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[Treebase-guts] SF.net SVN: treebase:[379] trunk/treebase-core/lib
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From: <rv...@us...> - 2009-12-15 18:35:51
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Revision: 379
http://treebase.svn.sourceforge.net/treebase/?rev=379&view=rev
Author: rvos
Date: 2009-12-15 18:35:41 +0000 (Tue, 15 Dec 2009)
Log Message:
-----------
Adding mesquite classes
Added Paths:
-----------
trunk/treebase-core/lib/mesquite/
trunk/treebase-core/lib/mesquite/align/
trunk/treebase-core/lib/mesquite/align/AlignDNAToProtein/
trunk/treebase-core/lib/mesquite/align/AlignDNAToProtein/AlignDNAToProtein.class
trunk/treebase-core/lib/mesquite/align/AlignScoreForTaxon/
trunk/treebase-core/lib/mesquite/align/AlignScoreForTaxon/AlignScoreForTaxon.class
trunk/treebase-core/lib/mesquite/align/AlignScoreForTaxonRC/
trunk/treebase-core/lib/mesquite/align/AlignScoreForTaxonRC/AlignScoreForTaxonRC.class
trunk/treebase-core/lib/mesquite/align/AlignSequences/
trunk/treebase-core/lib/mesquite/align/AlignSequences/AlignSequences.class
trunk/treebase-core/lib/mesquite/align/AlignSequences/AlignThread.class
trunk/treebase-core/lib/mesquite/align/AlignToDropped/
trunk/treebase-core/lib/mesquite/align/AlignToDropped/AlignToDropped.class
trunk/treebase-core/lib/mesquite/align/AlignToDropped/alignToDropped.gif
trunk/treebase-core/lib/mesquite/align/AlignToDropped/alignToDropped32.gif
trunk/treebase-core/lib/mesquite/align/AlignToDropped/alignToDropped64.gif
trunk/treebase-core/lib/mesquite/align/ClustalAlign/
trunk/treebase-core/lib/mesquite/align/ClustalAlign/ClustalAlign.class
trunk/treebase-core/lib/mesquite/align/ColorForAlignment/
trunk/treebase-core/lib/mesquite/align/ColorForAlignment/ColorForAlignment.class
trunk/treebase-core/lib/mesquite/align/ColorMisaligned/
trunk/treebase-core/lib/mesquite/align/ColorMisaligned/ColorMisaligned.class
trunk/treebase-core/lib/mesquite/align/aAlignIntro/
trunk/treebase-core/lib/mesquite/align/aAlignIntro/Templates/
trunk/treebase-core/lib/mesquite/align/aAlignIntro/Templates/standard.dwt
trunk/treebase-core/lib/mesquite/align/aAlignIntro/_notes/
trunk/treebase-core/lib/mesquite/align/aAlignIntro/_notes/2col_leftNav.css.mno
trunk/treebase-core/lib/mesquite/align/aAlignIntro/aAlignIntro.class
trunk/treebase-core/lib/mesquite/align/aAlignIntro/acknowledgements.html
trunk/treebase-core/lib/mesquite/align/aAlignIntro/additions.html
trunk/treebase-core/lib/mesquite/align/aAlignIntro/automated.html
trunk/treebase-core/lib/mesquite/align/aAlignIntro/citation.html
trunk/treebase-core/lib/mesquite/align/aAlignIntro/colorMisaligned.jpg
trunk/treebase-core/lib/mesquite/align/aAlignIntro/faq.html
trunk/treebase-core/lib/mesquite/align/aAlignIntro/future.html
trunk/treebase-core/lib/mesquite/align/aAlignIntro/images/
trunk/treebase-core/lib/mesquite/align/aAlignIntro/images/BlockMover.gif
trunk/treebase-core/lib/mesquite/align/aAlignIntro/images/alignToDropped.gif
trunk/treebase-core/lib/mesquite/align/aAlignIntro/images/email.jpg
trunk/treebase-core/lib/mesquite/align/aAlignIntro/images/leftGrab.gif
trunk/treebase-core/lib/mesquite/align/aAlignIntro/images/mesquiteIcon.gif
trunk/treebase-core/lib/mesquite/align/aAlignIntro/images/rightGrab.gif
trunk/treebase-core/lib/mesquite/align/aAlignIntro/images/splashAlign.psd
trunk/treebase-core/lib/mesquite/align/aAlignIntro/images/splashAlign2.psd
trunk/treebase-core/lib/mesquite/align/aAlignIntro/index.html
trunk/treebase-core/lib/mesquite/align/aAlignIntro/manualAlignment.html
trunk/treebase-core/lib/mesquite/align/aAlignIntro/overview.html
trunk/treebase-core/lib/mesquite/align/aAlignIntro/sourceCode.html
trunk/treebase-core/lib/mesquite/align/aAlignIntro/splash.gif
trunk/treebase-core/lib/mesquite/align/aAlignIntro/statistics.html
trunk/treebase-core/lib/mesquite/align/aAlignIntro/styles/
trunk/treebase-core/lib/mesquite/align/aAlignIntro/styles/mesquitePackage.css
trunk/treebase-core/lib/mesquite/align/aAlignIntro/visualization.html
Added: trunk/treebase-core/lib/mesquite/align/AlignDNAToProtein/AlignDNAToProtein.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/align/AlignDNAToProtein/AlignDNAToProtein.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/AlignScoreForTaxon/AlignScoreForTaxon.class
===================================================================
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Property changes on: trunk/treebase-core/lib/mesquite/align/AlignScoreForTaxon/AlignScoreForTaxon.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/AlignScoreForTaxonRC/AlignScoreForTaxonRC.class
===================================================================
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___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/AlignSequences/AlignSequences.class
===================================================================
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Property changes on: trunk/treebase-core/lib/mesquite/align/AlignSequences/AlignSequences.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/AlignSequences/AlignThread.class
===================================================================
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Property changes on: trunk/treebase-core/lib/mesquite/align/AlignSequences/AlignThread.class
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Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/AlignToDropped/AlignToDropped.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/align/AlignToDropped/AlignToDropped.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/AlignToDropped/alignToDropped.gif
===================================================================
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Property changes on: trunk/treebase-core/lib/mesquite/align/AlignToDropped/alignToDropped.gif
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Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/AlignToDropped/alignToDropped32.gif
===================================================================
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Property changes on: trunk/treebase-core/lib/mesquite/align/AlignToDropped/alignToDropped32.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/AlignToDropped/alignToDropped64.gif
