<?xml version="1.0" encoding="ascii"?> <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "DTD/xhtml1-transitional.dtd"> <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> <head> <title>Bio.Align</title> <link rel="stylesheet" href="epydoc.css" type="text/css" /> <script type="text/javascript" src="epydoc.js"></script> </head> <body bgcolor="white" text="black" link="blue" vlink="#204080" alink="#204080"> <!-- ==================== NAVIGATION BAR ==================== --> <table class="navbar" border="0" width="100%" cellpadding="0" bgcolor="#a0c0ff" cellspacing="0"> <tr valign="middle"> <!-- Tree link --> <th> <a href="module-tree.html">Trees</a> </th> <!-- Index link --> <th> <a href="identifier-index.html">Indices</a> </th> <!-- Help link --> <th> <a href="help.html">Help</a> </th> <th class="navbar" width="100%"></th> </tr> </table> <table width="100%" cellpadding="0" cellspacing="0"> <tr valign="top"> <td width="100%"> <span class="breadcrumbs"> <a href="Bio-module.html">Package Bio</a> :: Package Align </span> </td> <td> <table cellpadding="0" cellspacing="0"> <!-- hide/show private --> <tr><td align="right"><span class="options">[<a href="javascript:void(0);" class="privatelink" onclick="toggle_private();">hide private</a>]</span></td></tr> <tr><td align="right"><span class="options" >[<a href="frames.html" target="_top">frames</a >] | <a href="Bio.Align-module.html" target="_top">no frames</a>]</span></td></tr> </table> </td> </tr> </table> <!-- ==================== PACKAGE DESCRIPTION ==================== --> <h1 class="epydoc">Package Align</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.Align-pysrc.html">source code</a></span></p> <p>Code for dealing with sequence alignments.</p> <p>One of the most important things in this module is the MultipleSeqAlignment class, used in the Bio.AlignIO module.</p> <!-- ==================== SUBMODULES ==================== --> <a name="section-Submodules"></a> <table class="summary" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr bgcolor="#70b0f0" class="table-header"> <td colspan="2" class="table-header"> <table border="0" cellpadding="0" cellspacing="0" width="100%"> <tr valign="top"> <td align="left"><span class="table-header">Submodules</span></td> <td align="right" valign="top" ><span class="options">[<a href="#section-Submodules" class="privatelink" onclick="toggle_private();" >hide private</a>]</span></td> </tr> </table> </td> </tr> <tr><td class="summary"> <ul class="nomargin"> <li> <strong class="uidlink"><a href="Bio.Align.AlignInfo-module.html">Bio.Align.AlignInfo</a></strong>: <em class="summary">Extract information from alignment objects.</em> </li> <li> <strong class="uidlink"><a href="Bio.Align.Applications-module.html">Bio.Align.Applications</a></strong>: <em class="summary">Alignment command line tool wrappers.</em> <ul> <li class="private"> <strong class="uidlink"><a href="Bio.Align.Applications._Clustalw-module.html" onclick="show_private();">Bio.Align.Applications._Clustalw</a></strong>: <em class="summary">Command line wrapper for the multiple alignment program Clustal W.</em> </li> <li class="private"> <strong class="uidlink"><a href="Bio.Align.Applications._Dialign-module.html" onclick="show_private();">Bio.Align.Applications._Dialign</a></strong>: <em class="summary">Command line wrapper for the multiple alignment program DIALIGN2-2.</em> </li> <li class="private"> <strong class="uidlink"><a href="Bio.Align.Applications._Mafft-module.html" onclick="show_private();">Bio.Align.Applications._Mafft</a></strong>: <em class="summary">Command line wrapper for the multiple alignment programme MAFFT.</em> </li> <li class="private"> <strong class="uidlink"><a href="Bio.Align.Applications._Muscle-module.html" onclick="show_private();">Bio.Align.Applications._Muscle</a></strong>: <em class="summary">Command line wrapper for the multiple alignment program MUSCLE.</em> </li> <li class="private"> <strong class="uidlink"><a href="Bio.Align.Applications._Prank-module.html" onclick="show_private();">Bio.Align.Applications._Prank</a></strong>: <em class="summary">Command line wrapper for the multiple alignment program PRANK.</em> </li> <li class="private"> <strong class="uidlink"><a href="Bio.Align.Applications._Probcons-module.html" onclick="show_private();">Bio.Align.Applications._Probcons</a></strong>: <em class="summary">Command line wrapper for the multiple alignment program PROBCONS.</em> </li> <li class="private"> <strong class="uidlink"><a href="Bio.Align.Applications._TCoffee-module.html" onclick="show_private();">Bio.Align.Applications._TCoffee</a></strong>: <em class="summary">Command line wrapper for the multiple alignment program TCOFFEE.