.
+  * Updated my email address.
+  * Updated debian/watch to new version scheme and download location.
+  * Repack usptream archive and implemented a get-orig-source target
+    (debian/rules, debian/README.source, debian/copyright).
+  * Use Debhelper 8 (debian/control, debian/compat).
+  * Build directly from debian/rules targets.
+  * Corrected VCS URLs in debian/control.
+  * Conforms to Debian Policy 3.9.2 (debian/control, no changes needed).
+
+  [ David Paleino ]
+  * removed myself from Uploaders (debian/control).
+
+ -- Charles Plessy <plessy@debian.org>  Sun, 13 Nov 2011 18:38:06 +0900
+
+muscle (3.70+fix1-2) unstable; urgency=low
+
+  * debian/control Conflicts: and Replaces: muscle-doc (Closes: #465607)
+
+ -- Charles Plessy <charles-debian-nospam@plessy.org>  Thu, 14 Feb 2008 10:44:17 +0900
+
+muscle (3.70+fix1-1) unstable; urgency=low
+
+  [ Charles Plessy ]
+  * New upstream version, buildable with GCC 4.3 (Closes: #462707)
+    The version number was not increased upstream when the sources were
+    changed. We name this new version in Debian "3.70+fix1".
+  * Updated manual page.
+  * Converted the source package to CDBS, dropped Makefile patch.
+  * Fused muscle and muscle-doc.
+
+  [ Nelson A. de Oliveira ]
+  * Fixed watch file (Closes: #462827)
+
+ -- Charles Plessy <charles-debian-nospam@plessy.org>  Wed, 06 Feb 2008 12:04:31 +0900
+
+muscle (3.70-1) unstable; urgency=low
+
+  [ Charles Plessy ]
+  * New upstream release (bugfixes plus undocumented new features).
+  * debian/control:
+    - Add Subversion repository.
+    - Swiched to quilt.
+    - Enhaces: seaview because SeaView can call muscle to re-align sequences.
+    - Moved the Homepage: field out from the package's description.
+    - Using debhelper 5.
+    - Removed [Biology] from package description as there are Debtags now.
+    - Checked that muscle conforms to Policy 3.7.3.
+    - Updated Steffen's email address.
+  * Handling nostrip build option (policy 10.1) (Closes: #437599).
+  * Updated manpage.
+  * debian/copyright made machine-readable.
+
+  [ Nelson A. de Oliveira ]
+  * Added watch file.
+
+  [ David Paleino ]
+  * debian/manpage.xml moved to debian/muscle.1.xml
+  * debian/muscle.1 added - statically built
+  * debian/manpages removed - passing arguments to dh_installman
+    directly
+  * debian/control:
+    - B-D updated (see above)
+    - added myself to Uploaders
+    - moved XS-Vcs-* to Vcs-*
+  * debian/rules:
+    - manpages statically built
+    - minor changes
+
+ -- Charles Plessy <charles-debian-nospam@plessy.org>  Sat, 12 Jan 2008 16:55:48 +0900
+
+muscle (3.60-1) unstable; urgency=low
+
+  * New upstram release (Closes: Bug#361742).
+  * New maintainers email addresses. 
+
+ -- Charles Plessy <charles-debian-nospam@plessy.org>  Sat,  5 Aug 2006 09:57:27 +0900
+
+muscle (3.52-2) unstable; urgency=low
+
+  * Added missing build dependencies (Closes: Bug#287684).
+
+ -- Steffen Moeller <moeller@pzr.uni-rostock.de>  Wed, 29 Dec 2004 21:50:47 +0200 
+
+muscle (3.52-1) unstable; urgency=low
+
+  * New upstream version.
+  * Fix build on arch other than Pentium (Closes: Bug#285000).
+
+ -- Steffen Moeller <moeller@pzr.uni-rostock.de>  Sun, 18 Dec 2004 00:06:00 +0200
+
+muscle (3.51-1) unstable; urgency=low
+
+  * Initial Release (Closes: Bug#280411).
+
+ -- Steffen Moeller <moeller@pzr.uni-rostock.de>  Sun, 19 Sep 2004 00:51:19 +0200
--- muscle-3.8.31.orig/debian/copyright
+++ muscle-3.8.31/debian/copyright
@@ -0,0 +1,24 @@
+Format: http://dep.debian.net/deps/dep5/
+Source: http://www.drive5.com/muscle/downloads3.8.31/muscle3.8.31_src.tar.gz
+Comment: This release contains a potentially sourceless binary file, muscle21, that was removed.
+
+Files: *
+Copyright: © Robert C. Edgar "Bob" <muscle@drive5.com>
+License: PD-dedication
+ MUSCLE is public domain software
+ The MUSCLE software, including object and source code, is hereby donated
+ to the public domain.
+ .
+ Disclaimer of warranty
+ THIS SOFTWARE IS PROVIDED "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER
+ EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION IMPLIED WARRANTIES OF
+ MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+
+Files: debian/*
+Copyright: © 2004 Steffen Moeller <steffen_moeller@gmx.de>
+           © 2007 Nelson A. de Oliveira <naoliv@debian.org>
+           © 2007 David Paleino <d.paleino@gmail.com>
+           © 2006-2008 Charles Plessy <charles-debian-nospam@plessy.org>
+License: PD-dedication
+ Please treat this work as if it were in public domain.
+
--- muscle-3.8.31.orig/debian/muscle.1
+++ muscle-3.8.31/debian/muscle.1
@@ -0,0 +1,135 @@
+.\"     Title: MUSCLE
+.\"    Author: Robert Elgar
+.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
+.\"      Date: 02/06/2008
+.\"    Manual: Muscle Manual
+.\"    Source: muscle 3.7
+.\"
+.TH "MUSCLE" "1" "02/06/2008" "muscle 3.7" "Muscle Manual"
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.SH "NAME"
+muscle - Multiple Protein Sequence Alignment
+.SH "SYNOPSIS"
+.HP 7
+\fBmuscle\fR \fB\-in\ \fR\fB\fIinput\ file\ (fasta)\fR\fR [\fB\-out\ \fR\fB\fIoutput\ file\ (default\ fasta)\fR\fR] [\fB\-diags\fR] [\fB\-log\ \fR\fB\fIlog\ file\fR\fR] [\fB\-maxiters\ \fR\fB\fIn\fR\fR] [\fB\-maxhours\ \fR\fB\fIn\fR\fR] [\fB\-maxmb\ \fR\fB\fIm\fR\fR] [\fB\-html\fR] [\fB\-msf\fR] [\fB\-clw\fR] [\fB\-clwstrict\fR] [\fB\-log[a]\ \fR\fB\fIlogfile\fR\fR] [\fB\-quiet\fR] [\fB\-stable\fR] [\fB\-group\fR] [\fB\-version\fR]
+.SH "DESCRIPTION"
+.PP
+This manual page documents briefly the
+\fBmuscle\fR
+command\.
+.PP
+\fBmuscle\fR
+aligns protein sequences and is considered superior and faster than Clustal\ W\.
+.SH "OPTIONS"
+.PP
+\fB\-in \fR\fB\fIinput file\fR\fR
+.RS 4
+Path to FASTA formatted input file
+.RE
+.PP
+\fB\-out \fR\fB\fIoutput file\fR\fR
+.RS 4
+Path to output file, FASTA formatted by default
+.RE
+.PP
+\fB\-diags\fR
+.RS 4
+Find diagonals (faster for similar sequences)
+.RE
+.PP
+\fB\-maxiters \fR\fB\fIn\fR\fR
+.RS 4
+Maximum number of iterations (integer, default 16)
+.RE
+.PP
+\fB\-maxhours \fR\fB\fIn\fR\fR
+.RS 4
+Maximum time to iterate in hours (default no limit)
+.RE
+.PP
+\fB\-maxmb \fR\fB\fIm\fR\fR
+.RS 4
+Maximum memory to allocate in Mb (default 80% of RAM)
+.RE
+.PP
+\fB\-html\fR
+.RS 4
+Write output in HTML format (default FASTA)
+.RE
+.PP
+\fB\-msf\fR
+.RS 4
+Write output in MSF format (default FASTA)
+.RE
+.PP
+\fB\-clw\fR
+.RS 4
+Write output in Clustal\ W format (default FASTA)
+.RE
+.PP
+\fB\-clwstrict\fR
+.RS 4
+As \-clw, with \'CLUSTAL W (1\.81)\' header
+.RE
+.PP
+\fB\-log[a] \fR\fB\fIlogfile\fR\fR
+.RS 4
+Log to file (append if \-loga, overwrite if \-log)
+.RE
+.PP
+\fB\-quiet\fR
+.RS 4
+Do not write progress messages to stderr
+.RE
+.PP
+\fB\-stable\fR
+.RS 4
+Output sequences in input order (default is \-group)
+.RE
+.PP
+\fB\-group\fR
+.RS 4
+Group sequences by similarity (this is the default)
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+Display version information and exit
+.RE
+.SH "SEE ALSO"
+.PP
+
+\fBclustalw\fR(1),
+\fBseaview\fR(1),
+\fBt_coffee\fR(1)\.
+.SH "AUTHORS"
+.PP
+\fBRobert Elgar\fR
+.sp -1n
+.IP "" 4
+Wrote Muscle\.
+.PP
+\fBSteffen Moeller\fR <\&moeller@debian\.org\&>
+.sp -1n
+.IP "" 4
+Wrote this manpage\.
+.PP
+\fBCharles Plessy\fR <\&charles\-debian\-nospam@plessy\.org\&>
+.sp -1n
+.IP "" 4
+Updated this manpage\.
+.SH "COPYRIGHT"
+Copyright \(co 2003, 2004 Steffen Moeller (manpage)
+.br
+Copyright \(co 2007, 2008 Charles Plessy (manpage)
+.br
+.PP
+Muscle is in the public domain, and therefore not subjected to copyright\.
+.PP
+This manual page was written by Steffen Moeller moeller@debian\.org for the
+Debian(TM)
+system (but may be used by others)\. Permission is granted to copy, distribute and/or modify this document as if it were in public domain\.
+.sp
--- muscle-3.8.31.orig/debian/muscle.html
+++ muscle-3.8.31/debian/muscle.html
@@ -0,0 +1,2042 @@
+<html>
+
+<head>
+<meta http-equiv=Content-Type content="text/html; charset=windows-1252">
+<meta name=Generator content="Microsoft Word 10 (filtered)">
+<title>MUSCLE User Guide</title>
+
+<style>
+<!--
+ /* Font Definitions */
+ @font-face
+	{font-family:"MS Mincho";
+	panose-1:2 2 6 9 4 2 5 8 3 4;}
+@font-face
+	{font-family:Sendnya;
+	panose-1:0 0 4 0 0 0 0 0 0 0;}
+@font-face
+	{font-family:"Arial Black";
+	panose-1:2 11 10 4 2 1 2 2 2 4;}
+@font-face
+	{font-family:"\@MS Mincho";
+	panose-1:2 2 6 9 4 2 5 8 3 4;}
+ /* Style Definitions */
+ p.MsoNormal, li.MsoNormal, div.MsoNormal
+	{margin:0in;
+	margin-bottom:.0001pt;
+	font-size:10.0pt;
+	font-family:"Times New Roman";}
+h1
+	{margin-top:12.0pt;
+	margin-right:0in;
+	margin-bottom:3.0pt;
+	margin-left:0in;
+	text-indent:0in;
+	page-break-after:avoid;
+	font-size:16.0pt;
+	font-family:Arial;}
+h2
+	{margin-top:12.0pt;
+	margin-right:0in;
+	margin-bottom:3.0pt;
+	margin-left:0in;
+	text-indent:0in;
+	page-break-after:avoid;
+	font-size:12.0pt;
+	font-family:Arial;
+	font-weight:normal;}
+h3
+	{margin-top:12.0pt;
+	margin-right:0in;
+	margin-bottom:3.0pt;
+	margin-left:0in;
+	text-indent:0in;
+	page-break-after:avoid;
+	font-size:10.0pt;
+	font-family:"Times New Roman";}
+p.MsoToc1, li.MsoToc1, div.MsoToc1
+	{margin:0in;
+	margin-bottom:.0001pt;
+	font-size:10.0pt;
+	font-family:"Times New Roman";}
+p.MsoToc2, li.MsoToc2, div.MsoToc2
+	{margin-top:0in;
+	margin-right:0in;
+	margin-bottom:0in;
+	margin-left:10.0pt;
+	margin-bottom:.0001pt;
+	font-size:10.0pt;
+	font-family:"Times New Roman";}
+p.MsoToc3, li.MsoToc3, div.MsoToc3
+	{margin-top:0in;
+	margin-right:0in;
+	margin-bottom:0in;
+	margin-left:20.0pt;
+	margin-bottom:.0001pt;
+	font-size:10.0pt;
+	font-family:"Times New Roman";}
+p.MsoHeader, li.MsoHeader, div.MsoHeader
+	{margin:0in;
+	margin-bottom:.0001pt;
+	font-size:10.0pt;
+	font-family:"Times New Roman";}
+p.MsoFooter, li.MsoFooter, div.MsoFooter
+	{margin:0in;
+	margin-bottom:.0001pt;
+	font-size:10.0pt;
+	font-family:"Times New Roman";}
+p.MsoDate, li.MsoDate, div.MsoDate
+	{margin:0in;
+	margin-bottom:.0001pt;
+	font-size:10.0pt;
+	font-family:"Times New Roman";}
+a:link, span.MsoHyperlink
+	{color:blue;
+	text-decoration:underline;}
+a:visited, span.MsoHyperlinkFollowed
+	{color:purple;
+	text-decoration:underline;}
+p.EquationNumber, li.EquationNumber, div.EquationNumber
+	{margin-top:0in;
+	margin-right:0in;
+	margin-bottom:0in;
+	margin-left:.5in;
+	margin-bottom:.0001pt;
+	text-align:right;
+	text-indent:-.25in;
+	font-size:10.0pt;
+	font-family:"Times New Roman";}
+p.Code, li.Code, div.Code
+	{margin-top:0in;
+	margin-right:0in;
+	margin-bottom:0in;
+	margin-left:.25in;
+	margin-bottom:.0001pt;
+	font-size:9.0pt;
+	font-family:"Courier New";}
+@page Section1
+	{size:8.5in 11.0in;
+	margin:1.0in 1.25in 1.0in 1.25in;}
+div.Section1
+	{page:Section1;}
+ /* List Definitions */
+ ol
+	{margin-bottom:0in;}
+ul
+	{margin-bottom:0in;}
+-->
+</style>
+
+</head>
+
+<body lang=EN-US link=blue vlink=purple>
+
+<div class=Section1>
+
+<p class=MsoNormal>&nbsp;</p>
+
+<p class=MsoNormal>&nbsp;</p>
+
+<p class=MsoNormal>&nbsp;</p>
+
+<p class=MsoNormal>&nbsp;</p>
+
+<p class=MsoNormal align=right style='text-align:right'><span style='font-size:
+24.0pt;font-family:"Arial Black"'>MUSCLE User Guide</span></p>
+
+<p class=MsoNormal align=right style='text-align:right'><u>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</u></p>
+
+<p class=MsoNormal align=right style='text-align:right'><b><span
+style='font-family:Arial'>&nbsp;</span></b></p>
+
+<p class=MsoNormal><span style='font-family:Arial'>&nbsp;</span></p>
+
+<p class=MsoNormal><span style='font-family:Arial'>&nbsp;</span></p>
+
+<p class=MsoNormal><span style='font-family:Arial'>&nbsp;</span></p>
+
+<p class=MsoNormal><span style='font-family:Arial'>&nbsp;</span></p>
+
+<p class=MsoNormal><span style='font-family:Arial'>&nbsp;</span></p>
+
+<p class=MsoNormal><span style='font-family:Arial'>Multiple sequence comparison
+by log-expectation</span></p>
+
+<p class=MsoNormal><span style='font-family:Arial'>by Robert C. Edgar</span></p>
+
+<p class=MsoNormal><span style='font-family:Arial'>&nbsp;</span></p>
+
+<p class=MsoNormal><span style='font-family:Arial'>Version 3.5</span></p>
+
+<p class=MsoNormal><span style='font-family:Arial'>August 2004</span></p>
+
+<p class=MsoNormal><span style='font-family:Arial'>&nbsp;</span></p>
+
+<p class=MsoNormal><span style='font-family:Arial'>&nbsp;</span></p>
+
+<p class=MsoNormal><span style='font-family:Arial'><a
+href="http://www.drive5.com/muscle">http://www.drive5.com/muscle</a></span></p>
+
+<p class=MsoNormal><span style='font-family:Arial'>email: muscle (at) drive5.com</span></p>
+
+<p class=MsoNormal><span style='font-family:Arial'>&nbsp;</span></p>
+
+<p class=MsoNormal><span style='font-family:Arial'>MUSCLE is updated regularly.