===================================================================
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Property changes on: trunk/treebase-core/lib/mesquite/align/AlignToDropped/alignToDropped64.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/ClustalAlign/ClustalAlign.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/align/ClustalAlign/ClustalAlign.class
___________________________________________________________________
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+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/ColorForAlignment/ColorForAlignment.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/align/ColorForAlignment/ColorForAlignment.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/ColorMisaligned/ColorMisaligned.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/align/ColorMisaligned/ColorMisaligned.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/aAlignIntro/Templates/standard.dwt
===================================================================
--- trunk/treebase-core/lib/mesquite/align/aAlignIntro/Templates/standard.dwt (rev 0)
+++ trunk/treebase-core/lib/mesquite/align/aAlignIntro/Templates/standard.dwt 2009-12-15 18:35:41 UTC (rev 379)
@@ -0,0 +1,58 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"
+"http://www.w3.org/TR/html4/loose.dtd">
+<html>
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=">
+<!-- TemplateBeginEditable name="doctitle" -->
+<title>Untitled Document</title>
+<!-- TemplateEndEditable -->
+<link rel="stylesheet" href="../styles/mesquitePackage.css" type="text/css">
+<!-- TemplateBeginEditable name="head" --><!-- TemplateEndEditable -->
+</head>
+
+
+<body>
+<div id="masthead">
+ <div id="banner"><img src="../splash.gif" width="164" height="64"></div>
+ <div id="mainTitle"><font id="packageName"><b>Align</b></font><font id="version"><br>
+ Version 1.11<br>
+ 20 November 2007</font><BR>
+ David R. Maddison, Travis J. Wheeler, and Wayne P. Maddison </div>
+ <div id="subtitle"><!-- TemplateBeginEditable name="subtitle" -->subtitle<!-- TemplateEndEditable --></div>
+
+</div>
+<div>
+<!-- end masthead -->
+<div id="content"><!-- TemplateBeginEditable name="content" -->content<!-- TemplateEndEditable --></div>
+<!--end content -->
+<div id="navBar">
+ <div id="sectionLinks">
+ <ul>
+ <li><a href="../index.html">Home</a></li>
+ <li><a href="../manualAlignment.html">Manual Alignment</a></li>
+ <li><a href="../automated.html">Automated Alignment</a></li>
+ <li><a href="../visualization.html">Visualization Features</a></li>
+ <li><a href="../statistics.html">Statistics</a></li>
+ <li><a href="../citation.html">Citation</a></li>
+ <li><a href="../faq.html">FAQs</a></li>
+ <li><a href="../future.html">Future Directions</a></li>
+ <li><a href="../acknowledgements.html">Acknowledgements</a></li>
+ <li style="margin-top: 20px;"></li>
+ <li><a href="../sourceCode.html">Source Code</a></li>
+ <li style="margin-top: 20px;"></li>
+ <li><protectedURL>a href="../../../docs/mesquite/manual.html"</protectedURL>Mesquite Manual</a></li>
+ </ul>
+ <p> </p>
+ <ul><li> <a href="http://mesquiteproject.org" style="border: 0px;"><img src="../images/mesquiteIcon.gif" alt="Mesquite Home" width="32" height="32"> Mesquite Home</a> </li>
+ </ul>
+ </div>
+</div>
+</div>
+<div id="navBarExtension"> </div>
+<!--end navbar -->
+<div id="siteInfo"> Copyright © 2007 <a href="http://david.bembidion.org">David
+R. Maddison, </a><a href="http://traviswheeler.com/">Travis J. Wheeler</a>, and <a href="http://salticidae.org/wpm/home.html">Wayne
+P. Maddison</a></div>
+<br>
+</body>
+</html>
Added: trunk/treebase-core/lib/mesquite/align/aAlignIntro/_notes/2col_leftNav.css.mno
===================================================================
--- trunk/treebase-core/lib/mesquite/align/aAlignIntro/_notes/2col_leftNav.css.mno (rev 0)
+++ trunk/treebase-core/lib/mesquite/align/aAlignIntro/_notes/2col_leftNav.css.mno 2009-12-15 18:35:41 UTC (rev 379)
@@ -0,0 +1,4 @@
+<?xml version="1.0" encoding="utf-8" ?>
+<info>
+ <infoitem key="mm_new_doc_type" value="exclude" />
+</info>
Property changes on: trunk/treebase-core/lib/mesquite/align/aAlignIntro/_notes/2col_leftNav.css.mno
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/treebase-core/lib/mesquite/align/aAlignIntro/aAlignIntro.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/align/aAlignIntro/aAlignIntro.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/aAlignIntro/acknowledgements.html
===================================================================
--- trunk/treebase-core/lib/mesquite/align/aAlignIntro/acknowledgements.html (rev 0)
+++ trunk/treebase-core/lib/mesquite/align/aAlignIntro/acknowledgements.html 2009-12-15 18:35:41 UTC (rev 379)
@@ -0,0 +1,60 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"
+"http://www.w3.org/TR/html4/loose.dtd">
+<html><!-- InstanceBegin template="/Templates/standard.dwt" codeOutsideHTMLIsLocked="false" -->
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=">
+<!-- InstanceBeginEditable name="doctitle" -->
+<title>Acknowledgements</title>
+<!-- InstanceEndEditable -->
+<link rel="stylesheet" href="styles/mesquitePackage.css" type="text/css">
+<!-- InstanceBeginEditable name="head" --><!-- InstanceEndEditable -->
+</head>
+
+
+<body>
+<div id="masthead">
+ <div id="banner"><img src="splash.gif" width="164" height="64"></div>
+ <div id="mainTitle"><font id="packageName"><b>Align</b></font><font id="version"><br>
+ Version 1.11<br>
+ 20 November 2007</font><BR>
+ David R. Maddison, Travis J. Wheeler, and Wayne P. Maddison </div>
+ <div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Acknowledgements<!-- InstanceEndEditable --></div>
+
+</div>
+<div>
+<!-- end masthead -->
+<div id="content"><!-- InstanceBeginEditable name="content" -->
+ <p>We can't really think of anyone to thank at the moment. </p>
+ <!-- InstanceEndEditable --></div>
+<!--end content -->
+<div id="navBar">
+ <div id="sectionLinks">
+ <ul>
+ <li><a href="index.html">Home</a></li>
+ <li><a href="manualAlignment.html">Manual Alignment</a></li>
+ <li><a href="automated.html">Automated Alignment</a></li>
+ <li><a href="visualization.html">Visualization Features</a></li>
+ <li><a href="statistics.html">Statistics</a></li>
+ <li><a href="citation.html">Citation</a></li>