</em> </li> </ul> </li> <li> <strong class="uidlink"><a href="Bio.Align.Generic-module.html">Bio.Align.Generic</a></strong>: <em class="summary">Contains classes to deal with generic sequence alignment stuff not specific to a particular program or format.</em> </li> </ul></td></tr> </table> <br /> <!-- ==================== CLASSES ==================== --> <a name="section-Classes"></a> <table class="summary" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr bgcolor="#70b0f0" class="table-header"> <td colspan="2" class="table-header"> <table border="0" cellpadding="0" cellspacing="0" width="100%"> <tr valign="top"> <td align="left"><span class="table-header">Classes</span></td> <td align="right" valign="top" ><span class="options">[<a href="#section-Classes" class="privatelink" onclick="toggle_private();" >hide private</a>]</span></td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Bio.Align.MultipleSeqAlignment-class.html" class="summary-name">MultipleSeqAlignment</a><br /> Represents a classical multiple sequence alignment (MSA). </td> </tr> </table> <!-- ==================== FUNCTIONS ==================== --> <a name="section-Functions"></a> <table class="summary" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr bgcolor="#70b0f0" class="table-header"> <td colspan="2" class="table-header"> <table border="0" cellpadding="0" cellspacing="0" width="100%"> <tr valign="top"> <td align="left"><span class="table-header">Functions</span></td> <td align="right" valign="top" ><span class="options">[<a href="#section-Functions" class="privatelink" onclick="toggle_private();" >hide private</a>]</span></td> </tr> </table> </td> </tr> <tr class="private"> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a href="Bio.Align-module.html#_test" class="summary-sig-name" onclick="show_private();">_test</a>()</span><br /> Run the Bio.Align module's doctests.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Align-pysrc.html#_test">source code</a></span> </td> </tr> </table> </td> </tr> </table> <!-- ==================== VARIABLES ==================== --> <a name="section-Variables"></a> <table class="summary" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr bgcolor="#70b0f0" class="table-header"> <td colspan="2" class="table-header"> <table border="0" cellpadding="0" cellspacing="0" width="100%"> <tr valign="top"> <td align="left"><span class="table-header">Variables</span></td> <td align="right" valign="top" ><span class="options">[<a href="#section-Variables" class="privatelink" onclick="toggle_private();" >hide private</a>]</span></td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a name="__package__"></a><span class="summary-name">__package__</span> = <code title="'Bio.Align'"><code class="variable-quote">'</code><code class="variable-string">Bio.Align</code><code class="variable-quote">'</code></code> </td> </tr> </table> <!-- ==================== FUNCTION DETAILS ==================== --> <a name="section-FunctionDetails"></a> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr bgcolor="#70b0f0" class="table-header"> <td colspan="2" class="table-header"> <table border="0" cellpadding="0" cellspacing="0" width="100%"> <tr valign="top"> <td align="left"><span class="table-header">Function Details</span></td> <td align="right" valign="top" ><span class="options">[<a href="#section-FunctionDetails" class="privatelink" onclick="toggle_private();" >hide private</a>]</span></td> </tr> </table> </td> </tr> </table> <a name="_test"></a> <div class="private"> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr><td> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr valign="top"><td> <h3 class="epydoc"><span class="sig"><span class="sig-name">_test</span>()</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.Align-pysrc.html#_test">source code</a></span> </td> </tr></table> <p>Run the Bio.Align module's doctests.</p> <p>This will try and locate the unit tests directory, and run the doctests from there in order that the relative paths used in the examples work.</p> <dl class="fields"> </dl> </td></tr></table> </div> <br /> <!-- ==================== NAVIGATION BAR ==================== --> <table class="navbar" border="0" width="100%" cellpadding="0" bgcolor="#a0c0ff" cellspacing="0"> <tr valign="middle"> <!-- Tree link --> <th> <a href="module-tree.html">Trees</a> </th> <!-- Index link --> <th> <a href="identifier-index.html">Indices</a> </th> <!-- Help link --> <th> <a href="help.html">Help</a> </th> <th class="navbar" width="100%"></th> </tr> </table> <table 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