+Send me an e-mail if you would like to be notified of new releases.</span></p>
+
+<p class=MsoNormal><span style='font-family:Arial'> </span></p>
+
+<p class=MsoNormal><span style='font-family:Arial'>&nbsp;</span></p>
+
+<p class=MsoNormal><i><span style='font-family:Arial'>Citation:</span></i></p>
+
+<p class=MsoNormal><span style='font-family:Arial'>&nbsp;</span></p>
+
+<p class=MsoNormal><span style='font-family:Arial'><a
+href="http://nar.oupjournals.org/cgi/content/full/32/5/1792?ijkey=48Nmt1tta0fMg&amp;keytype=ref">Edgar,
+Robert C. (2004), MUSCLE: multiple sequence alignment with high accuracy and
+high throughput, <i>Nucleic Acids Research</i> <b>32</b>(5), 1792-97</a>.</span></p>
+
+<span style='font-size:10.0pt;font-family:Arial'><br clear=all
+style='page-break-before:always'>
+</span>
+
+<p class=MsoNormal><b><span style='font-size:16.0pt;font-family:Arial'>Table of
+Contents</span></b></p>
+
+<p class=MsoToc1><span
+class=MsoHyperlink><a href="#_Toc81224823">1 Introduction<span
+style='color:windowtext;display:none;text-decoration:none'>. </span><span
+style='color:windowtext;display:none;text-decoration:none'>3</span></a></span></p>
+
+<p class=MsoToc1><span class=MsoHyperlink><a href="#_Toc81224824">2 Quick Start<span
+style='color:windowtext;display:none;text-decoration:none'> </span><span
+style='color:windowtext;display:none;text-decoration:none'>3</span></a></span></p>
+
+<p class=MsoToc2><span class=MsoHyperlink><a href="#_Toc81224825">2.1
+Installation<span style='color:windowtext;display:none;text-decoration:none'>. </span><span
+style='color:windowtext;display:none;text-decoration:none'>3</span></a></span></p>
+
+<p class=MsoToc2><span class=MsoHyperlink><a href="#_Toc81224826">2.2 Making an
+alignment<span style='color:windowtext;display:none;text-decoration:none'> </span><span
+style='color:windowtext;display:none;text-decoration:none'>3</span></a></span></p>
+
+<p class=MsoToc2><span class=MsoHyperlink><a href="#_Toc81224827">2.3 Large
+alignments<span style='color:windowtext;display:none;text-decoration:none'>. </span><span
+style='color:windowtext;display:none;text-decoration:none'>3</span></a></span></p>
+
+<p class=MsoToc2><span class=MsoHyperlink><a href="#_Toc81224828">2.4 Fastest
+speed<span style='color:windowtext;display:none;text-decoration:none'>. </span><span
+style='color:windowtext;display:none;text-decoration:none'>3</span></a></span></p>
+
+<p class=MsoToc2><span class=MsoHyperlink><a href="#_Toc81224829">2.5 Huge
+alignments<span style='color:windowtext;display:none;text-decoration:none'>. </span><span
+style='color:windowtext;display:none;text-decoration:none'>4</span></a></span></p>
+
+<p class=MsoToc2><span class=MsoHyperlink><a href="#_Toc81224830">2.6 Accuracy:
+caveat emptor<span style='color:windowtext;display:none;text-decoration:none'> </span><span
+style='color:windowtext;display:none;text-decoration:none'>4</span></a></span></p>
+
+<p class=MsoToc2><span class=MsoHyperlink><a href="#_Toc81224831">2.7
+Pipelining<span style='color:windowtext;display:none;text-decoration:none'>. </span><span
+style='color:windowtext;display:none;text-decoration:none'>4</span></a></span></p>
+
+<p class=MsoToc2><span class=MsoHyperlink><a href="#_Toc81224832">2.8 Refining
+an existing alignment<span style='color:windowtext;display:none;text-decoration:
+none'> </span><span
+style='color:windowtext;display:none;text-decoration:none'>4</span></a></span></p>
+
+<p class=MsoToc2><span class=MsoHyperlink><a href="#_Toc81224833">2.9
+Profile-profile alignment<span style='color:windowtext;display:none;text-decoration:
+none'> </span><span
+style='color:windowtext;display:none;text-decoration:none'>4</span></a></span></p>
+
+<p class=MsoToc2><span class=MsoHyperlink><a href="#_Toc81224834">2.10 Sequence
+clustering<span style='color:windowtext;display:none;text-decoration:none'>. </span><span
+style='color:windowtext;display:none;text-decoration:none'>5</span></a></span></p>
+
+<p class=MsoToc1><span class=MsoHyperlink><a href="#_Toc81224835">3 File
+Formats<span style='color:windowtext;display:none;text-decoration:none'>. </span><span
+style='color:windowtext;display:none;text-decoration:none'>5</span></a></span></p>
+
+<p class=MsoToc2><span class=MsoHyperlink><a href="#_Toc81224836">3.1 Input
+files<span style='color:windowtext;display:none;text-decoration:none'>. </span><span
+style='color:windowtext;display:none;text-decoration:none'>5</span></a></span></p>
+
+<p class=MsoToc3><span class=MsoHyperlink><a href="#_Toc81224837">3.1.1 Amino
+acid sequences<span style='color:windowtext;display:none;text-decoration:none'>. </span><span
+style='color:windowtext;display:none;text-decoration:none'>5</span></a></span></p>
+
+<p class=MsoToc3><span class=MsoHyperlink><a href="#_Toc81224838">3.1.2
+Nucleotide sequences<span style='color:windowtext;display:none;text-decoration:
+none'>. </span><span
+style='color:windowtext;display:none;text-decoration:none'>5</span></a></span></p>
+
+<p class=MsoToc3><span class=MsoHyperlink><a href="#_Toc81224839">3.1.3
+Determining sequence type<span style='color:windowtext;display:none;text-decoration:
+none'>. </span><span
+style='color:windowtext;display:none;text-decoration:none'>5</span></a></span></p>
+
+<p class=MsoToc2><span class=MsoHyperlink><a href="#_Toc81224840">3.2 Output
+files<span style='color:windowtext;display:none;text-decoration:none'>. </span><span
+style='color:windowtext;display:none;text-decoration:none'>6</span></a></span></p>
+
+<p class=MsoToc3><span class=MsoHyperlink><a href="#_Toc81224841">3.2.1
+Sequence grouping<span style='color:windowtext;display:none;text-decoration:
+none'>. </span><span
+style='color:windowtext;display:none;text-decoration:none'>6</span></a></span></p>
+
+<p class=MsoToc2><span class=MsoHyperlink><a href="#_Toc81224842">3.3 CLUSTALW
+format<span style='color:windowtext;display:none;text-decoration:none'> </span><span
+style='color:windowtext;display:none;text-decoration:none'>6</span></a></span></p>
+
+<p class=MsoToc2><span class=MsoHyperlink><a href="#_Toc81224843">3.4 MSF format<span
+style='color:windowtext;display:none;text-decoration:none'> </span><span
+style='color:windowtext;display:none;text-decoration:none'>6</span></a></span></p>
+
+<p class=MsoToc2><span class=MsoHyperlink><a href="#_Toc81224844">3.5 HTML
+format<span style='color:windowtext;display:none;text-decoration:none'> </span><span
+style='color:windowtext;display:none;text-decoration:none'>6</span></a></span></p>
+
+<p class=MsoToc1><span class=MsoHyperlink><a href="#_Toc81224845">4 Using
+MUSCLE<span style='color:windowtext;display:none;text-decoration:none'>. </span><span
+style='color:windowtext;display:none;text-decoration:none'>6</span></a></span></p>
+
+<p class=MsoToc2><span class=MsoHyperlink><a href="#_Toc81224846">4.1 How the
+algorithm works<span style='color:windowtext;display:none;text-decoration:none'>. </span><span
+style='color:windowtext;display:none;text-decoration:none'>6</span></a></span></p>
+
+<p class=MsoToc2><span class=MsoHyperlink><a href="#_Toc81224847">4.2
+Command-line options<span style='color:windowtext;display:none;text-decoration:
+none'>. </span><span
+style='color:windowtext;display:none;text-decoration:none'>7</span></a></span></p>
+
+<p class=MsoToc2><span class=MsoHyperlink><a href="#_Toc81224848">4.3 The
+maxiters option<span style='color:windowtext;display:none;text-decoration:none'>. </span><span
+style='color:windowtext;display:none;text-decoration:none'>7</span></a></span></p>
+
+<p class=MsoToc2><span class=MsoHyperlink><a href="#_Toc81224849">4.4 The
+maxtrees option<span style='color:windowtext;display:none;text-decoration:none'>. </span><span
+style='color:windowtext;display:none;text-decoration:none'>8</span></a></span></p>
+
+<p class=MsoToc2><span class=MsoHyperlink><a href="#_Toc81224850">4.5 The
+maxhours option<span style='color:windowtext;display:none;text-decoration:none'>. </span><span
+style='color:windowtext;display:none;text-decoration:none'>8</span></a></span></p>
+
+<p class=MsoToc2><span class=MsoHyperlink><a href="#_Toc81224851">4.6 The
+profile scoring function<span style='color:windowtext;display:none;text-decoration:
+none'>. </span><span
+style='color:windowtext;display:none;text-decoration:none'>8</span></a></span></p>
+
+<p class=MsoToc2><span class=MsoHyperlink><a href="#_Toc81224852">4.7 Diagonal
+optimization<span style='color:windowtext;display:none;text-decoration:none'>. </span><span
+style='color:windowtext;display:none;text-decoration:none'>8</span></a></span></p>
+
+<p class=MsoToc2><span class=MsoHyperlink><a href="#_Toc81224853">4.8 Anchor
+optimization<span style='color:windowtext;display:none;text-decoration:none'>. </span><span
+style='color:windowtext;display:none;text-decoration:none'>8</span></a></span></p>
+
+<p class=MsoToc2><span class=MsoHyperlink><a href="#_Toc81224854">4.9 Log file<span
+style='color:windowtext;display:none;text-decoration:none'>. </span><span
+style='color:windowtext;display:none;text-decoration:none'>8</span></a></span></p>
+
+<p class=MsoToc2><span class=MsoHyperlink><a href="#_Toc81224855">4.10 Progress
+messages<span style='color:windowtext;display:none;text-decoration:none'>. </span><span
+style='color:windowtext;display:none;text-decoration:none'>9</span></a></span></p>
+
+<p class=MsoToc2><span class=MsoHyperlink><a href="#_Toc81224856">4.11 Running
+out of memory<span style='color:windowtext;display:none;text-decoration:none'>. </span><span
+style='color:windowtext;display:none;text-decoration:none'>9</span></a></span></p>
+
+<p class=MsoToc2><span class=MsoHyperlink><a href="#_Toc81224857">4.12
+Troubleshooting<span style='color:windowtext;display:none;text-decoration:none'>. </span><span
+style='color:windowtext;display:none;text-decoration:none'>9</span></a></span></p>
+
+<p class=MsoToc2><span class=MsoHyperlink><a href="#_Toc81224858">4.13
+Technical support<span style='color:windowtext;display:none;text-decoration:
+none'> </span><span
+style='color:windowtext;display:none;text-decoration:none'>10</span></a></span></p>
+
+<p class=MsoToc1><span class=MsoHyperlink><a href="#_Toc81224859">5 Command
+Line Reference<span style='color:windowtext;display:none;text-decoration:none'>. </span><span
+style='color:windowtext;display:none;text-decoration:none'>10</span></a></span></p>
+
+<p class=MsoNormal><span style='font-family:Arial'>&nbsp;</span></p>
+
+<b><span style='font-size:16.0pt;font-family:Arial'><br clear=all
+style='page-break-before:always'>
+</span></b>
+
+<h1 style='margin-left:0in;text-indent:0in'><a name="_Toc81224823">1 Introduction</a></h1>
+
+<p class=MsoNormal>MUSCLE is a program for creating multiple alignments of
+amino acid or nucleotide sequences. A range of options is provided that give
+you the choice of optimizing accuracy, speed, or some compromise between the
+two. Default parameters are those that give the best average accuracy in our
+tests. Using versions current at the time of writing, my tests show that MUSCLE
+can achieve both better average accuracy and better speed than CLUSTALW or T&#8209;Coffee,
+depending on the chosen options.</p>
+
+<h1 style='margin-left:0in;text-indent:0in'><a name="_Toc81224824">2 Quick
+Start</a></h1>
+
+<p class=MsoNormal>The MUSCLE algorithm is delivered as a command-line program
+called <i>muscle</i>. If you are running under Linux or Unix you will be
+working at a shell prompt. If you are running under Windows, you should be in a
+command window (nostalgically known to us older people as a DOS prompt). If you
+don't know how to use command-line programs, you should get help from a local
+guru.</p>
+
+<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc81224825">2.1 Installation</a></h2>
+
+<p class=MsoNormal>Copy the <i>muscle</i> binary file to a directory that is
+accessible from your computer. That's it—there are no configuration files,
+libraries, environment variables or other settings to worry about. If you are
+using Windows, then the binary file is named <i>muscle.exe</i>. From now on <i>muscle</i>
+should be understood to mean &quot;<i>muscle</i> if you are using Linux or Unix,
+<i>muscle.exe</i> if you are using Windows&quot;.</p>
+
+<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc81224826">2.2 Making an
+alignment</a></h2>
