<?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.Applications</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> ::
<a href="Bio.Align-module.html">Package Align</a> ::
Package Applications
</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.Applications-pysrc.html"
target="_top">no frames</a>]</span></td></tr>
</table>
</td>
</tr>
</table>
<h1 class="epydoc">Source Code for <a href="Bio.Align.Applications-module.html">Package Bio.Align.Applications</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-comment"># Copyright 2009 by Peter Cock & Cymon J. Cox. All rights reserved.</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-comment"># This code is part of the Biopython distribution and governed by its</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-comment"># license. Please see the LICENSE file that should have been included</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-comment"># as part of this package.</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-docstring">"""Alignment command line tool wrappers."""</tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-name">__docformat__</tt> <tt class="py-op">=</tt> <tt class="py-string">"epytext en"</tt> <tt class="py-comment">#Don't just use plain text in epydoc API pages!</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-0" class="py-name" targets="Module Bio.Align.Applications._Muscle=Bio.Align.Applications._Muscle-module.html"><a title="Bio.Align.Applications._Muscle" class="py-name" href="#" onclick="return doclink('link-0', '_Muscle', 'link-0');">_Muscle</a></tt> <tt class="py-keyword">import</tt> <tt id="link-1" class="py-name" targets="Class Bio.Align.Applications._Muscle.MuscleCommandline=Bio.Align.Applications._Muscle.MuscleCommandline-class.html"><a title="Bio.Align.Applications._Muscle.MuscleCommandline" class="py-name" href="#" onclick="return doclink('link-1', 'MuscleCommandline', 'link-1');">MuscleCommandline</a></tt> </tt>
<a name="L10"></a><tt class="py-lineno">10</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-2" class="py-name" targets="Module Bio.Align.Applications._Clustalw=Bio.Align.Applications._Clustalw-module.html"><a title="Bio.Align.Applications._Clustalw" class="py-name" href="#" onclick="return doclink('link-2', '_Clustalw', 'link-2');">_Clustalw</a></tt> <tt class="py-keyword">import</tt> <tt id="link-3" class="py-name" targets="Class Bio.Align.Applications._Clustalw.ClustalwCommandline=Bio.Align.Applications._Clustalw.ClustalwCommandline-class.html"><a title="Bio.Align.Applications._Clustalw.ClustalwCommandline" class="py-name" href="#" onclick="return doclink('link-3', 'ClustalwCommandline', 'link-3');">ClustalwCommandline</a></tt> </tt>
<a name="L11"></a><tt class="py-lineno">11</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-4" class="py-name" targets="Module Bio.Align.Applications._Prank=Bio.Align.Applications._Prank-module.html"><a title="Bio.Align.Applications._Prank" class="py-name" href="#" onclick="return doclink('link-4', '_Prank', 'link-4');">_Prank</a></tt> <tt class="py-keyword">import</tt> <tt id="link-5" class="py-name" targets="Class Bio.Align.Applications._Prank.PrankCommandline=Bio.Align.Applications._Prank.PrankCommandline-class.html"><a title="Bio.Align.Applications._Prank.PrankCommandline" class="py-name" href="#" onclick="return doclink('link-5', 'PrankCommandline', 'link-5');">PrankCommandline</a></tt> </tt>
<a name="L12"></a><tt class="py-lineno">12</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-6" class="py-name" targets="Module Bio.Align.Applications._Mafft=Bio.Align.Applications._Mafft-module.html"><a title="Bio.Align.Applications._Mafft" class="py-name" href="#" onclick="return doclink('link-6', '_Mafft', 'link-6');">_Mafft</a></tt> <tt class="py-keyword">import</tt> <tt id="link-7" class="py-name" targets="Class Bio.Align.Applications._Mafft.MafftCommandline=Bio.Align.Applications._Mafft.MafftCommandline-class.html"><a title="Bio.Align.Applications._Mafft.MafftCommandline" class="py-name" href="#" onclick="return doclink('link-7', 'MafftCommandline', 'link-7');">MafftCommandline</a></tt> </tt>