+ <li><a href="faq.html">FAQs</a></li>
+ <li><a href="future.html">Future Directions</a></li>
+ <li><a href="acknowledgements.html">Acknowledgements</a></li>
+ <li style="margin-top: 20px;"></li>
+ <li><a href="sourceCode.html">Source Code</a></li>
+ <li style="margin-top: 20px;"></li>
+ <li><protectedURL>a href="../../../docs/mesquite/manual.html"</protectedURL>Mesquite Manual</a></li>
+ </ul>
+ <p> </p>
+ <ul><li> <a href="http://mesquiteproject.org" style="border: 0px;"><img src="images/mesquiteIcon.gif" alt="Mesquite Home" width="32" height="32"> Mesquite Home</a> </li>
+ </ul>
+ </div>
+</div>
+</div>
+<div id="navBarExtension"> </div>
+<!--end navbar -->
+<div id="siteInfo"> Copyright © 2007 <a href="http://david.bembidion.org">David
+R. Maddison, </a><a href="http://traviswheeler.com/">Travis J. Wheeler</a>, and <a href="http://salticidae.org/wpm/home.html">Wayne
+P. Maddison</a></div>
+<br>
+</body>
+<!-- InstanceEnd --></html>
Added: trunk/treebase-core/lib/mesquite/align/aAlignIntro/additions.html
===================================================================
--- trunk/treebase-core/lib/mesquite/align/aAlignIntro/additions.html (rev 0)
+++ trunk/treebase-core/lib/mesquite/align/aAlignIntro/additions.html 2009-12-15 18:35:41 UTC (rev 379)
@@ -0,0 +1,52 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html>
+<head>
+<title>Untitled Document</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+</head>
+
+<body>
+<h3>Coloring Cells for Alignment</h3>
+<p>Manual alignment can be made easier by appropriate choice of a method to color
+ cells. You can set the method to color cells using the Matrix>Color cells
+ submenu. Three useful methods are:</p>
+<ul>
+ <li><strong>Character State</strong> — This colors cells according to
+ nucleotide. This is the default coloring, but in case it has been turned off,
+ you can turn it back on by going to Matrix>Color Cells>Character State.</li>
+ <li><strong>Aligning Colors</strong> — This colors pyrimidines by similar
+ colors, and likewise purines</li>
+ <li><strong>Highlight Apparently Slightly Misaligned</strong> — This highlights
+ subsequences that appear better shifted one or two sites left or right:<br>
+ <img src="colorMisaligned.jpg" width="249" height="252"> <br>
+ It bases its calculations on the dominant nucleotides in the columns, and
+ hence is useful only in a matrix that is mostly well aligned. Shifts more
+ distant than one or two sites are not considered. Do not consider this a definitive
+ indication that the cells should move; its purpose is only to help you find
+ possible issues, but the decision as to whether to shift or not is still up
+ to you. The highlight does not specify which direction the subsequences might
+ be best shifted; to learn this, hold the cursor over the sites in question.</li>
+</ul>
+<h3>Selecting Hint</h3>
+<p>To select from one cell to the end of the sequence, select the cell and then
+ hit Shift-Alt-Arrow key (or, on OS X, Shift-Option-Arrow key), where the arrow
+ key is either the right or left arrow key.</p>
+<h3>Preparing the Matrix</h3>
+<p>Several options under Matrix>Alter/Transform may be useful to modify the
+ matrix in preparation for alignment. Some of these options are under "Other
+ Choices...".</p>
+<ul>
+ <li>Collapse Gaps to Left</li>
+ <li>Collapse Gaps to Right</li>
+ <li>Trim Terminal Gaps Character</li>
+ <li>Gaps to Missing </li>
+ <li>Missing to Gaps</li>
+ <li>Terminal Gaps to ?</li>
+ <li>Terminal ? to Gaps</li>
+ <li>Reverse Complement</li>
+ <li>Reverse</li>
+ <li>Nucleotide Complement</li>
+</ul>
+<p> </p>
+</body>
+</html>
Added: trunk/treebase-core/lib/mesquite/align/aAlignIntro/automated.html
===================================================================
--- trunk/treebase-core/lib/mesquite/align/aAlignIntro/automated.html (rev 0)
+++ trunk/treebase-core/lib/mesquite/align/aAlignIntro/automated.html 2009-12-15 18:35:41 UTC (rev 379)
@@ -0,0 +1,110 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"
+"http://www.w3.org/TR/html4/loose.dtd">
+<html><!-- InstanceBegin template="/Templates/standard.dwt" codeOutsideHTMLIsLocked="false" -->
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=">
+<!-- InstanceBeginEditable name="doctitle" -->
+<title>Automated Alignment Tools</title>
+<!-- InstanceEndEditable -->
+<link rel="stylesheet" href="styles/mesquitePackage.css" type="text/css">
+<!-- InstanceBeginEditable name="head" --><!-- InstanceEndEditable -->
+</head>
+
+
+<body>
+<div id="masthead">
+ <div id="banner"><img src="splash.gif" width="164" height="64"></div>
+ <div id="mainTitle"><font id="packageName"><b>Align</b></font><font id="version"><br>
+ Version 1.11<br>
+ 20 November 2007</font><BR>
+ David R. Maddison, Travis J. Wheeler, and Wayne P. Maddison </div>
+ <div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Automated Alignment <!-- InstanceEndEditable --></div>
+
+</div>
+<div>
+<!-- end masthead -->
+<div id="content"><!-- InstanceBeginEditable name="content" -->
+ <h3><img src="images/alignToDropped.gif" alt="Pairwise Aligner" width="16" height="16">Pairwise Alignment tool </h3>
+ <p>This tool allows one to drop one or a selected set of sequences onto a reference sequence; the sequences dropped will then be aligned to the reference sequence, preserving whatever gaps are present in the reference sequence. In the process, if gaps need to be inserted into the reference sequence, then they will be also inserted into other, non-selected sequences. </p>
+ <p>The dropdown menu for this tool allows you to change the gap opening cost (default
+ 8) the gap extension cost (default 3) within bases of a sequences, as well
+ as the equivalent costs at the ends of the sequence (default 2 and 2, respectively). </p>
+ <p>The default substitution costs
+ are:</p>
+ <ul>
+ <li>for DNA and RNA data, 5 for a transition and 10 for a transversion</li>
+ <li>for protein data, 5 for each substitution.</li>
+ </ul>
+ <p>These costs can be changed using the Substitution Costs dialog box available from the tool's dropdown menu.</p>
+
+
+ <h3>Aligning nucleotide sequences to match an amino acid alignment </h3>
+ <p>This feature allows one to take a matrix of nucleotides, and an existing alignment of their translated amino acids, and have the nucleotides realigned to match the amino acid alignment.