+
+<p class=MsoNormal>Make a FASTA file containing some sequences. (If you are not
+familiar with FASTA format, it is described in detail later in this Guide.) For
+now, just to make things fast, limit the number of sequence in the file to no
+more than 50 and the sequence length to be no more than 500. Call the input
+file <i>seqs.fa</i>. (An example file named <i>seqs.fa</i> is distributed with
+the standard MUSCLE package). Make sure the directory containing the <i>muscle</i>
+binary is in your path. (If it isn't, you can run it by typing the full path
+name, and the following example command lines must be changed accordingly). Now
+type:</p>
+
+<p class=MsoNormal>&nbsp;</p>
+
+<p class=Code>muscle -in seqs.fa -out seqs.afa</p>
+
+<p class=MsoNormal>&nbsp;</p>
+
+<p class=MsoNormal>You should see some progress messages. If <i>muscle</i>
+completes successfully, it will create a file <i>seqs.afa</i> containing the
+alignment. By default, output is created in &quot;aligned FASTA&quot; format
+(hence the <i>.afa</i> extension). This is just like regular FASTA except that
+gaps are added in order to align the sequences. This is a nice format for
+computers but not very readable for people, so to look at the alignment you
+will want an alignment viewer such as Belvu, or a script that converts FASTA to
+a more readable format. You can also use the –<i>msf</i> command-line option to
+request output in MSF format, which is easier to understand for people. If <i>muscle</i>
+gives an error message and you don't know how to fix it, please read the
+Troubleshooting section.</p>
+
+<p class=MsoNormal>&nbsp;</p>
+
+<p class=MsoNormal>The default settings are designed to give the best accuracy,
+so this may be all you need to know.</p>
+
+<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc81224827">2.3 Large
+alignments</a></h2>
+
+<p class=MsoNormal>If you have a large number of sequences (a few thousand), or
+they are very long, then the default settings of may be too slow for practical
+use. A good compromise between speed and accuracy is to run just the first two
+iterations of the algorithm. On average, this gives accuracy equal to T-Coffee
+and speeds much faster than CLUSTALW. This is done by the option <i>–maxiters 2</i>,
+as in the following example.</p>
+
+<p class=MsoNormal>&nbsp;</p>
+
+<p class=Code>muscle -in seqs.fa -out seqs.afa -maxiters 2</p>
+
+<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc81224828">2.4 Fastest
+speed</a></h2>
+
+<p class=MsoNormal>If you want the fastest possible speed, then the following
+example shows the applicable options for proteins.</p>
+
+<p class=MsoNormal>&nbsp;</p>
+
+<p class=Code>muscle -in seqs.fa -out seqs.afa -maxiters 1 -diags1 -sv -distance1
+kbit20_3</p>
+
+<p class=Code>&nbsp;</p>
+
+<p class=MsoNormal>For nucleotides, use:</p>
+
+<p class=MsoNormal>&nbsp;</p>
+
+<p class=Code>muscle -in seqs.fa -out seqs.afa -maxiters 1 -diags1</p>
+
+<p class=MsoNormal>&nbsp;</p>
+
+<p class=MsoNormal>At the time of writing, <i>muscle</i> with these options is faster
+than any other multiple sequence alignment program that I have tested. The
+alignments are not bad, especially when the sequences are closely related.
+However, as you might expect, this blazing speed comes at the cost of the
+lowest average accuracy of the options that <i>muscle</i> provides.</p>
+
+<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc81224829">2.5 Huge
+alignments</a></h2>
+
+<p class=MsoNormal>If you have a <i>very</i> large number of sequences (several
+thousand), or they are very long, then the <i>kbit20_3</i> option may cause
+problems because it needs a relatively large amount of memory. Better is to use
+the default distance measure, which is roughly 2× or 3× slower but needs less
+memory, like this:</p>
+
+<p class=MsoNormal>&nbsp;</p>
+
+<p class=Code>muscle -in seqs.fa -out seqs.afa -maxiters 1 -diags1 -sv</p>
+
+<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc81224830">2.6 Accuracy:
+caveat emptor</a></h2>
+
+<p class=MsoNormal>Why do I keep using the clumsy phrase &quot;average
+accuracy&quot; instead of just saying &quot;accuracy&quot;? That's because the
+quality of alignments produced by MUSCLE varies, as do those produced other programs
+such as CLUSTALW and T-Coffee. The state of the art leaves plenty of room for
+improvement. Sometimes the fastest speed options to <i>muscle</i> give
+alignments that are better than T-Coffee, though the reverse will more often be
+the case. With challenging sets of sequences, it is a good idea to make several
+different alignments using different <i>muscle</i> options and to try other programs
+too. Regions where different alignments agree are more believable than regions
+where they disagree. </p>
+
+<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc81224831">2.7 Pipelining</a></h2>
+
+<p class=MsoNormal>Input can be taken from standard input, and output can be
+written to standard output. This is the default, so our first example would
+also work like this:</p>
+
+<p class=MsoNormal>&nbsp;</p>
+
+<p class=Code>muscle &lt; seqs.fa &gt; seqs.afa</p>
+
+<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc81224832">2.8 Refining
+an existing alignment</a></h2>
+
+<p class=MsoNormal>You can ask <i>muscle</i> to try to improve an existing alignment
+by using the –<i>refine</i> option. The input file must then be a FASTA file
+containing an alignment. All sequences must be of equal length, gaps can be
+specified using dots &quot;.&quot; or dashes &quot;–&quot;. For example:</p>
+
+<p class=MsoNormal>&nbsp;</p>
+
+<p class=Code>muscle -in seqs.afa -out refined.afa -refine</p>
+
+<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc81224833">2.9 Profile-profile
+alignment</a></h2>
+
+<p class=MsoNormal>A fundamental step in the MUSCLE algorithm is aligning two
+multiple sequence alignments, each of which contain some of the input
+sequences. This operation is sometimes called &quot;profile-profile
+alignment&quot;. If you have two existing alignments of related sequences you
+can use the <i>–profile</i> option of MUSCLE to align those two sequences.
+Typical usage is:</p>
+
+<p class=MsoNormal>&nbsp;</p>
+
+<p class=Code>muscle -profile -in1 one.afa -in2 two.afa -out both.afa</p>
+
+<p class=MsoNormal>&nbsp;</p>
+
+<p class=MsoNormal>The alignments in <i>one.afa</i> and <i>two.afa</i>, which
+must be in aligned FASTA format, are aligned to each other, keeping input
+columns intact and inserting columns of gaps where needed. Output is stored in <i>both.afa</i>.</p>
+
+<p class=MsoNormal>&nbsp;</p>
+
+<p class=MsoNormal>MUSCLE does not compute a similarity measure or measure of
+statistical significance (such as an E-value), so this option is not useful for
+discriminating homologs from unrelated sequences. For this task, I recommend Sadreyev
+&amp; Grishin's COMPASS program.</p>
+
+<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc81224834">2.10 Sequence
+clustering</a></h2>
+
+<p class=MsoNormal>The first stage in MUSCLE is a fast clustering algorithm.
+This may be of use in other applications. Typical usage is:</p>
+
+<p class=MsoNormal>&nbsp;</p>
+
+<p class=Code>muscle -cluster -in seqs.fa -tree1 tree.phy</p>
+
+<p class=MsoNormal>&nbsp;</p>
+
+<p class=MsoNormal>The sequences will be clustered, and a tree written to <i>tree.phy</i>.
+Options –<i>weight1</i>, –<i>distance1</i>, –<i>cluster1</i> and –<i>root1</i> can
+be applied if desired. Note that by default, UPGMA clustering is used. You can
+use</p>
+
+<p class=MsoNormal> –<i>neighborjoining</i> if you prefer, but note that this
+is substantially slower than UPGMA for large numbers of sequences.</p>
+
+<h1 style='margin-left:0in;text-indent:0in'><a name="_Toc81224835">3 File
+Formats</a></h1>
+
+<p class=MsoNormal>MUSCLE uses FASTA format for both input and output. For
+output only, it also offers CLUSTALW, MSF and HTML formats using the –<i>clw</i>,
+–<i>msf</i> and –<i>html</i> command-line options.</p>
+
+<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc81224836">3.1 Input
+files</a></h2>
+
+<p class=MsoNormal>Input files must be in FASTA format. These are plain text
+files (word processing files such as Word documents are not understood!). Unix,
+Windows and DOS text files are supported (end-of-line may be NL or CR NL). There
+is no explicit limit on the length of a sequence, however if you are running a
+32-bit version of <i>muscle</i> then the maximum will be very roughly 10,000 letters
+due to maximum addressable size of tables required in memory. Each sequence starts
+with an annotation line, which is recognized by having a greater-than symbol
+&quot;&gt;&quot; as its first character. There is no limit on the length of an
+annotation line (this is new as of version 3.5), and there is no requirement
+that the annotation be unique. The sequence itself follows on one or more
+subsequent lines, and is terminated either by the next annotation line or by
+the end of the file. </p>
+
+<h3 style='margin-left:0in;text-indent:0in'><a name="_Toc81224837">3.1.1 Amino
+acid sequences</a></h3>
+
+<p class=MsoNormal>The standard single-letter amino acid alphabet is used. Upper
+and lower case is allowed, the case is not significant. The special characters
+X, B, Z and U are understood. X means &quot;unknown amino acid&quot;, B is D or
+N, Z is E or Q. U is understood to be the 21st amino acid Selenocysteine. White
+space (spaces, tabs and the end-of-line characters CR and NL) is allowed inside
+sequence data. Dots &quot;.&quot; and dashes &quot;–&quot; in sequences are
+allowed and are discarded unless the input is expected to be aligned (e.g. for
+the –<i>refine</i> option). </p>
+
+<h3 style='margin-left:0in;text-indent:0in'><a name="_Toc81224838">3.1.2 Nucleotide
+sequences</a></h3>
+
+<p class=MsoNormal>The usual letters A, G, C, T and U stand for nucleotides.
+The letters T and U are equivalent as far as MUSCLE is concerned. N is the
+wildcard meaning &quot;unknown nucleotide&quot;. R means A or G, Y means C or
+T/U. Other wildcards, such as those used by RFAM, are not understood in this
+version and will be replaced by Ns. If you would like support for other DNA /
+RNA alphabets, please let me know.</p>
+
+<h3 style='margin-left:0in;text-indent:0in'><a name="_Toc81224839">3.1.3 Determining
+sequence type</a></h3>
+
+<p class=MsoNormal>By default, MUSCLE looks at the first 100 letters in the
+input sequence data (excluding gaps). If 95% or more of those letters are valid
+nucleotides (AGCTUN), then the file is treated as nucleotides, otherwise as
+amino acids. This method almost always guesses correctly, but you can make sure
+by specifying the sequence type on the command line. This is done using the –<i>seqtype</i>
+option, which can take the following values:</p>
+
+<p class=MsoNormal>&nbsp;</p>
+
+<p class=MsoNormal>        –­<i>seqtype protein</i>                          Amino
+acid</p>
+
+<p class=MsoNormal>        –s<i>eqtype nucleo</i>                          Nucleotide</p>
+
+<p class=MsoNormal>        –<i>seqtype auto</i>                               Automatic
+detection (default).</p>
+
+<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc81224840">3.2 Output
+files</a></h2>
+
+<p class=MsoNormal>By default, output is also written in FASTA format. All
+letters are upper-case and gaps are represented by dashes &quot;–&quot;.</p>
+
+<h3 style='margin-left:0in;text-indent:0in'><a name="_Toc81224841">3.2.1 Sequence
+grouping</a></h3>
+
+<p class=MsoNormal>By default, MUSCLE re-arranges sequences so that similar
+sequences are adjacent in the output file. (This is done by ordering sequences
+according to a prefix traversal of the guide tree). This makes the alignment
+easier to evaluate by eye. If you want to the sequences to be output in the
+same order as the input file, you can use the –<i>stable</i> option.</p>
+
+<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc81224842">3.3 CLUSTALW
+format</a></h2>
+
+<p class=MsoNormal>You can request CLUSTALW output by using the –<i>clw</i>
+option. This should be compatible with CLUSTALW, with the exception of the
+program name in the file header. You can ask MUSCLE to impersonate CLUSTALW by
+writing &quot;CLUSTAL W (1.81)&quot; as the program name by using –<i>clwstrict</i>.