<a name="L13"></a><tt class="py-lineno">13</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-8" class="py-name" targets="Module Bio.Align.Applications._Dialign=Bio.Align.Applications._Dialign-module.html"><a title="Bio.Align.Applications._Dialign" class="py-name" href="#" onclick="return doclink('link-8', '_Dialign', 'link-8');">_Dialign</a></tt> <tt class="py-keyword">import</tt> <tt id="link-9" class="py-name" targets="Class Bio.Align.Applications._Dialign.DialignCommandline=Bio.Align.Applications._Dialign.DialignCommandline-class.html"><a title="Bio.Align.Applications._Dialign.DialignCommandline" class="py-name" href="#" onclick="return doclink('link-9', 'DialignCommandline', 'link-9');">DialignCommandline</a></tt> </tt>
<a name="L14"></a><tt class="py-lineno">14</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-10" class="py-name" targets="Module Bio.Align.Applications._Probcons=Bio.Align.Applications._Probcons-module.html"><a title="Bio.Align.Applications._Probcons" class="py-name" href="#" onclick="return doclink('link-10', '_Probcons', 'link-10');">_Probcons</a></tt> <tt class="py-keyword">import</tt> <tt id="link-11" class="py-name" targets="Class Bio.Align.Applications._Probcons.ProbconsCommandline=Bio.Align.Applications._Probcons.ProbconsCommandline-class.html"><a title="Bio.Align.Applications._Probcons.ProbconsCommandline" class="py-name" href="#" onclick="return doclink('link-11', 'ProbconsCommandline', 'link-11');">ProbconsCommandline</a></tt> </tt>
<a name="L15"></a><tt class="py-lineno">15</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-12" class="py-name" targets="Module Bio.Align.Applications._TCoffee=Bio.Align.Applications._TCoffee-module.html"><a title="Bio.Align.Applications._TCoffee" class="py-name" href="#" onclick="return doclink('link-12', '_TCoffee', 'link-12');">_TCoffee</a></tt> <tt class="py-keyword">import</tt> <tt id="link-13" class="py-name" targets="Class Bio.Align.Applications._TCoffee.TCoffeeCommandline=Bio.Align.Applications._TCoffee.TCoffeeCommandline-class.html"><a title="Bio.Align.Applications._TCoffee.TCoffeeCommandline" class="py-name" href="#" onclick="return doclink('link-13', 'TCoffeeCommandline', 'link-13');">TCoffeeCommandline</a></tt> </tt>
<a name="L16"></a><tt class="py-lineno">16</tt> <tt class="py-line"> </tt>
<a name="L17"></a><tt class="py-lineno">17</tt> <tt class="py-line"><tt class="py-comment">#Make this explicit, then they show up in the API docs</tt> </tt>
<a name="L18"></a><tt class="py-lineno">18</tt> <tt class="py-line"><tt class="py-name">__all__</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-string">"MuscleCommandline"</tt><tt class="py-op">,</tt> </tt>
<a name="L19"></a><tt class="py-lineno">19</tt> <tt class="py-line"> <tt class="py-string">"ClustalwCommandline"</tt><tt class="py-op">,</tt> </tt>
<a name="L20"></a><tt class="py-lineno">20</tt> <tt class="py-line"> <tt class="py-string">"PrankCommandline"</tt><tt class="py-op">,</tt> </tt>
<a name="L21"></a><tt class="py-lineno">21</tt> <tt class="py-line"> <tt class="py-string">"MafftCommandline"</tt><tt class="py-op">,</tt> </tt>
<a name="L22"></a><tt class="py-lineno">22</tt> <tt class="py-line"> <tt class="py-string">"DialignCommandline"</tt><tt class="py-op">,</tt> </tt>
<a name="L23"></a><tt class="py-lineno">23</tt> <tt class="py-line"> <tt class="py-string">"ProbconsCommandline"</tt><tt class="py-op">,</tt> </tt>
<a name="L24"></a><tt class="py-lineno">24</tt> <tt class="py-line"> <tt class="py-string">"TCoffeeCommandline"</tt><tt class="py-op">,</tt> </tt>
<a name="L25"></a><tt class="py-lineno">25</tt> <tt class="py-line"> <tt class="py-op">]</tt> </tt>
<a name="L26"></a><tt class="py-lineno">26</tt> <tt class="py-line"> </tt><script type="text/javascript">
<!--
expandto(location.href);
// -->
</script>
</pre>
<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 border="0" cellpadding="0" cellspacing="0" width="100%%">
<tr>
<td align="left" class="footer">
Generated by Epydoc 3.0.1 on Thu Aug 18 18:22:28 2011
</td>
<td align="right" class="footer">
<a target="mainFrame" href="http://epydoc.sourceforge.net"
>http://epydoc.sourceforge.net</a>
</td>
</tr>
</table>
<script type="text/javascript">
<!--
// Private objects are initially displayed (because if
// javascript is turned off then we want them to be
// visible); but by default, we want to hide them. So hide
// them unless we have a cookie that says to show them.
checkCookie();
// -->
</script>
</body>
</html>