+ To do this, you will need to have in the same Mesquite file both the nucleotide matrix and the protein matrix. For example, you could do the following: </p>
+ <ul>
+ <li>Assign codon positions and genetic code to a nucleotide matrix (see the main Mesquite manual for details).</li>
+ <li>Adjust each sequence so that its reading frame is correct, by using the <a href="manualAlignment.html#shiftMinStops">Shift To Minimize Stops</a> feature.</li>
+ <li>Trim any incomplete codons from the ends of the sequences by selecting the
+ entire matrix and choosing <font size="-1"><u>Matrix>Alter/Transform>Other
+ Choices</u></font>... and selecting
+ Trim Terminal Incomplete Codons. "Terminal Incomplete Codons" are nucleotides
+ that are only part of a codon. For example, if one sequence starts at a third
+ position, then that third position nucleotide represents only one-third of a
+ codon, and it will be trimmed. Once this is done, only complete codons will
+ be left in the sequence </li>
+ <li>Translate the DNA matrix to amino acids by choosing <font size="-1"><u>Characters>Make New Matrix From>Translate
+ DNA To Protein</u></font>. You will now have the protein matrix in your file.</li>
+
+ <li>Align the protein matrix. You could use, for example, the Clustal Align
+ feature described below. If instead you export the matrix (e.g., using
+ the <u><font size="-1">File>Export</font></u> options), align the proteins in a separate program, you
+ will then need to choose <u><font size="-1">File>Include</font></u> file to include the output of the
+ alignment program into your file.</li>
+ <li>Finally, go to your DNA matrix, and choose <font size="-1"><u>Matrix>Alter/Transform>Align
+ DNA to Protein</u></font>. </li>
+ </ul>
+
+ <h3>ClustalW Align </h3>
+ <p>This feature allows one to select a single block of sequences, and then have ClustalW align them. To do this, select the block, then choose Matrix>Align Multiple Sequences>Clustal Align... </p>
+ <p>You will be presented first with a query as to whether you want to do the ClustalW alignment on a separate thread, or on the same thread. Mesquite can do multiple things at once, because it can have one thing running on one computational "thread", and another thing happening on a separate thread. There is a main thread of the program that is the thread the user deals with directly, and that allows you to give commands to Mesquite (via menus, etc.). If this main thread is busy with a calculation, then you will not be able to ask for new things to happen in Mesquite until the calculation is done. By choosing "Separate" in the query that appears, you are asking Mesquite to create a thread separate from the main thread, thus enabling you to do things in Mesquite while the Clustal alignment is proceeding. However, if you do this, you must remember not to edit the matrix or close the window showing the matrix; if you do, Mesquite will be very unhappy. The safest thing to do is choose "No" to that query. </p>
+ <p>Once you make that choice, you will see a dialog box in which you must enter the directory location of ClustalW; if you use the Browse button in the dialog box you can choose ClustalW and have the location filled in automatically. If you wish, you can also alter the options of clustalw. If you then press OK, Mesquite will send that section of the matrix to ClustalW and ask for it to be aligned; it will then harvest the results and reincorporate that piece into the matrix.</p>
+ <p>The version of ClustalW that is to be used by Mesquite <em>must</em> be a version of ClustalW that is executable from the command line of your operating system. </p>
+ <p> </p>
+
+ <h3>Muscle Align </h3>
+ <p>This tool is just like the ClustalW Align feature described above, except that it works for Robert C. Edgar's <a href="http://www.drive5.com/muscle/">MUSCLE</a> program. </p>
+ <p> </p>
+
+<!-- InstanceEndEditable --></div>
+<!--end content -->
+<div id="navBar">
+ <div id="sectionLinks">
+ <ul>
+ <li><a href="index.html">Home</a></li>
+ <li><a href="manualAlignment.html">Manual Alignment</a></li>
+ <li><a href="automated.html">Automated Alignment</a></li>
+ <li><a href="visualization.html">Visualization Features</a></li>
+ <li><a href="statistics.html">Statistics</a></li>
+ <li><a href="citation.html">Citation</a></li>
+ <li><a href="faq.html">FAQs</a></li>
+ <li><a href="future.html">Future Directions</a></li>
+ <li><a href="acknowledgements.html">Acknowledgements</a></li>
+ <li style="margin-top: 20px;"></li>
+ <li><a href="sourceCode.html">Source Code</a></li>
+ <li style="margin-top: 20px;"></li>
+ <li><protectedURL>a href="../../../docs/mesquite/manual.html"</protectedURL>Mesquite Manual</a></li>
+ </ul>
+ <p> </p>
+ <ul><li> <a href="http://mesquiteproject.org" style="border: 0px;"><img src="images/mesquiteIcon.gif" alt="Mesquite Home" width="32" height="32"> Mesquite Home</a> </li>
+ </ul>
+ </div>
+</div>
+</div>
+<div id="navBarExtension"> </div>
+<!--end navbar -->
+<div id="siteInfo"> Copyright © 2007 <a href="http://david.bembidion.org">David
+R. Maddison, </a><a href="http://traviswheeler.com/">Travis J. Wheeler</a>, and <a href="http://salticidae.org/wpm/home.html">Wayne
+P. Maddison</a></div>
+<br>
+</body>
+<!-- InstanceEnd --></html>
Added: trunk/treebase-core/lib/mesquite/align/aAlignIntro/citation.html
===================================================================
--- trunk/treebase-core/lib/mesquite/align/aAlignIntro/citation.html (rev 0)
+++ trunk/treebase-core/lib/mesquite/align/aAlignIntro/citation.html 2009-12-15 18:35:41 UTC (rev 379)
@@ -0,0 +1,64 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"
+"http://www.w3.org/TR/html4/loose.dtd">
+<html><!-- InstanceBegin template="/Templates/standard.dwt" codeOutsideHTMLIsLocked="false" -->
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=">
+<!-- InstanceBeginEditable name="doctitle" -->
+<title>Untitled Document</title>
+<!-- InstanceEndEditable -->
+<link rel="stylesheet" href="styles/mesquitePackage.css" type="text/css">
+<!-- InstanceBeginEditable name="head" --><!-- InstanceEndEditable -->
+</head>
+
+
+<body>
+<div id="masthead">
+ <div id="banner"><img src="splash.gif" width="164" height="64"></div>
+ <div id="mainTitle"><font id="packageName"><b>Align</b></font><font id="version"><br>
+ Version 1.11<br>
+ 20 November 2007</font><BR>
+ David R. Maddison, Travis J. Wheeler, and Wayne P. Maddison </div>
+ <div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Citation<!-- InstanceEndEditable --></div>
+
+</div>
+<div>
+<!-- end masthead -->
+<div id="content"><!-- InstanceBeginEditable name="content" -->
+ <p><font face="Trebuchet MS">Align should be cited as:</font></p>
+ <p><font face="Trebuchet MS"><br />
+ Maddison, D.R., T.J. Wheeler, and W.P. Maddison. 2006. Align: a Mesquite