+If you have problems parsing MUSCLE output with scripts designed for CLUSTALW,
+please let me know.</p>
+
+<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc81224843">3.4 MSF format</a></h2>
+
+<p class=MsoNormal>MSF format (similar to CLUSTALW) is requested by using the –<i>msf</i>
+option. As with CLUSTALW format, this is easier for people to read than FASTA.</p>
+
+<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc81224844">3.5 HTML
+format</a></h2>
+
+<p class=MsoNormal>I've added an experimental feature starting in version 3.4. To
+get a Web page as output, use the –<i>html</i> option. The alignment is colored
+using a color scheme from Eric Sonnhammer's Belvu editor, which is my personal
+favorite. A drawback of this option is that the Web page typically contains a
+very large number of HTML tags, which can be slow to display in the Internet
+Explorer browser. The Netscape browser works much better. If you have any ideas
+about good ways to make Web pages, please let me know.</p>
+
+<h1 style='margin-left:0in;text-indent:0in'><a name="_Toc81224845">4 Using
+MUSCLE</a></h1>
+
+<p class=MsoNormal>In this section we give more details of the MUSCLE algorithm
+and the more important options offered by the <i>muscle</i> implementation.</p>
+
+<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc81224846">4.1 How the
+algorithm works</a></h2>
+
+<p class=MsoNormal>We won't give a complete description of the MUSCLE algorithm
+here—for that, you will have to read the paper. But hopefully a summary will
+help explain what some of the command-line options do and how they might be
+useful in your work.</p>
+
+<p class=MsoNormal>&nbsp;</p>
+
+<p class=MsoNormal>The first step is to calculate a tree. In CLUSTALW, this is
+done as follows. Each pair of input sequences is aligned, and used to compute
+the pair-wise identity of the pair. Identities are converted to a measure of
+distance. Finally, the distance matrix is converted to a tree using a
+clustering method (CLUSTALW uses neighbor-joining). If you have 1,000
+sequences, there are (1,000 <span style='font-family:Symbol'>´</span> 999)/2 =
+499,500 pairs, so aligning every pair can take a while. MUSCLE uses a much
+faster, but somewhat more approximate, method to compute distances: it counts
+the number of short sub-sequences (known as <i>k</i>-mers, <i>k</i>-tuples or
+words) that two sequences have in common, without constructing an alignment.
+This is typically around 3,000 times faster that CLUSTALW's method, but the trees
+will generally be less accurate. We call this step &quot;<i>k</i>-mer
+clustering&quot;.</p>
+
+<p class=MsoNormal>&nbsp;</p>
+
+<p class=MsoNormal>The second step is to use the tree to construct what is
+known as a progressive alignment. At each node of the binary tree, a pair-wise
+alignment is constructed, progressing from the leaves towards the root. The
+first alignment will be made from two sequences. Later alignments will be one
+of the three following types: sequence-sequence, profile-sequence or
+profile-profile, where &quot;profile&quot; means the multiple alignment of the sequences
+under a given internal node of the tree. This is very similar to what CLUSTALW
+does once it has built a tree.</p>
+
+<p class=MsoNormal>&nbsp;</p>
+
+<p class=MsoNormal style='page-break-after:avoid'>Now we have a multiple
+alignment, which has been built very quickly compared with conventional methods,
+mainly because of the distance calculation using <i>k</i>-mers rather than
+alignments. The quality of this alignment is typically pretty good—it will
+often tie or beat a T-Coffee alignment on our tests. However, on average, we
+find that it can be improved by proceeding through the following steps.</p>
+
+<p class=MsoNormal style='page-break-after:avoid'>&nbsp;</p>
+
+<p class=MsoNormal style='page-break-after:avoid'>From the multiple alignment,
+we can now compute the pair-wise identities of each pair of sequences. This
+gives us a new distance matrix, from which we estimate a new tree. We compare
+the old and new trees, and re-align subgroups where needed to produce a
+progressive multiple alignment from the new tree. If the two trees are
+identical, there is nothing to do; if there are no subtrees that agree (very unusual),
+then the whole progressive alignment procedure must be repeated from scratch.
+Typically we find that the tree is pretty stable near the leaves, but some
+re-alignments are needed closer the root. This procedure (compute pair-wise
+identities, estimate new tree, compare trees, re-align) is iterated until the
+tree stabilizes or until a specified maximum number of iterations has been
+done. We call this process &quot;tree refinement&quot;, although it also tends
+to improve the alignment.</p>
+
+<p class=MsoNormal style='page-break-after:avoid'>&nbsp;</p>
+
+<p class=MsoNormal style='page-break-after:avoid'>We now keep the tree fixed
+and move to a new procedure which is designed to improve the multiple
+alignment. The set of sequences is divided into two subsets (i.e., we make a
+bipartition on the set of sequences). A profile is constructed for each of the
+two subsets based on the current multiple alignment. These two profiles are
+then re-aligned to each other using the same pair-wise alignment algorithm as
+used in the progressive stage. If this improves an &quot;objective score&quot;
+that measures the quality of the alignment, then the new multiple alignment is
+kept, otherwise it is discarded. By default, the objective score is the classic
+sum-of-pairs score that takes the (sequence weighted) average of the pair-wise
+alignment score of every pair of sequences in the alignment. Bipartitions are
+chosen by deleting an edge in the guide tree, each of the two resulting
+subtrees defines a subset of sequences. This procedure is called &quot;tree
+dependent refinement&quot;. One iteration of tree dependent refinement tries
+bipartitions produced by deleting every edge of the tree in depth order moving
+from the leaves towards the center of the tree. Iterations continue until
+convergence or up to a specified maximum.</p>
+
+<p class=MsoNormal style='page-break-after:avoid'>&nbsp;</p>
+
+<p class=MsoNormal style='page-break-after:avoid'>For convenience, the major
+steps in MUSCLE are described as &quot;iterations&quot;, though the first three
+iterations all do quite different things and may take very different lengths of
+time to complete. The tree-dependent refinement iterations 3, 4 ... are true
+iterations and will take similar lengths of time. </p>
+
+<p class=MsoNormal style='page-break-after:avoid'>&nbsp;</p>
+
+<table class=MsoTableGrid border=0 cellspacing=0 cellpadding=0
+ style='border-collapse:collapse'>
+ <tr>
+  <td width=89 valign=top style='width:66.6pt;border:none;border-bottom:solid windowtext 1.0pt;
+  padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal style='page-break-after:avoid'><b><span style='font-size:
+  9.0pt;font-family:Arial'>Iteration</span></b></p>
+  </td>
+  <td width=461 valign=top style='width:4.8in;border:none;border-bottom:solid windowtext 1.0pt;
+  padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal style='page-break-after:avoid'><b><span style='font-size:
+  9.0pt;font-family:Arial'>Actions</span></b></p>
+  </td>
+ </tr>
+ <tr>
+  <td width=89 valign=top style='width:66.6pt;border:none;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal style='page-break-after:avoid'>1</p>
+  </td>
+  <td width=461 valign=top style='width:4.8in;border:none;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal style='page-break-after:avoid'>Distance matrix by <i>k</i>-mer
+  clustering, estimate tree, progressive alignment according to this tree.</p>
+  <p class=MsoNormal style='page-break-after:avoid'>&nbsp;</p>
+  </td>
+ </tr>
+ <tr>
+  <td width=89 valign=top style='width:66.6pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal style='page-break-after:avoid'>2</p>
+  </td>
+  <td width=461 valign=top style='width:4.8in;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal style='page-break-after:avoid'>Distance matrix by
+  pair-wise identities from current multiple alignment, estimate tree,
+  progressive alignment according to new tree, repeat until convergence or specified
+  maximum number of times.</p>
+  <p class=MsoNormal style='page-break-after:avoid'>&nbsp;</p>
+  </td>
+ </tr>
+ <tr>
+  <td width=89 valign=top style='width:66.6pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal style='page-break-after:avoid'>3, 4 ...</p>
+  </td>
+  <td width=461 valign=top style='width:4.8in;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal style='page-break-after:avoid'>Tree-dependent refinement. One
+  iteration visits every edge in the tree one time.</p>
+  </td>
+ </tr>
+</table>
+
+<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc81224847">4.2 Command-line
+options</a></h2>
+
+<p class=MsoNormal>There are two types of command-line options: value options
+and flag options. Value options are followed by the value of the given
+parameter, for example –<i>in &lt;filename&gt;</i>; flag options just stand for
+themselves, such as –<i>msf</i>. All options are a dash (not two dashes!)
+followed by a long name; there are no single-letter equivalents. Value options
+must be separated from their values by white space in the command line. Thus, <i>muscle</i>
+does not follow Unix, Linux or Posix standards, for which we apologize. The
+order in which options are given is irrelevant unless two options contradict,
+in which case the right-most option silently wins.</p>
+
+<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc81224848">4.3 The
+maxiters option</a></h2>
+
+<p class=MsoNormal>You can control the number of iterations that MUSCLE does by
+specifying the <i>–maxiters</i> option. If you specify 1, 2 or 3, then this is
+exactly the number of iterations that will be performed. If the value is
+greater than 3, then <i>muscle</i> will continue up to the maximum you specify
+or until convergence is reached, which ever happens sooner. The default is 16.
+If you have a large number of sequences, refinement may be rather slow.</p>
+
+<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc81224849">4.4 The maxtrees
+option</a></h2>
+
+<p class=MsoNormal>This option controls the maximum number of new trees to
+create in iteration 2. Our experience suggests that a point of diminishing
+returns is typically reached after the first tree, so the default value is 1.
+If a larger value is given, the process will repeat until convergence or until
+this number of trees has been created, which ever comes first.</p>
+
+<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc81224850">4.5 The maxhours
+option</a></h2>
+
+<p class=MsoNormal>If you have a large alignment, <i>muscle</i> may take a long
+time to complete. It is sometimes convenient to say &quot;I want the best
+alignment I can get in 24 hours&quot; rather than specifying a set of options
+that will take an unknown length of time. This is done by using <i>–maxhours</i>,
+which specifies a floating-point number of hours. If this time is exceeded, <i>muscle</i>
+will write out current alignment and stop. For example,</p>
+
+<p class=MsoNormal>&nbsp;</p>
+
+<p class=Code>muscle -in huge.fa -out huge.afa -maxiters 9999 -maxhours 24.0</p>
+
+<p class=MsoNormal>&nbsp;</p>
+
+<p class=MsoNormal>Note that the actual time may exceed the specified limit by
+a few minutes while <i>muscle</i> finishes up on a step. It is also possible
+for no alignment to be produced if the time limit is too small.</p>
+
+<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc81224851">4.6 The
+profile scoring function</a></h2>
+
+<p class=MsoNormal>Three different protein profile scoring functions are
+supported, the log-expectation score (–<i>le</i> option) and a sum of pairs
+score using either the PAM200 matrix (–<i>sp</i>) or the VTML240 matrix (–<i>sv</i>).
