<?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</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">
Package Bio
</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-module.html"
target="_top">no frames</a>]</span></td></tr>
</table>
</td>
</tr>
</table>
<!-- ==================== PACKAGE DESCRIPTION ==================== -->
<h1 class="epydoc">Package Bio</h1><p class="nomargin-top"><span class="codelink"><a href="Bio-pysrc.html">source code</a></span></p>
<p>Collection of modules for dealing with biological data in Python.</p>
<p>The Biopython Project is an international association of developers of
freely available Python tools for computational molecular biology.</p>
<p>http://biopython.org</p>
<hr />
<div class="fields"> <p><strong>Version:</strong>
1.58
</p>
</div><!-- ==================== 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.Affy-module.html">Bio.Affy</a></strong>: <em class="summary">Deal with Affymetrix related data such as cel files.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.Affy.CelFile-module.html">Bio.Affy.CelFile</a></strong>: <em class="summary">Classes for accessing the information in Affymetrix cel files.</em> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.Align-module.html">Bio.Align</a></strong>: <em class="summary">Code for dealing with sequence alignments.</em>
<ul>
<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>
</li>
<li> <strong class="uidlink"><a href="Bio.AlignIO-module.html">Bio.AlignIO</a></strong>: <em class="summary">Multiple sequence alignment input/output as alignment objects.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.AlignIO.ClustalIO-module.html">Bio.AlignIO.ClustalIO</a></strong>: <em class="summary">Bio.AlignIO support for the "clustal" output from CLUSTAL
W and other tools.</em> </li>
<li> <strong class="uidlink"><a href="Bio.AlignIO.EmbossIO-module.html">Bio.AlignIO.EmbossIO</a></strong>: <em class="summary">Bio.AlignIO support for the "emboss" alignment output
from EMBOSS tools.</em> </li>
<li> <strong class="uidlink"><a href="Bio.AlignIO.FastaIO-module.html">Bio.AlignIO.FastaIO</a></strong>: <em class="summary">Bio.AlignIO support for "fasta-m10" output from Bill
Pearson's FASTA tools.</em> </li>
<li> <strong class="uidlink"><a href="Bio.AlignIO.Interfaces-module.html">Bio.AlignIO.Interfaces</a></strong>: <em class="summary">AlignIO support module (not for general use).</em> </li>
<li> <strong class="uidlink"><a href="Bio.AlignIO.NexusIO-module.html">Bio.AlignIO.NexusIO</a></strong>: <em class="summary">Bio.AlignIO support for the "nexus" file format.</em> </li>
<li> <strong class="uidlink"><a href="Bio.AlignIO.PhylipIO-module.html">Bio.AlignIO.PhylipIO</a></strong>: <em class="summary">AlignIO support for the "phylip" format used in Joe Felsenstein's PHYLIP tools.</em> </li>
<li> <strong class="uidlink"><a href="Bio.AlignIO.StockholmIO-module.html">Bio.AlignIO.StockholmIO</a></strong>: <em class="summary">Bio.AlignIO support for the "stockholm" format (used in
the PFAM database).</em> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.Alphabet-module.html">Bio.Alphabet</a></strong>: <em class="summary">Alphabets used in Seq objects etc to declare sequence type and
letters.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.Alphabet.IUPAC-module.html">Bio.Alphabet.IUPAC</a></strong>: <em class="summary">Standard nucleotide and protein alphabets defined by IUPAC.</em> </li>
<li> <strong class="uidlink"><a href="Bio.Alphabet.Reduced-module.html">Bio.Alphabet.Reduced</a></strong>: <em class="summary">Reduced alphabets which lump together several amino-acids into one
letter.</em> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.Application-module.html">Bio.Application</a></strong>: <em class="summary">General mechanisms to access applications in Biopython.</em> </li>