+ package for aligning sequence data. Version 1.0.<em> http://mesquiteproject.org</em></font></p>
+ <p> </p>
+ <!-- InstanceEndEditable --></div>
+<!--end content -->
+<div id="navBar">
+ <div id="sectionLinks">
+ <ul>
+ <li><a href="index.html">Home</a></li>
+ <li><a href="manualAlignment.html">Manual Alignment</a></li>
+ <li><a href="automated.html">Automated Alignment</a></li>
+ <li><a href="visualization.html">Visualization Features</a></li>
+ <li><a href="statistics.html">Statistics</a></li>
+ <li><a href="citation.html">Citation</a></li>
+ <li><a href="faq.html">FAQs</a></li>
+ <li><a href="future.html">Future Directions</a></li>
+ <li><a href="acknowledgements.html">Acknowledgements</a></li>
+ <li style="margin-top: 20px;"></li>
+ <li><a href="sourceCode.html">Source Code</a></li>
+ <li style="margin-top: 20px;"></li>
+ <li><protectedURL>a href="../../../docs/mesquite/manual.html"</protectedURL>Mesquite Manual</a></li>
+ </ul>
+ <p> </p>
+ <ul><li> <a href="http://mesquiteproject.org" style="border: 0px;"><img src="images/mesquiteIcon.gif" alt="Mesquite Home" width="32" height="32"> Mesquite Home</a> </li>
+ </ul>
+ </div>
+</div>
+</div>
+<div id="navBarExtension"> </div>
+<!--end navbar -->
+<div id="siteInfo"> Copyright © 2007 <a href="http://david.bembidion.org">David
+R. Maddison, </a><a href="http://traviswheeler.com/">Travis J. Wheeler</a>, and <a href="http://salticidae.org/wpm/home.html">Wayne
+P. Maddison</a></div>
+<br>
+</body>
+<!-- InstanceEnd --></html>
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Added: trunk/treebase-core/lib/mesquite/align/aAlignIntro/faq.html
===================================================================
--- trunk/treebase-core/lib/mesquite/align/aAlignIntro/faq.html (rev 0)
+++ trunk/treebase-core/lib/mesquite/align/aAlignIntro/faq.html 2009-12-15 18:35:41 UTC (rev 379)
@@ -0,0 +1,65 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"
+"http://www.w3.org/TR/html4/loose.dtd">
+<html><!-- InstanceBegin template="/Templates/standard.dwt" codeOutsideHTMLIsLocked="false" -->
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=">
+<!-- InstanceBeginEditable name="doctitle" -->
+<title>Frequently Asked Questions</title>
+<!-- InstanceEndEditable -->
+<link rel="stylesheet" href="styles/mesquitePackage.css" type="text/css">
+<!-- InstanceBeginEditable name="head" --><!-- InstanceEndEditable -->
+</head>
+
+
+<body>
+<div id="masthead">
+ <div id="banner"><img src="splash.gif" width="164" height="64"></div>
+ <div id="mainTitle"><font id="packageName"><b>Align</b></font><font id="version"><br>
+ Version 1.11<br>
+ 20 November 2007</font><BR>
+ David R. Maddison, Travis J. Wheeler, and Wayne P. Maddison </div>
+ <div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Frequently Asked Questions <!-- InstanceEndEditable --></div>
+
+</div>
+<div>
+<!-- end masthead -->
+<div id="content"><!-- InstanceBeginEditable name="content" -->
+ <p> </p>
+ <p>Q: Can I change the substitution costs used by the pairwise aligner tools? </p>
+ <p>A: Yes. You can now do this using the Substitution Costs menu item that
+ is available in the dropdown menu that appears if you touch down on the Pairwise
+ Aligner tool in the tool palette.</p>
+ <p> </p>
+<!-- InstanceEndEditable --></div>
+<!--end content -->
+<div id="navBar">
+ <div id="sectionLinks">
+ <ul>
+ <li><a href="index.html">Home</a></li>
+ <li><a href="manualAlignment.html">Manual Alignment</a></li>
+ <li><a href="automated.html">Automated Alignment</a></li>
+ <li><a href="visualization.html">Visualization Features</a></li>
+ <li><a href="statistics.html">Statistics</a></li>
+ <li><a href="citation.html">Citation</a></li>
+ <li><a href="faq.html">FAQs</a></li>
+ <li><a href="future.html">Future Directions</a></li>
+ <li><a href="acknowledgements.html">Acknowledgements</a></li>
+ <li style="margin-top: 20px;"></li>
+ <li><a href="sourceCode.html">Source Code</a></li>
+ <li style="margin-top: 20px;"></li>
+ <li><protectedURL>a href="../../../docs/mesquite/manual.html"</protectedURL>Mesquite Manual</a></li>
+ </ul>
+ <p> </p>
+ <ul><li> <a href="http://mesquiteproject.org" style="border: 0px;"><img src="images/mesquiteIcon.gif" alt="Mesquite Home" width="32" height="32"> Mesquite Home</a> </li>
+ </ul>
+ </div>
+</div>
+</div>
+<div id="navBarExtension"> </div>
+<!--end navbar -->
+<div id="siteInfo"> Copyright © 2007 <a href="http://david.bembidion.org">David
+R. Maddison, </a><a href="http://traviswheeler.com/">Travis J. Wheeler</a>, and <a href="http://salticidae.org/wpm/home.html">Wayne
+P. Maddison</a></div>
+<br>
+</body>
+<!-- InstanceEnd --></html>
Added: trunk/treebase-core/lib/mesquite/align/aAlignIntro/future.html
===================================================================
--- trunk/treebase-core/lib/mesquite/align/aAlignIntro/future.html (rev 0)
+++ trunk/treebase-core/lib/mesquite/align/aAlignIntro/future.html 2009-12-15 18:35:41 UTC (rev 379)
@@ -0,0 +1,68 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"
+"http://www.w3.org/TR/html4/loose.dtd">
+<html><!-- InstanceBegin template="/Templates/standard.dwt" codeOutsideHTMLIsLocked="false" -->
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=">
+<!-- InstanceBeginEditable name="doctitle" -->
+<title>Future Directions</title>
+<!-- InstanceEndEditable -->
+<link rel="stylesheet" href="styles/mesquitePackage.css" type="text/css">
+<!-- InstanceBeginEditable name="head" --><!-- InstanceEndEditable -->
+</head>
+
+
+<body>
+<div id="masthead">
+ <div id="banner"><img src="splash.gif" width="164" height="64"></div>
+ <div id="mainTitle"><font id="packageName"><b>Align</b></font><font id="version"><br>
+ Version 1.11<br>
+ 20 November 2007</font><BR>
+ David R. Maddison, Travis J. Wheeler, and Wayne P. Maddison </div>
+ <div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Future Directions <!-- InstanceEndEditable --></div>
+
+</div>
+<div>
+<!-- end masthead -->
+<div id="content"><!-- InstanceBeginEditable name="content" -->
+ <p>In the future, we plan to:</p>
+ <ul>
+ <li>allow more control by the user over the alignment parameters used by the pairwise aligner</li>
+ <li>add various graphical features for aiding with alignment of ribosomal DNA</li>
+ <li>add more manual alignment tools, including a tools that lets one manipulate multiple sequences at once <br>
+ </li>
+ <li>add more features derived from the pairwise aligner calculations. </li>
+ </ul>
+ <h3> </h3>
+ <!-- InstanceEndEditable --></div>
+<!--end content -->
+<div id="navBar">
+ <div id="sectionLinks">
+ <ul>
+ <li><a href="index.html">Home</a></li>
+ <li><a href="manualAlignment.html">Manual Alignment</a></li>
+ <li><a href="automated.html">Automated Alignment</a></li>