+The log-expectation score is the default as it gives better results on our
+tests, but is typically somewhere between two or three times slower than the
+sum-of-pairs score. For nucleotides, –<i>spn</i> is currently the only option
+(which is of course the default for nucleotide data, so you don't need to
+specify this option).</p>
+
+<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc81224852">4.7 Diagonal
+optimization</a></h2>
+
+<p class=MsoNormal>Creating a pair-wise alignment by dynamic programming
+requires computing an <i>L</i><sub>1</sub> <span style='font-family:Symbol'>´</span>
+<i>L</i><sub>2</sub> matrix, where <i>L</i><sub>1</sub> and <i>L</i><sub>2</sub>
+are the sequence lengths. A trick used in algorithms such as BLAST is to reduce
+the size of this matrix by using fast methods to find &quot;diagonals&quot;,
+i.e. short regions of high similarity between the two sequences. This speeds up
+the algorithm at the expense of some reduction in accuracy. MUSCLE uses a
+technique called <i>k</i>-mer extension to find diagonals. It is disabled by
+default because of the slight reduction in average accuracy and can be turned
+on by specifying the –<i>diags1</i> and <i>–diags2</i> options.</p>
+
+<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc81224853">4.8 Anchor
+optimization</a></h2>
+
+<p class=MsoNormal>Tree-dependent refinement (iterations 3, 4 ... ) can be
+speeded up by dividing the alignment vertically into blocks. Block boundaries
+are found by identifying high-scoring columns (e.g., a perfectly conserved
+column of Cs or Ws would be a candidate). Each vertical block is then refined
+independently before reassembling the complete alignment, which is faster
+because of the <i>L</i><sup>2</sup> factor in dynamic programming (e.g.,
+suppose the alignment is split into two vertical blocks, then 2 <span
+style='font-family:Symbol'>´</span> 0.5<sup>2</sup> = 0.5, so the dynamic
+programming time is roughly halved). The –<i>noanchors</i> option is used to disable
+this feature. This option has no effect if <i>–maxiters 1</i> or –<i>maxiters 2</i>
+is specified. On benchmark tests, enabling anchors has little or no effect on
+accuracy, but if you want to be very conservative and are striving for the best
+possible accuracy then –<i>noanchors</i> is a reasonable choice.</p>
+
+<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc81224854">4.9 Log file</a></h2>
+
+<p class=MsoNormal>You can specify a log file by using –<i>log &lt;filename&gt;</i>
+or –<i>loga &lt;filename&gt;</i>. Using –<i>log</i> causes any existing file to
+be deleted, –<i>loga</i> appends to any existing file. A message will be
+written to the log file when <i>muscle</i> starts and stops. Error and warning
+messages will also be written to the log. If –<i>verbose</i> is specified, then
+more information will be written, including the command line used to invoke <i>muscle</i>,
+the resulting internal parameter settings, and also progress messages. The
+content and format of verbose log file output is subject to change in future
+versions. </p>
+
+<p class=MsoNormal>&nbsp;</p>
+
+<p class=MsoNormal>The use of a log file may seem contrary to Unix conventions for
+using standard output and standard error. I like these conventions, but never
+found a fully satisfactory way to use them. I like progress messages (see
+below), but they mess up a file if you re-direct standard error and there are
+errors or warning messages too. I could try to detect whether a standard file
+handle is a <i>tty</i> device or a disk file and change behavior accordingly,
+but I regard this as too complicated and too hard for the user to understand. On
+Windows it can be hard to re-direct standard file handles, especially when
+working in a GUI debugger. Maybe one day I will figure out a better solution
+(suggestions welcomed).</p>
+
+<p class=MsoNormal>&nbsp;</p>
+
+<p class=MsoNormal>I highly recommend using –<i>verbose </i>and ­–<i>log[a]</i>,
+especially when running <i>muscle</i> in a batch mode. This enables you to
+verify whether a particular alignment was completed and to review any errors or
+warnings that occurred.</p>
+
+<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc81224855">4.10 Progress
+messages</a></h2>
+
+<p class=MsoNormal>By default, <i>muscle</i> writes progress messages to
+standard error periodically so that you know it's doing something and get some
+feedback about the time and memory requirements for the alignment. Here is a
+typical progress message.</p>
+
+<p class=MsoNormal>&nbsp;</p>
+
+<p class=Code>00:00:23     25 Mb  Iter   2  87.20%  Build guide tree</p>
+
+<p class=MsoNormal>&nbsp;</p>
+
+<p class=MsoNormal style='page-break-after:avoid'>The fields are as follows.</p>
+
+<p class=MsoNormal style='page-break-after:avoid'>&nbsp;</p>
+
+<table class=MsoTableGrid border=0 cellspacing=0 cellpadding=0
+ style='border-collapse:collapse'>
+ <tr>
+  <td width=118 valign=top style='width:88.2pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=Code style='page-break-after:avoid'>00:00:23</p>
+  </td>
+  <td width=408 valign=top style='width:306.05pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal style='page-break-after:avoid'>Elapsed time since <i>muscle</i>
+  started.</p>
+  </td>
+ </tr>
+ <tr>
+  <td width=118 valign=top style='width:88.2pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=Code style='page-break-after:avoid'>25 Mb</p>
+  </td>
+  <td width=408 valign=top style='width:306.05pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal style='page-break-after:avoid'>Peak memory use in megabytes
+  (i.e., not the current usage, but the maximum amount of memory used since <i>muscle</i>
+  started).</p>
+  </td>
+ </tr>
+ <tr>
+  <td width=118 valign=top style='width:88.2pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=Code style='page-break-after:avoid'>Iter 2</p>
+  </td>
+  <td width=408 valign=top style='width:306.05pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal style='page-break-after:avoid'>Iteration currently in
+  progress.</p>
+  </td>
+ </tr>
+ <tr>
+  <td width=118 valign=top style='width:88.2pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=Code style='page-break-after:avoid'>87.20%</p>
+  </td>
+  <td width=408 valign=top style='width:306.05pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal style='page-break-after:avoid'>How much of the current step
+  has been completed (percentage).</p>
+  </td>
+ </tr>
+ <tr>
+  <td width=118 valign=top style='width:88.2pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=Code>Build...</p>
+  </td>
+  <td width=408 valign=top style='width:306.05pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal>A brief description of the current step.</p>
+  </td>
+ </tr>
+</table>
+
+<p class=MsoNormal>&nbsp;</p>
+
+<p class=MsoNormal>The –<i>quiet</i> command-line option disables writing
+progress messages to standard error. If the –<i>verbose</i> command-line option
+is specified, a progress message will be written to the log file when each
+iteration completes. So –<i>quiet</i> and –<i>verbose</i> are not
+contradictory.</p>
+
+<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc81224856">4.11 Running
+out of memory</a></h2>
+
+<p class=MsoNormal>The <i>muscle</i> code tries to deal gracefully with
+low-memory conditions by using the following technique. A block of &quot;emergency
+reserve&quot; memory is allocated when <i>muscle</i> starts. If a later request
+to allocate memory fails, this reserve block is made available, and <i>muscle</i>
+attempts to save the current alignment. With luck, the reserved memory will be
+enough to allow <i>muscle</i> to save the alignment and exit gracefully with an
+informative error message.</p>
+
+<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc81224857">4.12 Troubleshooting</a></h2>
+
+<p class=MsoNormal>Here is some general advice on what to do if <i>muscle</i>
+fails and you don't understand what happened. The code is designed to fail
+gracefully with an informative error message when something goes wrong, but
+there will no doubt be situations I haven't anticipated (not to mention bugs).</p>
+
+<p class=MsoNormal>&nbsp;</p>
+
+<p class=MsoNormal>Check the MUSCLE web site for updates, bug reports and other
+relevant information.</p>
+
+<p class=MsoNormal>&nbsp;</p>
+
+<p class=MsoNormal style='page-break-after:avoid'>        <a
+href="http://www.drive5.com/muscle">http://www.drive5.com/muscle</a></p>
+
+<p class=MsoNormal>&nbsp;</p>
+
+<p class=MsoNormal>Check the input file to make sure it is in valid FASTA format.
+Try giving it to another sequence analysis program that can accept large FASTA
+files (e.g., the NCBI <i>formatdb</i> utility) to see if you get an informative
+error message. Try dividing the file into two halves and using each half
+individually as input. If one half fails and the other does not, repeat until
+the problem is localized as far as possible.</p>
+
+<p class=MsoNormal>&nbsp;</p>
+
+<p class=MsoNormal>Use –<i>log</i> or –<i>loga</i> and –­<i>verbose</i> and
+check the log file to see if there are any messages that give you a hint about the
+problem. Look at the peak memory requirements (reported in progress messages)
+to see if you may be exceeding the physical or virtual memory capacity of your
+computer.</p>
+
+<p class=MsoNormal>&nbsp;</p>
+
+<p class=MsoNormal>If <i>muscle</i> crashes without giving an error message, or
+hangs, then you may need to refer to the source code or use a debugger. A
+&quot;debug&quot; version, <i>muscled</i>, may be provided. This is built from
+the same source code but with the DEBUG macro defined and without compiler
+optimizations. This version runs much more slowly (perhaps by a factor of three
+or more), but does a lot more internal checking and may be able to catch
+something that is going wrong in the code. The –­<i>core</i> option specifies
+that <i>muscle</i> should not catch exceptions. When –<i>core</i> is specified,
+an exception may result in a debugger trap or a core dump, depending on the
+execution environment. The –<i>nocore</i> option has the opposite effect. In <i>muscle</i>,
+–<i>nocore</i> is the default, –­<i>core</i> is the default in <i>muscled</i>.</p>
+
+<h2 style='margin-left:0in;text-indent:0in'><a name="_Toc81224858">4.13 Technical
+support</a></h2>
+
+<p class=MsoNormal>I am happy to provide support. But I am busy, and am
+offering this program at no charge, so I ask you to make a reasonable effort to
+figure things out for yourself before contacting me.</p>
+
+<h1 style='margin-left:0in;text-indent:0in'><a name="_Toc81224859">5 Command Line
+Reference</a></h1>
+
+<p class=MsoNormal style='page-break-after:avoid'>&nbsp;</p>
+
+<table class=MsoTableGrid border=0 cellspacing=0 cellpadding=0
+ style='border-collapse:collapse'>
+ <thead>
+  <tr>
+   <td width=110 valign=top style='width:82.85pt;border:none;border-bottom:
+   solid windowtext 1.0pt;padding:0in 5.4pt 0in 5.4pt'>
+   <p class=MsoNormal style='page-break-after:avoid'><b><span style='font-size:
+   9.0pt;font-family:Arial'>Value option</span></b></p>
+   </td>
+   <td width=113 valign=top style='width:84.8pt;border:none;border-bottom:solid windowtext 1.0pt;
+   padding:0in 5.4pt 0in 5.4pt'>
+   <p class=MsoNormal style='page-break-after:avoid'><b><span style='font-size:
+   9.0pt;font-family:Arial'>Legal values</span></b></p>
+   </td>
+   <td width=103 valign=top style='width:77.35pt;border:none;border-bottom:
+   solid windowtext 1.0pt;padding:0in 5.4pt 0in 5.4pt'>
+   <p class=MsoNormal style='page-break-after:avoid'><b><span style='font-size:
+   9.0pt;font-family:Arial'>Default</span></b></p>
+   </td>
+   <td width=264 valign=top style='width:197.8pt;border:none;border-bottom:
+   solid windowtext 1.0pt;padding:0in 5.4pt 0in 5.4pt'>
+   <p class=MsoNormal style='page-break-after:avoid'><b><span style='font-size:
+   9.0pt;font-family:Arial'>Description</span></b></p>
+   </td>
+  </tr>
+ </thead>
+ <tr>
+  <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
+  8.0pt;font-family:"Courier New"'>anchorspacing</span></p>
+  </td>
+  <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal style='page-break-after:avoid'>Integer</p>
+  </td>
+  <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
+  8.0pt;font-family:"Courier New"'>32</span></p>
+  </td>
+  <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal style='page-break-after:avoid'>Minimum spacing between
+  anchor columns.</p>
+  <p class=MsoNormal style='page-break-after:avoid'>&nbsp;</p>
+  </td>
+ </tr>
+ <tr>
+  <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
+  8.0pt;font-family:"Courier New"'>center</span></p>
+  </td>
+  <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal style='page-break-after:avoid'>Floating point</p>
+  </td>
+  <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal style='page-break-after:avoid'>[1]</p>
+  </td>
+  <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal style='page-break-after:avoid'>Center parameter. Should be
+  negative.</p>
+  <p class=MsoNormal style='page-break-after:avoid'>&nbsp;</p>
+  </td>
+ </tr>
+ <tr>
+  <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
+  8.0pt;font-family:"Courier New"'>cluster1</span></p>
+  <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
+  8.0pt;font-family:"Courier New"'>cluster2</span></p>
+  </td>
+  <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
+  8.0pt;font-family:"Courier New"'>upgma</span></p>
+  <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
+  8.0pt;font-family:"Courier New"'>upgmb</span></p>
+  <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
+  8.0pt;font-family:"Courier New"'>neighborjoining</span></p>
+  </td>
+  <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
+  8.0pt;font-family:"Courier New"'>upgmb</span></p>
+  </td>
+  <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal style='page-break-after:avoid'>Clustering method. cluster1
+  is used in iteration 1 and 2, cluster2 in later iterations.</p>
+  <p class=MsoNormal style='page-break-after:avoid'>&nbsp;</p>
+  </td>
+ </tr>
+ <tr>
+  <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
+  8.0pt;font-family:"Courier New"'>diaglength</span></p>
+  </td>
+  <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal style='page-break-after:avoid'>Integer</p>
+  </td>
+  <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
+  8.0pt;font-family:"Courier New"'>24</span></p>
+  </td>
+  <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal style='page-break-after:avoid'>Minimum length of diagonal.</p>
+  <p class=MsoNormal style='page-break-after:avoid'>&nbsp;</p>
+  </td>
+ </tr>
+ <tr>
+  <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
+  8.0pt;font-family:"Courier New"'>diagmargin</span></p>
+  </td>
+  <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal style='page-break-after:avoid'>Integer</p>
+  </td>
+  <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
+  8.0pt;font-family:"Courier New"'>5</span></p>
+  </td>
+  <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal style='page-break-after:avoid'>Discard this many positions
+  at ends of diagonal.</p>
+  <p class=MsoNormal style='page-break-after:avoid'>&nbsp;</p>
+  </td>
+ </tr>
+ <tr>
+  <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>distance1</span></p>
+  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>&nbsp;</span></p>
+  </td>
+  <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>kmer6_6</span></p>
+  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>kmer20_3</span></p>
+  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>kmer20_4</span></p>
+  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>kbit20_3</span></p>
+  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>kmer4_6</span></p>
+  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>&nbsp;</span></p>
+  </td>
+  <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>Kmer6_6
+  (amino) or Kmer4_6 (nucleo)</span></p>
+  </td>
+  <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal>Distance measure for iteration 1.</p>
+  </td>
+ </tr>
+ <tr>
+  <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>distance2</span></p>
+  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>&nbsp;</span></p>
+  </td>
+  <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>kmer6_6</span></p>
+  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>kmer20_3</span></p>
+  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>kmer20_4</span></p>
+  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>kbit20_3</span></p>
+  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>pctid_kimura</span></p>
+  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>pctid_log</span></p>
+  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>&nbsp;</span></p>
+  </td>
+  <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>pctid_kimura</span></p>
+  </td>
+  <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal>Distance measure for iterations 2, 3 ...</p>
+  <p class=MsoNormal>&nbsp;</p>
+  <p class=MsoNormal>&nbsp;</p>
+  <p class=MsoNormal>&nbsp;</p>
+  <p class=MsoNormal>&nbsp;</p>
+  </td>
+ </tr>
+ <tr>
+  <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>gapopen</span></p>
+  </td>
+  <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal>Floating point</p>
+  </td>
+  <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal>[1]</p>
+  </td>
+  <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal>The gap open score. Must be negative.</p>
+  <p class=MsoNormal>&nbsp;</p>
+  </td>
+ </tr>
+ <tr>
+  <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>hydro</span></p>
+  </td>
+  <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal>Integer</p>
+  </td>
+  <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>5</span></p>
+  </td>
+  <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal>Window size for determining whether a region is
+  hydrophobic.</p>
+  <p class=MsoNormal>&nbsp;</p>
+  </td>
+ </tr>
+ <tr>
+  <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>hydrofactor</span></p>
+  </td>
+  <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal>Floating point</p>
+  </td>
+  <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>1.2</span></p>
+  </td>
+  <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal>Multiplier for gap open/close penalties in hydrophobic
+  regions.</p>
+  <p class=MsoNormal>&nbsp;</p>
+  </td>
+ </tr>
+ <tr>
+  <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>in</span></p>
+  </td>
+  <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal>Any file name</p>
+  </td>
+  <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal>standard input</p>
+  </td>
+  <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal>Where to find the input sequences.</p>
+  <p class=MsoNormal>&nbsp;</p>
+  </td>
+ </tr>
+ <tr>
+  <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>log</span></p>
+  </td>
+  <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal>File name</p>
+  </td>
+  <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal>None.</p>
+  </td>
+  <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal>Log file name (delete existing file).</p>
+  <p class=MsoNormal>&nbsp;</p>
+  </td>
+ </tr>
+ <tr>
+  <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>loga</span></p>
+  </td>
+  <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal>File name</p>
+  </td>
+  <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal>None.</p>
+  </td>
+  <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal>Log file name (append to existing file).</p>
+  <p class=MsoNormal>&nbsp;</p>
+  </td>
+ </tr>
+ <tr>
+  <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>maxdiagbreak</span></p>
+  </td>
+  <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal>Integer</p>
+  </td>
+  <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal>1</p>
+  </td>
+  <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal>Maximum distance between two diagonals that allows them to
+  merge into one diagonal.</p>
+  <p class=MsoNormal>&nbsp;</p>
+  </td>
+ </tr>
+ <tr>
+  <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>maxhours</span></p>
+  </td>
+  <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal>Floating point</p>
+  </td>
+  <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal>None.</p>
+  </td>
+  <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal>Maximum time to run in hours. The actual time may exceed
+  the requested limit by a few minutes. Decimals are allowed, so 1.5 means one
+  hour and 30 minutes.</p>
+  <p class=MsoNormal>&nbsp;</p>
+  </td>
+ </tr>
+ <tr>
+  <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>maxiters</span></p>
+  </td>
+  <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal>Integer 1, 2 ...</p>
+  </td>
+  <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>16</span></p>
+  </td>
+  <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal>Maximum number of iterations.</p>
+  <p class=MsoNormal>&nbsp;</p>
+  </td>
+ </tr>
+ <tr>
+  <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>maxtrees</span></p>
+  </td>
+  <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal>Integer</p>
+  </td>
+  <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>1</span></p>
+  </td>
+  <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal>Maximum number of new trees to build in iteration 2.</p>
+  <p class=MsoNormal>&nbsp;</p>
+  </td>
+ </tr>
+ <tr>
+  <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
+  8.0pt;font-family:"Courier New"'>minbestcolscore</span></p>
+  </td>
+  <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal style='page-break-after:avoid'>Floating point </p>
+  </td>
+  <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal style='page-break-after:avoid'>[1]</p>
+  </td>
+  <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal style='page-break-after:avoid'>Minimum score a column must
+  have to be an anchor.</p>
+  <p class=MsoNormal style='page-break-after:avoid'>&nbsp;</p>
+  </td>
+ </tr>
+ <tr>
+  <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
+  8.0pt;font-family:"Courier New"'>minsmoothscore</span></p>
+  </td>
+  <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal style='page-break-after:avoid'>Floating point</p>
+  </td>
+  <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal style='page-break-after:avoid'>[1]</p>
+  </td>
+  <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal style='page-break-after:avoid'>Minimum smoothed score a
+  column must have to be an anchor.</p>
+  <p class=MsoNormal style='page-break-after:avoid'>&nbsp;</p>
+  </td>
+ </tr>
+ <tr>
+  <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>objscore</span></p>
+  </td>
+  <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>sp</span></p>
+  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>ps</span></p>
+  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>dp</span></p>
+  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>xp</span></p>
+  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>spf</span></p>
+  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>spm</span></p>
+  </td>
+  <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>spm</span></p>
+  </td>
+  <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal>Objective score used by tree dependent refinement.</p>
+  <p class=MsoNormal>sp=sum-of-pairs score.</p>
+  <p class=MsoNormal>spf=sum-of-pairs score (dimer approximation)</p>
+  <p class=MsoNormal>spm=sp for &lt; 100 seqs, otherwise spf</p>
+  <p class=MsoNormal>dp=dynamic programming score.</p>
+  <p class=MsoNormal>ps=average profile-sequence score.</p>
+  <p class=MsoNormal>xp=cross profile score.</p>
+  <p class=MsoNormal>&nbsp;</p>
+  </td>
+ </tr>
+ <tr>
+  <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>out</span></p>
+  </td>
+  <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal>File name</p>
+  </td>
+  <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal>standard output</p>
+  </td>
+  <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal>Where to write the alignment.</p>
+  <p class=MsoNormal>&nbsp;</p>
+  </td>
+ </tr>
+ <tr>
+  <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>root1</span></p>
+  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>root2</span></p>
+  </td>
+  <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>pseudo</span></p>
+  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>midlongestspan</span></p>
+  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>minavgleafdist</span></p>
+  </td>
+  <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>psuedo</span></p>
+  </td>
+  <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal>Method used to root tree; root1 is used in iteration 1 and
+  2, root2 in later iterations.</p>
+  <p class=MsoNormal>&nbsp;</p>
+  <p class=MsoNormal>&nbsp;</p>
+  </td>
+ </tr>
+ <tr>
+  <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>seqtype</span></p>
+  </td>
+  <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>protein</span></p>
+  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>nucleo</span></p>
+  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>auto</span></p>
+  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>&nbsp;</span></p>
+  </td>
+  <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>auto</span></p>
+  </td>
+  <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal>Sequence type.</p>
+  </td>
+ </tr>
+ <tr>
+  <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>smoothscoreceil</span></p>
+  </td>
+  <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal>Floating point</p>
+  </td>
+  <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal>[1]</p>
+  </td>
+  <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal>Maximum value of column score for smoothing purposes.</p>
+  <p class=MsoNormal>&nbsp;</p>
+  </td>
+ </tr>
+ <tr>
+  <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>smoothwindow</span></p>
+  </td>
+  <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal>Integer</p>
+  </td>
+  <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>7</span></p>
+  </td>
+  <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal>Window used for anchor column smoothing.</p>
+  <p class=MsoNormal>&nbsp;</p>
+  </td>
+ </tr>
+ <tr>
+  <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>SUEFF</span></p>
+  </td>
+  <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal>Floating point value between 0 and 1.</p>
+  <p class=MsoNormal>&nbsp;</p>
+  </td>
+  <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>0.1</span></p>
+  </td>
+  <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal>Constant used in UPGMB clustering. Determines the relative
+  fraction of average linkage (SUEFF) vs. nearest-neighbor linkage (1 – SUEFF).<br>
+  <br>
+  </p>
+  </td>
+ </tr>
+ <tr>
+  <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>tree1</span></p>
+  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>tree2</span></p>
+  </td>
+  <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal>File name</p>
+  </td>
+  <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal>None</p>
+  </td>
+  <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal>Save tree produced in first or second iteration to given
+  file in Newick (Phylip-compatible) format.</p>
+  <p class=MsoNormal>&nbsp;</p>
+  </td>
+ </tr>
+ <tr>
+  <td width=110 valign=top style='width:82.85pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
+  8.0pt;font-family:"Courier New"'>weight1</span></p>
+  <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
+  8.0pt;font-family:"Courier New"'>weight2</span></p>
+  </td>
+  <td width=113 valign=top style='width:84.8pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
+  8.0pt;font-family:"Courier New"'>none</span></p>
+  <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
+  8.0pt;font-family:"Courier New"'>henikoff</span></p>
+  <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
+  8.0pt;font-family:"Courier New"'>henikoffpb</span></p>
+  <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
+  8.0pt;font-family:"Courier New"'>gsc</span></p>
+  <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
+  8.0pt;font-family:"Courier New"'>clustalw</span></p>
+  <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
+  8.0pt;font-family:"Courier New"'>threeway</span></p>
+  </td>
+  <td width=103 valign=top style='width:77.35pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
+  8.0pt;font-family:"Courier New"'>clustalw</span></p>
+  <p class=MsoNormal style='page-break-after:avoid'>&nbsp;</p>
+  </td>
+  <td width=264 valign=top style='width:197.8pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal style='page-break-after:avoid'>Sequence weighting scheme.</p>
+  <p class=MsoNormal style='page-break-after:avoid'>weight1 is used in
+  iterations 1 and 2.</p>
+  <p class=MsoNormal style='page-break-after:avoid'>weight2 is used for
+  tree-dependent refinement.</p>
+  <p class=MsoNormal style='page-break-after:avoid'>none=all sequences have
+  equal weight.</p>
+  <p class=MsoNormal style='page-break-after:avoid'>henikoff=Henikoff &amp;
+  Henikoff weighting scheme.</p>
+  <p class=MsoNormal style='page-break-after:avoid'>henikoffpb=Modified
+  Henikoff scheme as used in PSI-BLAST.</p>
+  <p class=MsoNormal style='page-break-after:avoid'>clustalw=CLUSTALW method.</p>
+  <p class=MsoNormal style='page-break-after:avoid'>threeway=Gotoh three-way
+  method.</p>
+  <p class=MsoNormal style='page-break-after:avoid'>&nbsp;</p>
+  </td>
+ </tr>
+</table>
+
+<p class=MsoNormal>&nbsp;</p>
+
+<table class=MsoTableGrid border=0 cellspacing=0 cellpadding=0
+ style='border-collapse:collapse'>
+ <thead>
+  <tr>
+   <td width=137 valign=top style='width:102.6pt;border:none;border-bottom:
+   solid windowtext 1.0pt;padding:0in 5.4pt 0in 5.4pt'>
+   <p class=MsoNormal style='page-break-after:avoid'><b><span style='font-size:
+   9.0pt;font-family:Arial'>Flag option</span></b></p>
+   </td>
+   <td width=106 valign=top style='width:1.1in;border:none;border-bottom:solid windowtext 1.0pt;
+   padding:0in 5.4pt 0in 5.4pt'>
+   <p class=MsoNormal style='page-break-after:avoid'><b><span style='font-size:
+   9.0pt;font-family:Arial'>Set by default?</span></b></p>
+   </td>
+   <td width=348 valign=top style='width:261.0pt;border:none;border-bottom:
+   solid windowtext 1.0pt;padding:0in 5.4pt 0in 5.4pt'>
+   <p class=MsoNormal style='page-break-after:avoid'><b><span style='font-size:
+   9.0pt;font-family:Arial'>Description</span></b></p>
+   </td>
+  </tr>
+ </thead>
+ <tr style='height:6.25pt'>
+  <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;
+  height:6.25pt'>
+  <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
+  8.0pt;font-family:"Courier New"'>anchors</span></p>
+  </td>
+  <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;
+  height:6.25pt'>
+  <p class=MsoNormal style='page-break-after:avoid'>yes</p>
+  </td>
+  <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;
+  height:6.25pt'>
+  <p class=MsoNormal style='page-break-after:avoid'>Use anchor optimization in
+  tree dependent refinement iterations.</p>
+  <p class=MsoNormal style='page-break-after:avoid'>&nbsp;</p>
+  </td>
+ </tr>
+ <tr style='height:6.25pt'>
+  <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;
+  height:6.25pt'>
+  <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
+  8.0pt;font-family:"Courier New"'>clw</span></p>
+  </td>
+  <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;
+  height:6.25pt'>
+  <p class=MsoNormal style='page-break-after:avoid'>no</p>
+  </td>