+ <li><a href="visualization.html">Visualization Features</a></li>
+ <li><a href="statistics.html">Statistics</a></li>
+ <li><a href="citation.html">Citation</a></li>
+ <li><a href="faq.html">FAQs</a></li>
+ <li><a href="future.html">Future Directions</a></li>
+ <li><a href="acknowledgements.html">Acknowledgements</a></li>
+ <li style="margin-top: 20px;"></li>
+ <li><a href="sourceCode.html">Source Code</a></li>
+ <li style="margin-top: 20px;"></li>
+ <li><protectedURL>a href="../../../docs/mesquite/manual.html"</protectedURL>Mesquite Manual</a></li>
+ </ul>
+ <p> </p>
+ <ul><li> <a href="http://mesquiteproject.org" style="border: 0px;"><img src="images/mesquiteIcon.gif" alt="Mesquite Home" width="32" height="32"> Mesquite Home</a> </li>
+ </ul>
+ </div>
+</div>
+</div>
+<div id="navBarExtension"> </div>
+<!--end navbar -->
+<div id="siteInfo"> Copyright © 2007 <a href="http://david.bembidion.org">David
+R. Maddison, </a><a href="http://traviswheeler.com/">Travis J. Wheeler</a>, and <a href="http://salticidae.org/wpm/home.html">Wayne
+P. Maddison</a></div>
+<br>
+</body>
+<!-- InstanceEnd --></html>
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Added: trunk/treebase-core/lib/mesquite/align/aAlignIntro/index.html
===================================================================
--- trunk/treebase-core/lib/mesquite/align/aAlignIntro/index.html (rev 0)
+++ trunk/treebase-core/lib/mesquite/align/aAlignIntro/index.html 2009-12-15 18:35:41 UTC (rev 379)
@@ -0,0 +1,93 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"
+"http://www.w3.org/TR/html4/loose.dtd">
+<html><!-- InstanceBegin template="/Templates/standard.dwt" codeOutsideHTMLIsLocked="false" -->
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=">
+<!-- InstanceBeginEditable name="doctitle" -->
+<title>Mesquite: Chromaseq</title>
+<!-- InstanceEndEditable -->
+<link rel="stylesheet" href="styles/mesquitePackage.css" type="text/css">
+<!-- InstanceBeginEditable name="head" -->
+<style type="text/css">
+<!--
+.style1 {
+ color: #009999;
+ font-weight: bold;
+}
+-->
+</style>
+<!-- InstanceEndEditable -->
+</head>
+
+
+<body>
+<div id="masthead">
+ <div id="banner"><img src="splash.gif" width="164" height="64"></div>
+ <div id="mainTitle"><font id="packageName"><b>Align</b></font><font id="version"><br>
+ Version 1.11<br>
+ 20 November 2007</font><BR>
+ David R. Maddison, Travis J. Wheeler, and Wayne P. Maddison </div>
+ <div id="subtitle"><!-- InstanceBeginEditable name="subtitle" --><!-- InstanceEndEditable --></div>
+
+</div>
+<div>
+<!-- end masthead -->
+<div id="content"><!-- InstanceBeginEditable name="content" -->
+ <h2><font face="Trebuchet MS">Align: a Mesquite
+ package for aligning sequence data </font></h2>
+ <p>The Align package provides some basic tools involving alignment of sequence data. The Align package contains:</p>
+ <ul>
+ <li>Tools for <a href="manualAlignment.html">manual alignment</a>
+ <ul>
+ <li>a Move Blocks tool</li>
+ <li>a Push Sequence tool</li>
+ <li>commands to remove gaps <em>en masse</em> </li>
+ </ul>
+ </li>
+ <li>Tools for <a href="automated.html">automated alignment </a>
+ <ul>
+ <li>a Pairwise Aligner tool</li>
+ <li>the ability to have a nucleotide matrix realigned to match an amino acid alignment</li>
+ <li>the ability to send a block of the matrix to ClustalW or MUSCLE to align </li>
+ </ul>
+ </li>
+ <li>Various <a href="statistics.html">statistics</a> about taxa based about alignments
+ <ul>
+ <li>the alignment score of a taxon against a reference taxon</li>
+ <li>the ratio of the alignment score of a taxon and its reverse complement against a reference taxon; this allows one to quickly detect sequences that are reverse complements of others.</li>
+ </ul>
+ </li>
+ </ul>
+<!-- InstanceEndEditable --></div>
+<!--end content -->
+<div id="navBar">
+ <div id="sectionLinks">
+ <ul>
+ <li><a href="index.html">Home</a></li>
+ <li><a href="manualAlignment.html">Manual Alignment</a></li>
+ <li><a href="automated.html">Automated Alignment</a></li>
+ <li><a href="visualization.html">Visualization Features</a></li>
+ <li><a href="statistics.html">Statistics</a></li>
+ <li><a href="citation.html">Citation</a></li>
+ <li><a href="faq.html">FAQs</a></li>
+ <li><a href="future.html">Future Directions</a></li>
+ <li><a href="acknowledgements.html">Acknowledgements</a></li>
+ <li style="margin-top: 20px;"></li>
+ <li><a href="sourceCode.html">Source Code</a></li>
+ <li style="margin-top: 20px;"></li>
+ <li><protectedURL>a href="../../../docs/mesquite/manual.html"</protectedURL>Mesquite Manual</a></li>
+ </ul>
+ <p> </p>
+ <ul><li> <a href="http://mesquiteproject.org" style="border: 0px;"><img src="images/mesquiteIcon.gif" alt="Mesquite Home" width="32" height="32"> Mesquite Home</a> </li>
+ </ul>
+ </div>
+</div>
+</div>
+<div id="navBarExtension"> </div>
+<!--end navbar -->
+<div id="siteInfo"> Copyright © 2007 <a href="http://david.bembidion.org">David
+R. Maddison, </a><a href="http://traviswheeler.com/">Travis J. Wheeler</a>, and <a href="http://salticidae.org/wpm/home.html">Wayne
+P. Maddison</a></div>
+<br>
+</body>
+<!-- InstanceEnd --></html>
Added: trunk/treebase-core/lib/mesquite/align/aAlignIntro/manualAlignment.html
===================================================================
--- trunk/treebase-core/lib/mesquite/align/aAlignIntro/manualAlignment.html (rev 0)
+++ trunk/treebase-core/lib/mesquite/align/aAlignIntro/manualAlignment.html 2009-12-15 18:35:41 UTC (rev 379)
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"
+"http://www.w3.org/TR/html4/loose.dtd">
+<html><!-- InstanceBegin template="/Templates/standard.dwt" codeOutsideHTMLIsLocked="false" -->
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=">
+<!-- InstanceBeginEditable name="doctitle" -->
+<title>Manual Alignment Tools</title>
+<!-- InstanceEndEditable -->
+<link rel="stylesheet" href="styles/mesquitePackage.css" type="text/css">
+<!-- InstanceBeginEditable name="head" --><!-- InstanceEndEditable -->
+</head>
+
+
+<body>
+<div id="masthead">
+ <div id="banner"><img src="splash.gif" width="164" height="64"></div>
+ <div id="mainTitle"><font id="packageName"><b>Align</b></font><font id="version"><br>
+ Version 1.11<br>
+ 20 November 2007</font><BR>
+ David R. Maddison, Travis J. Wheeler, and Wayne P. Maddison </div>
+ <div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Manual Alignment <!-- InstanceEndEditable --></div>
+
+</div>
+<div>
+<!-- end masthead -->
+<div id="content"><!-- InstanceBeginEditable name="content" -->
+ <h2>Moving bases by hand </h2>
+ <p>There are two tools available for moving bases by hand. One is the Move Blocks tool (<img src="images/BlockMover.gif" alt="Block Mover" width="16" height="16">), the other is the Push Sequence tool (<img src="images/rightGrab.gif" alt="Push Sequence" width="16" height="16">). </p>