+  <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;
+  height:6.25pt'>
+  <p class=MsoNormal style='page-break-after:avoid'>Write output in CLUSTALW
+  format (default is FASTA).</p>
+  <p class=MsoNormal style='page-break-after:avoid'>&nbsp;</p>
+  </td>
+ </tr>
+ <tr style='height:6.25pt'>
+  <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;
+  height:6.25pt'>
+  <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
+  8.0pt;font-family:"Courier New"'>clwstrict</span></p>
+  </td>
+  <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;
+  height:6.25pt'>
+  <p class=MsoNormal style='page-break-after:avoid'>no</p>
+  </td>
+  <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;
+  height:6.25pt'>
+  <p class=MsoNormal style='page-break-after:avoid'>Write output in CLUSTALW
+  format with the &quot;CLUSTAL W (1.81)&quot; header rather than the MUSCLE
+  version. This is useful when a post-processing step is picky about the file
+  header.</p>
+  <p class=MsoNormal style='page-break-after:avoid'>&nbsp;</p>
+  </td>
+ </tr>
+ <tr style='height:6.25pt'>
+  <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;
+  height:6.25pt'>
+  <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
+  8.0pt;font-family:"Courier New"'>core</span></p>
+  </td>
+  <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;
+  height:6.25pt'>
+  <p class=MsoNormal style='page-break-after:avoid'>yes in muscle,</p>
+  <p class=MsoNormal style='page-break-after:avoid'>no in muscled.</p>
+  </td>
+  <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;
+  height:6.25pt'>
+  <p class=MsoNormal style='page-break-after:avoid'>Do not catch exceptions.</p>
+  <p class=MsoNormal style='page-break-after:avoid'>&nbsp;</p>
+  <p class=MsoNormal style='page-break-after:avoid'>&nbsp;</p>
+  </td>
+ </tr>
+ <tr style='height:6.25pt'>
+  <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;
+  height:6.25pt'>
+  <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
+  8.0pt;font-family:"Courier New"'>fasta</span></p>
+  </td>
+  <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;
+  height:6.25pt'>
+  <p class=MsoNormal style='page-break-after:avoid'>yes</p>
+  </td>
+  <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;
+  height:6.25pt'>
+  <p class=MsoNormal style='page-break-after:avoid'>Write output in FASTA
+  format. Alternatives include –<i>clw</i>,</p>
+  <p class=MsoNormal style='page-break-after:avoid'>–<i>clwstrict, –msf</i> and
+  –<i>html</i>.</p>
+  <p class=MsoNormal style='page-break-after:avoid'>&nbsp;</p>
+  </td>
+ </tr>
+ <tr style='height:6.25pt'>
+  <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;
+  height:6.25pt'>
+  <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
+  8.0pt;font-family:"Courier New"'>group</span></p>
+  </td>
+  <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;
+  height:6.25pt'>
+  <p class=MsoNormal style='page-break-after:avoid'>yes</p>
+  </td>
+  <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;
+  height:6.25pt'>
+  <p class=MsoNormal style='page-break-after:avoid'>Group similar sequences
+  together in the output. This is the default. See also –<i>stable</i>.</p>
+  <p class=MsoNormal style='page-break-after:avoid'>&nbsp;</p>
+  </td>
+ </tr>
+ <tr style='height:6.25pt'>
+  <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;
+  height:6.25pt'>
+  <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
+  8.0pt;font-family:"Courier New"'>html</span></p>
+  </td>
+  <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;
+  height:6.25pt'>
+  <p class=MsoNormal style='page-break-after:avoid'>no</p>
+  </td>
+  <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;
+  height:6.25pt'>
+  <p class=MsoNormal style='page-break-after:avoid'>Write output in HTML format
+  (default is FASTA).</p>
+  <p class=MsoNormal style='page-break-after:avoid'>&nbsp;</p>
+  </td>
+ </tr>
+ <tr>
+  <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
+  8.0pt;font-family:"Courier New"'>le</span></p>
+  </td>
+  <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal>maybe</p>
+  </td>
+  <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt'>
+  <p class=MsoNormal>Use log-expectation profile score (VTML240). Alternatives
+  are to use –<i>sp</i> or <i>–sv</i>. This is the default for amino acid
+  sequences.</p>
+  <p class=MsoNormal>&nbsp;</p>
+  </td>
+ </tr>
+ <tr style='height:6.25pt'>
+  <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;
+  height:6.25pt'>
+  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>msf</span></p>
+  </td>
+  <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;
+  height:6.25pt'>
+  <p class=MsoNormal>no</p>
+  </td>
+  <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;
+  height:6.25pt'>
+  <p class=MsoNormal>Write output in MSF format (default is FASTA).</p>
+  <p class=MsoNormal>&nbsp;</p>
+  </td>
+ </tr>
+ <tr style='height:6.25pt'>
+  <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;
+  height:6.25pt'>
+  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>noanchors</span></p>
+  </td>
+  <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;
+  height:6.25pt'>
+  <p class=MsoNormal>no</p>
+  </td>
+  <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;
+  height:6.25pt'>
+  <p class=MsoNormal>Disable anchor optimization. Default is –<i>anchors</i>.</p>
+  <p class=MsoNormal>&nbsp;</p>
+  </td>
+ </tr>
+ <tr style='height:6.25pt'>
+  <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;
+  height:6.25pt'>
+  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>nocore</span></p>
+  </td>
+  <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;
+  height:6.25pt'>
+  <p class=MsoNormal>no in muscle,</p>
+  <p class=MsoNormal>yes in muscled.</p>
+  </td>
+  <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;
+  height:6.25pt'>
+  <p class=MsoNormal>Catch exceptions and give an error message if possible.</p>
+  <p class=MsoNormal>&nbsp;</p>
+  <p class=MsoNormal>&nbsp;</p>
+  </td>
+ </tr>
+ <tr style='height:6.25pt'>
+  <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;
+  height:6.25pt'>
+  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>quiet</span></p>
+  </td>
+  <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;
+  height:6.25pt'>
+  <p class=MsoNormal>no</p>
+  </td>
+  <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;
+  height:6.25pt'>
+  <p class=MsoNormal>Do not display progress messages.</p>
+  <p class=MsoNormal>&nbsp;</p>
+  </td>
+ </tr>
+ <tr style='height:6.25pt'>
+  <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;
+  height:6.25pt'>
+  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>refine</span></p>
+  </td>
+  <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;
+  height:6.25pt'>
+  <p class=MsoNormal>no</p>
+  </td>
+  <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;
+  height:6.25pt'>
+  <p class=MsoNormal>Input file is already aligned, skip first two iterations
+  and begin tree dependent refinement.</p>
+  <p class=MsoNormal>&nbsp;</p>
+  </td>
+ </tr>
+ <tr style='height:6.25pt'>
+  <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;
+  height:6.25pt'>
+  <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
+  8.0pt;font-family:"Courier New"'>sp</span></p>
+  </td>
+  <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;
+  height:6.25pt'>
+  <p class=MsoNormal>no</p>
+  </td>
+  <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;
+  height:6.25pt'>
+  <p class=MsoNormal>Use sum-of-pairs protein profile score (PAM200). Default
+  is –<i>le.</i></p>
+  <p class=MsoNormal>&nbsp;</p>
+  </td>
+ </tr>
+ <tr style='height:6.25pt'>
+  <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;
+  height:6.25pt'>
+  <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
+  8.0pt;font-family:"Courier New"'>spn</span></p>
+  </td>
+  <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;
+  height:6.25pt'>
+  <p class=MsoNormal>maybe</p>
+  <p class=MsoNormal>&nbsp;</p>
+  </td>
+  <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;
+  height:6.25pt'>
+  <p class=MsoNormal>Use sum-of-pairs nucleotide profile score (BLASTZ
+  parameters). This is the only option for nucleotides, and is therefore the
+  default.</p>
+  <p class=MsoNormal>&nbsp;</p>
+  </td>
+ </tr>
+ <tr style='height:6.25pt'>
+  <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;
+  height:6.25pt'>
+  <p class=MsoNormal style='page-break-after:avoid'><span style='font-size:
+  8.0pt;font-family:"Courier New"'>stable</span></p>
+  </td>
+  <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;
+  height:6.25pt'>
+  <p class=MsoNormal>no</p>
+  </td>
+  <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;
+  height:6.25pt'>
+  <p class=MsoNormal>Preserve input order of sequences in output file. Default
+  is to group sequences by similarity (–<i>group</i>).</p>
+  <p class=MsoNormal>&nbsp;</p>
+  </td>
+ </tr>
+ <tr style='height:6.25pt'>
+  <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;
+  height:6.25pt'>
+  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>sv</span></p>
+  </td>
+  <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;
+  height:6.25pt'>
+  <p class=MsoNormal>no</p>
+  </td>
+  <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;
+  height:6.25pt'>
+  <p class=MsoNormal>Use sum-of-pairs profile score (VTML240). Default is –<i>le.</i></p>
+  <p class=MsoNormal>&nbsp;</p>
+  </td>
+ </tr>
+ <tr style='height:6.25pt'>
+  <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;
+  height:6.25pt'>
+  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>termgapsfull</span></p>
+  </td>
+  <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;
+  height:6.25pt'>
+  <p class=MsoNormal>no</p>
+  </td>
+  <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;
+  height:6.25pt'>
+  <p class=MsoNormal>Terminal gaps penalized with full penalty.</p>
+  <p class=MsoNormal>[1] Not fully supported in this version.</p>
+  <p class=MsoNormal>&nbsp;</p>
+  </td>
+ </tr>
+ <tr style='height:6.25pt'>
+  <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;
+  height:6.25pt'>
+  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>termgapshalf</span></p>
+  </td>
+  <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;
+  height:6.25pt'>
+  <p class=MsoNormal>yes</p>
+  </td>
+  <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;
+  height:6.25pt'>
+  <p class=MsoNormal>Terminal gaps penalized with half penalty.</p>
+  <p class=MsoNormal>[1] Not fully supported in this version.</p>
+  <p class=MsoNormal>&nbsp;</p>
+  </td>
+ </tr>
+ <tr style='height:6.25pt'>
+  <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;
+  height:6.25pt'>
+  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>termgapshalflonger</span></p>
+  </td>
+  <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;
+  height:6.25pt'>
+  <p class=MsoNormal>no</p>
+  </td>
+  <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;
+  height:6.25pt'>
+  <p class=MsoNormal>Terminal gaps penalized with half penalty if gap relative
+  to </p>
+  <p class=MsoNormal>longer sequence, otherwise with full penalty.</p>
+  <p class=MsoNormal>[1] Not fully supported in this version.</p>
+  <p class=MsoNormal>&nbsp;</p>
+  </td>
+ </tr>
+ <tr style='height:6.25pt'>
+  <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;
+  height:6.25pt'>
+  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>verbose</span></p>
+  </td>
+  <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;
+  height:6.25pt'>
+  <p class=MsoNormal>no</p>
+  </td>
+  <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;
+  height:6.25pt'>
+  <p class=MsoNormal>Write parameter settings and progress messages to log
+  file.</p>
+  <p class=MsoNormal>&nbsp;</p>
+  </td>
+ </tr>
+ <tr style='height:6.25pt'>
+  <td width=137 valign=top style='width:102.6pt;padding:0in 5.4pt 0in 5.4pt;
+  height:6.25pt'>
+  <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>version</span></p>
+  </td>
+  <td width=106 valign=top style='width:1.1in;padding:0in 5.4pt 0in 5.4pt;
+  height:6.25pt'>
+  <p class=MsoNormal>no</p>
+  </td>
+  <td width=348 valign=top style='width:261.0pt;padding:0in 5.4pt 0in 5.4pt;
+  height:6.25pt'>
+  <p class=MsoNormal>Write version string to stdout and exit.</p>
+  </td>
+ </tr>
+</table>
+
+<p class=MsoNormal><i>&nbsp;</i></p>
+
+<p class=MsoNormal><i>Notes</i></p>
+
+<p class=MsoNormal>[1] Default depends on the profile scoring function. To
+determine the default, use –<i>verbose –log</i> and check the log file.</p>
+
+<p class=MsoNormal><u><span style='text-decoration:none'>&nbsp;</span></u></p>
+
+</div>
+
+</body>
+
+</html>
--- muscle-3.8.31.orig/debian/muscle.1.xml
+++ muscle-3.8.31/debian/muscle.1.xml
@@ -0,0 +1,270 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<?xml-stylesheet type="text/xsl"
+	href="http://docbook.sourceforge.net/release/xsl/current/manpages/docbook.xsl"?>
+<!DOCTYPE refentry PUBLIC "-//OASIS//DTD DocBook XML V4.4//EN"
+	"http://www.oasis-open.org/docbook/xml/4.4/docbookx.dtd" [
+
+<!--
+
+Process this file with an XSLT processor: `xsltproc \
+-''-nonet /usr/share/sgml/docbook/stylesheet/xsl/nwalsh/\
+manpages/docbook.xsl manpage.dbk'.  A manual page
+<package>.<section> will be generated.  You may view the
+manual page with: nroff -man <package>.<section> | less'.  A
+typical entry in a Makefile or Makefile.am is:
+
+DB2MAN=/usr/share/sgml/docbook/stylesheet/xsl/nwalsh/\
+manpages/docbook.xsl
+XP=xsltproc -''-nonet
+
+manpage.1: manpage.dbk
+        $(XP) $(DB2MAN) $<
+    
+The xsltproc binary is found in the xsltproc package.  The
+XSL files are in docbook-xsl.  Please remember that if you
+create the nroff version in one of the debian/rules file
+targets (such as build), you will need to include xsltproc
+and docbook-xsl in your Build-Depends control field.
+
+-->
+
+  <!ENTITY dhfirstname "Steffen">
+  <!ENTITY dhsurname   "Moeller">
+  <!ENTITY dhsection   "<manvolnum>1</manvolnum>">
+  <!ENTITY dhemail     "moeller@debian.org">
+  <!ENTITY dhusername  "Steffen Moeller">
+  <!ENTITY dhucpackage "<refentrytitle>MUSCLE</refentrytitle>">
+  <!ENTITY dhpackage   "muscle">
+  <!ENTITY debian      "<productname>Debian</productname>">
+  <!ENTITY gnu         "<acronym>GNU</acronym>">
+  <!ENTITY gpl         "&gnu; <acronym>GPL</acronym>">
+  <!ENTITY dhrelease   "3.7">
+  <!ENTITY dhtitle     "Muscle Manual">
+]>
+
+<refentry>
+  <refentryinfo>
+  		<title>&dhtitle;</title>
+		<productname>&dhpackage;</productname>
+		<releaseinfo role="version">&dhrelease;</releaseinfo>
+    <authorgroup>
+      <author>
+        <firstname>Robert</firstname>
+        <firstname>C.</firstname>
+        <surname>Elgar</surname>
+        <contrib>Wrote Muscle.</contrib>
+      </author>
+      <author>
+        <firstname>&dhfirstname;</firstname>
+        <surname>&dhsurname;</surname>
+        <contrib>Wrote this manpage.</contrib>
+        <address><email>&dhemail;</email></address>
+      </author>
+      <author>
+        <firstname>Charles</firstname>
+        <surname>Plessy</surname>
+        <contrib>Updated this manpage.</contrib>
+        <address><email>charles-debian-nospam@plessy.org</email></address>
+      </author>
+    </authorgroup>
+    <copyright>
+      <year>2003</year>
+      <year>2004</year>
+      <holder>&dhusername; (manpage)</holder>
+    </copyright>
+    <copyright>
+      <year>2007</year>
+      <year>2008</year>
+      <holder>Charles Plessy (manpage)</holder>
+    </copyright>
+    <legalnotice>
+      <para>
+        Muscle is in the public domain, and therefore not subjected to copyright.
+      </para>
+      
+      <para>
+        This manual page was written by &dhusername; &dhemail; for the &debian; system (but may be used by others). Permission is granted to copy, distribute and/or modify this document as if it were in public domain.