+ <p>Both of these tools have a "Live update analyses, etc." option in their popup menus. If this is chosen, then all calculations (e.g., charts, character tracings, etc.) that depend upon these data will be redone <em>as you use</em> these tools. (Recalculations will be done once you let go of the mouse button, in any event.) If some of these calculations take a while, this can dramatically slow down use of these tools. </p>
+ <p>There are some <a href="visualization.html">visualization features</a> in Mesquite that can aid in manual
+ alignment.</p>
+ <h3><img src="images/BlockMover.gif" alt="Block Mover" width="16" height="16"> Move Blocks Tool </h3>
+ <p>This tool will move a contiguous block of a single sequence. If you move the tool between two bases it will let you split a block in two, inserting gaps. </p>
+ <p>If you wish, you can move more than a single, contiguous block by turning on "Move Selected Block" within the tool's popup menu, then using the tool to move selected bases and gaps. </p>
+ <h3><img src="images/rightGrab.gif" alt="Push Sequence" width="16" height="16"> Push Sequence Tool</h3>
+ <p>This tool pushes to the right the entire sequence to the right of the tool, or, if you have the Option key held down, it pushes to the left the entire sequence to the left of the tool. </p>
+ <h2>Shifting sequences </h2>
+ <p>Select a portion of a single sequence. If you then choose Matrix>Alter/Transform>Shift Other to Match..., then you will be presented with a dialog box that lets you choose a range of taxa, as well as a percentage. By default the range of taxa is the remaining taxa in the matrix. The default percentage is 75%. </p>
+ <p>If you press OK, Mesquite will look at each of the taxa within the range, and see if it can find a portion of each that is at least as similar as the percentage indicated to the selected portion (no gaps allowed). For each taxon that it can find such a match, it will shift those sequence such that the matched regions are lined up with the selected region. </p>
+ <p>Note that this is not an alignment algorithm; it simply shifts the sequences, maintaining whatever gaps are there or not in the sequences to be shifted. </p>
+ <p><a name="shiftMinStops"></a> You can also choose Matrix>Alter/Transform>Shift To Minimize Stop
+ Codons to shifts each <br>
+sequence 0, 1, or 2 bases so as to minimize the number of stop codons. The amount
+each sequence will be shifted will vary from sequence to sequence. This feature
+requires that codon
+positions be designated.</p>
+ <h2>Removal of Gaps</h2>
+ <h3>Remove All-Gap Characters </h3>
+ <p>Choosing this from Matrix>Alter/Transform>Remove All-Gap Characters will remove all sites in the matrix that consist entirely of gaps. </p>
+ <h3>Collapse Gaps </h3>
+ <p>With a block of the matrix selected, choosing Matrix>Alter/Transform>Collapse Gaps will remove all gaps in the selected block, with the bases or amino acids pushed as far to the left as possible. </p>
+<h2>Selecting Hint</h2>
+<p>To select from one cell to the end of the sequence, select the cell and then
+ hit Shift-Alt-Arrow key (or, on OS X, Shift-Option-Arrow key), where the arrow
+ key is either the right or left arrow key.</p>
+<h2>Preparing the Matrix</h2>
+<p>Several options under Matrix>Alter/Transform may be useful to modify the
+ matrix in preparation for alignment. Some of these options are under "Other
+ Choices...".</p>
+<ul>
+ <li>Collapse Gaps to Left</li>
+ <li>Collapse Gaps to Right</li>
+ <li>Trim Terminal Gaps Character</li>
+ <li>Gaps to Missing </li>
+ <li>Missing to Gaps</li>
+ <li>Terminal Gaps to ?</li>
+ <li>Terminal ? to Gaps</li>
+ <li>Reverse Complement</li>
+ <li>Reverse</li>
+ <li>Nucleotide Complement</li>
+</ul>
+<!-- InstanceEndEditable --></div>
+<!--end content -->
+<div id="navBar">
+ <div id="sectionLinks">
+ <ul>
+ <li><a href="index.html">Home</a></li>
+ <li><a href="manualAlignment.html">Manual Alignment</a></li>
+ <li><a href="automated.html">Automated Alignment</a></li>
+ <li><a href="visualization.html">Visualization Features</a></li>
+ <li><a href="statistics.html">Statistics</a></li>
+ <li><a href="citation.html">Citation</a></li>
+ <li><a href="faq.html">FAQs</a></li>
+ <li><a href="future.html">Future Directions</a></li>
+ <li><a href="acknowledgements.html">Acknowledgements</a></li>
+ <li style="margin-top: 20px;"></li>
+ <li><a href="sourceCode.html">Source Code</a></li>
+ <li style="margin-top: 20px;"></li>
+ <li><protectedURL>a href="../../../docs/mesquite/manual.html"</protectedURL>Mesquite Manual</a></li>
+ </ul>
+ <p> </p>
+ <ul><li> <a href="http://mesquiteproject.org" style="border: 0px;"><img src="images/mesquiteIcon.gif" alt="Mesquite Home" width="32" height="32"> Mesquite Home</a> </li>
+ </ul>
+ </div>
+</div>
+</div>
+<div id="navBarExtension"> </div>
+<!--end navbar -->
+<div id="siteInfo"> Copyright © 2007 <a href="http://david.bembidion.org">David
+R. Maddison, </a><a href="http://traviswheeler.com/">Travis J. Wheeler</a>, and <a href="http://salticidae.org/wpm/home.html">Wayne
+P. Maddison</a></div>
+<br>
+</body>
+<!-- InstanceEnd --></html>
Added: trunk/treebase-core/lib/mesquite/align/aAlignIntro/overview.html
===================================================================
--- trunk/treebase-core/lib/mesquite/align/aAlignIntro/overview.html (rev 0)
+++ trunk/treebase-core/lib/mesquite/align/aAlignIntro/overview.html 2009-12-15 18:35:41 UTC (rev 379)
@@ -0,0 +1,81 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"
+"http://www.w3.org/TR/html4/loose.dtd">
+<html><!-- InstanceBegin template="/Templates/standard.dwt" codeOutsideHTMLIsLocked="false" -->
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=">
+<!-- InstanceBeginEditable name="doctitle" -->
+<title>Chromaseq Overview</title>
+<!-- InstanceEndEditable -->
+<link rel="stylesheet" href="styles/mesquitePackage.css" type="text/css">
+<!-- InstanceBeginEditable name="head" --><!-- InstanceEndEditable -->
+</head>
+
+
+<body>
+<div id="masthead">
+ <div id="banner"><img src="splash.gif" width="164" height="64"></div>
+ <div id="mainTitle"><font id="packageName"><b>Align</b></font><font id="version"><br>
+ Version 1.11<br>
+ 20 November 2007</font><BR>
+ David R. Maddison, Travis J. Wheeler, and Wayne P. Maddison </div>
+ <div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Overview<!-- InstanceEndEditable --></div>
+
+</div>
+<div>
+<!-- end masthead -->
+<div id="content"><!-- InstanceBeginEditable name="content" -->
+ <p>The Align package contains:</p>
+ <ul>
+ <li>Tools for <a href="manualAlignment.html">manual alignment</a>
+ <ul>
+ <li>a Move Blocks tool</li>
+ <li>a Push Sequence tool</li>
+ <li>commands to remove gaps <em>en masse</em> </li>
+ </ul>
+ </li>