+      </para>
+    </legalnotice>
+  </refentryinfo>
+  
+  <refmeta>
+    &dhucpackage;
+    &dhsection;
+  </refmeta>
+  
+  <refnamediv>
+    <refname>&dhpackage;</refname>
+    <refpurpose>Multiple Protein Sequence Alignment</refpurpose>
+  </refnamediv>
+  
+  <refsynopsisdiv>
+    <cmdsynopsis>
+      <command>&dhpackage;</command>
+      <arg choice="plain"><option>-in <replaceable>input file (fasta)</replaceable></option></arg>
+      <arg choice="opt"><option>-out <replaceable>output file (default fasta)</replaceable></option></arg>
+      <arg choice="opt"><option>-diags</option></arg>
+      <arg choice="opt"><option>-log <replaceable>log file</replaceable></option></arg>
+      <arg choice="opt"><option>-maxiters <replaceable>n</replaceable></option></arg>
+      <arg choice="opt"><option>-maxhours <replaceable>n</replaceable></option></arg>
+      <arg choice="opt"><option>-maxmb <replaceable>m</replaceable></option></arg>
+      <arg choice="opt"><option>-html</option></arg>
+      <arg choice="opt"><option>-msf</option></arg>
+      <arg choice="opt"><option>-clw</option></arg>
+      <arg choice="opt"><option>-clwstrict</option></arg>
+      <arg choice="opt"><option>-log[a] <replaceable>logfile</replaceable></option></arg>
+      <arg choice="opt"><option>-quiet</option></arg>
+      <arg choice="opt"><option>-stable</option></arg>
+      <arg choice="opt"><option>-group</option></arg>
+      <arg choice="opt"><option>-version</option></arg>
+    </cmdsynopsis>
+  </refsynopsisdiv>
+  
+  <refsect1>
+    <title>DESCRIPTION</title>
+
+    <para>This manual page documents briefly the
+      <command>&dhpackage;</command> command.
+   </para>
+
+    <para><command>&dhpackage;</command> aligns protein sequences and is considered superior and faster than Clustal W.</para>
+  </refsect1>
+  
+  <refsect1>
+    <title>OPTIONS</title>
+    <variablelist>
+      <varlistentry>
+        <term><option>-in <replaceable>input file</replaceable></option>
+        </term>
+        <listitem>
+          <para>Path to FASTA formatted input file
+	  </para>
+        </listitem>
+      </varlistentry>
+      <varlistentry>
+        <term><option>-out <replaceable>output file</replaceable></option>
+        </term>
+        <listitem>
+          <para>Path to output file, FASTA formatted by default
+	  </para>
+        </listitem>
+      </varlistentry>
+      <varlistentry>
+        <term><option>-diags</option>
+	</term>
+	<listitem>
+	  <para>Find diagonals (faster for similar sequences)
+	  </para>
+	</listitem>
+      </varlistentry>
+      <varlistentry>
+        <term><option>-maxiters <replaceable>n</replaceable></option>
+        </term>
+        <listitem>
+          <para>Maximum number of iterations (integer, default 16)
+	  </para>
+        </listitem>
+      </varlistentry>
+      <varlistentry>
+        <term><option>-maxhours <replaceable>n</replaceable></option>
+        </term>
+        <listitem>
+          <para>Maximum time to iterate in hours (default no limit)
+	  </para>
+        </listitem>
+      </varlistentry>
+      
+      <varlistentry>
+        <term><option>-maxmb <replaceable>m</replaceable></option></term>
+        <listitem>
+          <para>Maximum memory to allocate in Mb (default 80% of RAM)</para>
+        </listitem>
+      </varlistentry>
+      
+      <varlistentry>
+        <term><option>-html</option>
+        </term>
+        <listitem>
+          <para>Write output in HTML format (default FASTA)</para>
+        </listitem>
+      </varlistentry>
+      <varlistentry>
+        <term><option>-msf</option>
+        </term>
+        <listitem>
+          <para>Write output in MSF format (default FASTA)</para>
+        </listitem>
+      </varlistentry>
+      
+      <varlistentry>
+        <term><option>-clw</option>
+        </term>
+        <listitem>
+          <para>Write output in Clustal W format (default FASTA)</para>
+        </listitem>
+      </varlistentry>
+      <varlistentry>
+        <term><option>-clwstrict</option>
+        </term>
+        <listitem>
+          <para>As -clw, with 'CLUSTAL W (1.81)' header</para>
+        </listitem>
+      </varlistentry>
+ 
+      <varlistentry>
+        <term><option>-log[a] <replaceable>logfile</replaceable></option>
+        </term>
+        <listitem>
+          <para>Log to file (append if -loga, overwrite if -log)</para>
+        </listitem>
+      </varlistentry>
+      <varlistentry>
+        <term><option>-quiet</option>
+        </term>
+        <listitem>
+          <para>Do not write progress messages to stderr</para>
+        </listitem>
+      </varlistentry>
+      <varlistentry>
+        <term><option>-stable</option>
+        </term>
+        <listitem>
+          <para>Output sequences in input order (default is -group)</para>
+        </listitem>
+      </varlistentry>
+      <varlistentry>
+        <term><option>-group</option>
+        </term>
+        <listitem>
+          <para>Group sequences by similarity (this is the default)</para>
+        </listitem>
+      </varlistentry>
+      <varlistentry>
+        <term><option>-version</option>
+        </term>
+        <listitem>
+          <para>Display version information and exit</para>
+        </listitem>
+      </varlistentry>
+    </variablelist>
+  </refsect1>
+  <refsect1>
+    <title>SEE ALSO</title>
+    <para>
+      <citerefentry>
+        <refentrytitle>clustalw</refentrytitle>
+        <manvolnum>1</manvolnum>
+      </citerefentry>,
+      
+      <citerefentry>
+        <refentrytitle>seaview</refentrytitle>
+        <manvolnum>1</manvolnum>
+      </citerefentry>,
+      
+      <citerefentry>
+        <refentrytitle>t_coffee</refentrytitle>
+        <manvolnum>1</manvolnum>
+      </citerefentry>.
+    </para>
+  </refsect1>
+</refentry>
--- muscle-3.8.31.orig/debian/README.Debian
+++ muscle-3.8.31/debian/README.Debian
@@ -0,0 +1,23 @@
+muscle for Debian
+-----------------
+
+Please cite
+
+  Edgar, Robert C. (2004), MUSCLE: multiple sequence alignment with
+  high accuracy and high throughput, Nucleic Acids Research 32(5), 1792-97.
+
+when publishing results achieved with this software.
+
+Steffen
+
+ -- Steffen Moeller <steffen_moeller@gmx.de>, Sun, 19 Sep 2004 00:51:19 +0200
+
+
+
+There has been two different upstream releases with the same name,
+muscle3.7_src.tar.gz, the second one being corrected for building with GCC 4.3.
+The Debian package 3.70-1 contained the first release (md5sum:
+55c9fe99b9c0bccd41e3ed18f8b9d0d99). The Debian package 3.70+fix1-1 contains the
+corrected release (md5sum: 45930141f334b89d927b3cfee6fc7857).
+
+ -- Charles Plessy <charles-debian-nospam@plessy.org>  Wed, 06 Feb 2008 12:04:31 +0900
--- muscle-3.8.31.orig/debian/muscle.doc-base
+++ muscle-3.8.31/debian/muscle.doc-base
@@ -0,0 +1,15 @@
+Document: muscle-manual
+Title: MUSCLE User Guide 3.5
+Author: Robert C. Edgar
+Abstract: MUSCLE is a program for creating multiple alignments of amino acid or
+ nucleotide sequences. A range of options is provided that give you the choice
+ of optimizing accuracy, speed, or some compromise between the two. Default
+ parameters are those that give the best average accuracy in our tests. Using
+ versions current at the time of writing, my tests show that MUSCLE can achieve
+ both better average accuracy and better speed than Clustal W or T‑Coffee,
+ depending on the chosen options.
+Section: Science/Biology
+
+Format: HTML
+Index: /usr/share/doc/muscle/muscle.html
+Files: /usr/share/doc/muscle/muscle.html
--- muscle-3.8.31.orig/debian/rules
+++ muscle-3.8.31/debian/rules
@@ -0,0 +1,35 @@
+#!/usr/bin/make -f
+
+include /usr/share/cdbs/1/rules/debhelper.mk
+include /usr/share/cdbs/1/class/makefile-vars.mk
+
+DEB_MAKE_BUILD_TARGET   :=
+
+CPPNames = aligngivenpath aligngivenpathsw aligntwomsas aligntwoprofs aln alpha anchors bittraceback blosum62 blosumla clust cluster clwwt color cons diaglist diffobjscore diffpaths difftrees difftreese distcalc distfunc distpwkimura domuscle dosp dpreglist drawtree edgelist enumopts enumtostr estring fasta fasta2 fastclust fastdist fastdistjones fastdistkbit fastdistkmer fastdistmafft fastdistnuc fastscorepath2 finddiags finddiagsn glbalign glbalign352 glbaligndiag glbalignle glbalignsimple glbalignsp glbalignspn glbalignss glbalndimer globals globalslinux globalsosx globalsother globalswin32 gonnet henikoffweight henikoffweightpb html hydro intmath local main makerootmsa makerootmsab maketree mhack mpam200 msa msa2 msadistkimura msf muscle muscleout nucmx nwdasimple nwdasimple2 nwdasmall nwrec nwsmall objscore objscore2 objscoreda onexception options outweights pam200mafft params phy phy2 phy3 phy4 phyfromclust phyfromfile physeq phytofile posgap ppscore profdb profile profilefrommsa progalign progress progressivealign pwpath readmx realigndiffs realigndiffse refine refinehoriz refinesubfams refinetree refinetreee refinevert refinew savebest scoredist scoregaps scorehistory scorepp seq seqvect setblosumweights setgscweights setnewhandler spfast sptest stabilize subfam subfams sw termgaps textfile threewaywt tomhydro traceback tracebackopt tracebacksw treefrommsa typetostr upgma2 usage validateids vtml2 writescorefile
+
+ObjNames = aligngivenpath.o aligngivenpathsw.o aligntwomsas.o aligntwoprofs.o aln.o alpha.o anchors.o bittraceback.o blosum62.o blosumla.o clust.o cluster.o clwwt.o color.o cons.o diaglist.o diffobjscore.o diffpaths.o difftrees.o difftreese.o distcalc.o distfunc.o distpwkimura.o domuscle.o dosp.o dpreglist.o drawtree.o edgelist.o enumopts.o enumtostr.o estring.o fasta.o fasta2.o fastclust.o fastdist.o fastdistjones.o fastdistkbit.o fastdistkmer.o fastdistmafft.o fastdistnuc.o fastscorepath2.o finddiags.o finddiagsn.o glbalign.o glbalign352.o glbaligndiag.o glbalignle.o glbalignsimple.o glbalignsp.o glbalignspn.o glbalignss.o glbalndimer.o globals.o globalslinux.o globalsosx.o globalsother.o globalswin32.o gonnet.o henikoffweight.o henikoffweightpb.o html.o hydro.o intmath.o local.o main.o makerootmsa.o makerootmsab.o maketree.o mhack.o mpam200.o msa.o msa2.o msadistkimura.o msf.o muscle.o muscleout.o nucmx.o nwdasimple.o nwdasimple2.o nwdasmall.o nwrec.o nwsmall.o objscore.o objscore2.o objscoreda.o onexception.o options.o outweights.o pam200mafft.o params.o phy.o phy2.o phy3.o phy4.o phyfromclust.o phyfromfile.o physeq.o phytofile.o posgap.o ppscore.o profdb.o profile.o profilefrommsa.o progalign.o progress.o progressivealign.o pwpath.o readmx.o realigndiffs.o realigndiffse.o refine.o refinehoriz.o refinesubfams.o refinetree.o refinetreee.o refinevert.o refinew.o savebest.o scoredist.o scoregaps.o scorehistory.o scorepp.o seq.o seqvect.o setblosumweights.o setgscweights.o setnewhandler.o spfast.o sptest.o stabilize.o subfam.o subfams.o sw.o termgaps.o textfile.o threewaywt.o tomhydro.o traceback.o tracebackopt.o tracebacksw.o treefrommsa.o typetostr.o upgma2.o usage.o validateids.o vtml2.o writescorefile.o
+
+%.o: $.cpp
+	$(CXX) -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 $(LDLIBS) $(CXXFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $@ $<
+
+build/muscle:: $(ObjNames)
+	g++ $(LDLIBS) $(CXXFLAGS) $(CPPFLAGS) $(LDFLAGS) -o muscle $(ObjNames)
+
+clean::
+	$(RM) *.o make.err make.out muscle
+
+SRC_TMP    := $(shell mktemp --tmpdir --directory muscle-build.XXXXXXXXXX)
+UP_TARBALL := $(SRC_TMP)/muscle$(DEB_UPSTREAM_VERSION)_src.tar.gz
+REPACKED   := muscle-$(DEB_UPSTREAM_VERSION).orig
+TARBALLS   := $(CURDIR)/../tarballs
+
+get-orig-source:
+	rm -rf $(SRC_TMP)/$(REPACKED)
+	[ -f $(UP_TARBALL) ] || wget -q -O $(UP_TARBALL) http://www.drive5.com/muscle/downloads3.8.31/muscle$(DEB_UPSTREAM_VERSION)_src.tar.gz
+	cd $(SRC_TMP) && \
+	  tar xvf $(UP_TARBALL) && \
+	  find . -name "muscle21" -delete && \
+	  mv $(SRC_TMP)/muscle$(DEB_UPSTREAM_VERSION)/src $(SRC_TMP)/$(REPACKED)
+	[ -d $(TARBALLS) ] || mkdir $(TARBALLS)
+	cd $(SRC_TMP) && GZIP="--best --no-name" tar -czf $(TARBALLS)/muscle_$(DEB_UPSTREAM_VERSION).orig.tar.gz $(REPACKED)
+	rm -rf $(SRC_TMP)
--- muscle-3.8.31.orig/debian/compat
+++ muscle-3.8.31/debian/compat
@@ -0,0 +1 @@
+8