+ <li>Tools for <a href="automated.html">automated alignment </a>
+ <ul>
+ <li>a Pairwise Aligner tool</li>
+ <li>the ability to send a block of the matrix to ClustalW to align </li>
+ </ul>
+ </li>
+ <li>Various <a href="statistics.html">statistics</a> about taxa based about alignments
+ <ul>
+ <li>the alignment score of a taxon against a reference taxon</li>
+ <li>the ratio of the alignment score of a taxon and its reverse complement against a reference taxon; this allows one to quickly detect sequences that are reverse complements of others. </li>
+ </ul>
+ </li>
+ </ul>
+ <!-- InstanceEndEditable --></div>
+<!--end content -->
+<div id="navBar">
+ <div id="sectionLinks">
+ <ul>
+ <li><a href="index.html">Home</a></li>
+ <li><a href="manualAlignment.html">Manual Alignment</a></li>
+ <li><a href="automated.html">Automated Alignment</a></li>
+ <li><a href="visualization.html">Visualization Features</a></li>
+ <li><a href="statistics.html">Statistics</a></li>
+ <li><a href="citation.html">Citation</a></li>
+ <li><a href="faq.html">FAQs</a></li>
+ <li><a href="future.html">Future Directions</a></li>
+ <li><a href="acknowledgements.html">Acknowledgements</a></li>
+ <li style="margin-top: 20px;"></li>
+ <li><a href="sourceCode.html">Source Code</a></li>
+ <li style="margin-top: 20px;"></li>
+ <li><protectedURL>a href="../../../docs/mesquite/manual.html"</protectedURL>Mesquite Manual</a></li>
+ </ul>
+ <p> </p>
+ <ul><li> <a href="http://mesquiteproject.org" style="border: 0px;"><img src="images/mesquiteIcon.gif" alt="Mesquite Home" width="32" height="32"> Mesquite Home</a> </li>
+ </ul>
+ </div>
+</div>
+</div>
+<div id="navBarExtension"> </div>
+<!--end navbar -->
+<div id="siteInfo"> Copyright © 2007 <a href="http://david.bembidion.org">David
+R. Maddison, </a><a href="http://traviswheeler.com/">Travis J. Wheeler</a>, and <a href="http://salticidae.org/wpm/home.html">Wayne
+P. Maddison</a></div>
+<br>
+</body>
+<!-- InstanceEnd --></html>
Added: trunk/treebase-core/lib/mesquite/align/aAlignIntro/sourceCode.html
===================================================================
--- trunk/treebase-core/lib/mesquite/align/aAlignIntro/sourceCode.html (rev 0)
+++ trunk/treebase-core/lib/mesquite/align/aAlignIntro/sourceCode.html 2009-12-15 18:35:41 UTC (rev 379)
@@ -0,0 +1,60 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"
+"http://www.w3.org/TR/html4/loose.dtd">
+<html><!-- InstanceBegin template="/Templates/standard.dwt" codeOutsideHTMLIsLocked="false" -->
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=">
+<!-- InstanceBeginEditable name="doctitle" -->
+<title>Source Code</title>
+<!-- InstanceEndEditable -->
+<link rel="stylesheet" href="styles/mesquitePackage.css" type="text/css">
+<!-- InstanceBeginEditable name="head" --><!-- InstanceEndEditable -->
+</head>
+
+
+<body>
+<div id="masthead">
+ <div id="banner"><img src="splash.gif" width="164" height="64"></div>
+ <div id="mainTitle"><font id="packageName"><b>Align</b></font><font id="version"><br>
+ Version 1.11<br>
+ 20 November 2007</font><BR>
+ David R. Maddison, Travis J. Wheeler, and Wayne P. Maddison </div>
+ <div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Source Code<!-- InstanceEndEditable --></div>
+
+</div>
+<div>
+<!-- end masthead -->
+<div id="content"><!-- InstanceBeginEditable name="content" -->
+ <p><font face="Trebuchet MS">The source code for Align is distributed as part of the standard <a href="http://mesquiteproject.org/mesquite/download/source.html">source distribution</a> of Mesquite. </font></p>
+ <!-- InstanceEndEditable --></div>
+<!--end content -->
+<div id="navBar">
+ <div id="sectionLinks">
+ <ul>
+ <li><a href="index.html">Home</a></li>
+ <li><a href="manualAlignment.html">Manual Alignment</a></li>
+ <li><a href="automated.html">Automated Alignment</a></li>
+ <li><a href="visualization.html">Visualization Features</a></li>
+ <li><a href="statistics.html">Statistics</a></li>
+ <li><a href="citation.html">Citation</a></li>
+ <li><a href="faq.html">FAQs</a></li>
+ <li><a href="future.html">Future Directions</a></li>
+ <li><a href="acknowledgements.html">Acknowledgements</a></li>
+ <li style="margin-top: 20px;"></li>
+ <li><a href="sourceCode.html">Source Code</a></li>
+ <li style="margin-top: 20px;"></li>
+ <li><protectedURL>a href="../../../docs/mesquite/manual.html"</protectedURL>Mesquite Manual</a></li>
+ </ul>
+ <p> </p>
+ <ul><li> <a href="http://mesquiteproject.org" style="border: 0px;"><img src="images/mesquiteIcon.gif" alt="Mesquite Home" width="32" height="32"> Mesquite Home</a> </li>
+ </ul>
+ </div>
+</div>
+</div>
+<div id="navBarExtension"> </div>
+<!--end navbar -->
+<div id="siteInfo"> Copyright © 2007 <a href="http://david.bembidion.org">David
+R. Maddison, </a><a href="http://traviswheeler.com/">Travis J. Wheeler</a>, and <a href="http://salticidae.org/wpm/home.html">Wayne
+P. Maddison</a></div>
+<br>
+</body>
+<!-- InstanceEnd --></html>
Added: trunk/treebase-core/lib/mesquite/align/aAlignIntro/splash.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/align/aAlignIntro/splash.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/aAlignIntro/statistics.html
===================================================================
--- trunk/treebase-core/lib/mesquite/align/aAlignIntro/statistics.html (rev 0)
+++ trunk/treebase-core/lib/mesquite/align/aAlignIntro/statistics.html 2009-12-15 18:35:41 UTC (rev 379)
@@ -0,0 +1,63 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"
+"http://www.w3.org/TR/html4/loose.dtd">
+<html><!-- InstanceBegin template="/Templates/standard.dwt" codeOutsideHTMLIsLocked="false" -->
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=">
+<!-- InstanceBeginEditable name="doctitle" -->
+<title>Alignment Statistics</title>
+<!-- InstanceEndEditable -->
+<link rel="stylesheet" href="styles/mesquitePackage.css" type="text/css">
+<!-- InstanceBeginEditable name="head" --><!-- InstanceEndEditable -->
+</head>
+
+
+<body>
+<div id="masthead">
+ <div id="banner"><img src="splash.gif" width="164" height="64"></div>
+ <div id="mainTitle"><font id="packageName"><b>Align</b></font><font id="version"><br>
+ Version 1.11<br>
+ 20 November 2007</font><BR>
+ David R. Maddison, Travis J. Wheeler, and Wayne P. Maddison </div>
+ <div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Statistics<!-- InstanceEndEditable --></div>
+
+</div>
+<div>
+<!-- end masthead -->
+<div id="content"><!-- InstanceBeginEditable name="content" -->
+ <p>Align provides two statistics that can be calculate for each taxon in a matrix.
+ </p>
+ <p>The first, the <strong>Alignment Score</strong>, is simply the "cost" of the alignment between that taxon and a reference sequence, using Mesquite's defau...
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