<li> <strong class="uidlink"><a href="Bio.Blast-module.html">Bio.Blast</a></strong>: <em class="summary">Code for dealing with BLAST programs and output.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.Blast.Applications-module.html">Bio.Blast.Applications</a></strong>: <em class="summary">Definitions for interacting with BLAST related applications.</em> </li>
<li> <strong class="uidlink"><a href="Bio.Blast.NCBIStandalone-module.html">Bio.Blast.NCBIStandalone</a></strong>: <em class="summary">Code for calling standalone BLAST and parsing plain text output
(OBSOLETE).</em> </li>
<li> <strong class="uidlink"><a href="Bio.Blast.NCBIWWW-module.html">Bio.Blast.NCBIWWW</a></strong>: <em class="summary">This module provides code to work with the WWW version of BLAST
provided by the NCBI.</em> </li>
<li> <strong class="uidlink"><a href="Bio.Blast.NCBIXML-module.html">Bio.Blast.NCBIXML</a></strong>: <em class="summary">This module provides code to work with the BLAST XML output
following the DTD available on the NCBI FTP
ftp://ftp.ncbi.nlm.nih.gov/blast/documents/xml/NCBI_BlastOutput.dtd</em> </li>
<li> <strong class="uidlink"><a href="Bio.Blast.ParseBlastTable-module.html">Bio.Blast.ParseBlastTable</a></strong>: <em class="summary">A parser for the NCBI blastpgp version 2.2.5 output format.</em> </li>
<li> <strong class="uidlink"><a href="Bio.Blast.Record-module.html">Bio.Blast.Record</a></strong>: <em class="summary">Record classes to hold BLAST output.</em> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.CAPS-module.html">Bio.CAPS</a></strong>: <em class="summary">This module deals with CAPS markers.</em> </li>
<li> <strong class="uidlink"><a href="Bio.Cluster-module.html">Bio.Cluster</a></strong> </li>
<li> <strong class="uidlink"><a href="Bio.Compass-module.html">Bio.Compass</a></strong>: <em class="summary">Code to deal with COMPASS output, a program for profile/profile
comparison.</em> </li>
<li> <strong class="uidlink"><a href="Bio.Crystal-module.html">Bio.Crystal</a></strong>: <em class="summary">Module to represent the NDB Atlas structure (a minimal subset of
PDB format).</em> </li>
<li> <strong class="uidlink"><a href="Bio.Data-module.html">Bio.Data</a></strong>: <em class="summary">Collections of various bits of useful biological data.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.Data.CodonTable-module.html">Bio.Data.CodonTable</a></strong>: <em class="summary">Codon tables based on those from the NCBI.</em> </li>
<li> <strong class="uidlink"><a href="Bio.Data.IUPACData-module.html">Bio.Data.IUPACData</a></strong> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.DocSQL-module.html">Bio.DocSQL</a></strong>: <em class="summary">Bio.DocSQL: easy access to DB API databases.</em> </li>
<li> <strong class="uidlink"><a href="Bio.Emboss-module.html">Bio.Emboss</a></strong>: <em class="summary">Code to interact with the ever-so-useful EMBOSS programs.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.Emboss.Applications-module.html">Bio.Emboss.Applications</a></strong>: <em class="summary">Code to interact with and run various EMBOSS programs.</em> </li>
<li> <strong class="uidlink"><a href="Bio.Emboss.Primer3-module.html">Bio.Emboss.Primer3</a></strong>: <em class="summary">Code to parse output from the EMBOSS eprimer3 program.</em> </li>
<li> <strong class="uidlink"><a href="Bio.Emboss.PrimerSearch-module.html">Bio.Emboss.PrimerSearch</a></strong>: <em class="summary">Code to interact with the primersearch program from EMBOSS.</em> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.Entrez-module.html">Bio.Entrez</a></strong>: <em class="summary">Provides code to access NCBI over the WWW.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.Entrez.Parser-module.html">Bio.Entrez.Parser</a></strong>: <em class="summary">Parser for XML results returned by NCBI's Entrez Utilities.</em> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.ExPASy-module.html">Bio.ExPASy</a></strong>: <em class="summary">This module provides code to access resources at ExPASy over the
WWW.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.ExPASy.Enzyme-module.html">Bio.ExPASy.Enzyme</a></strong>: <em class="summary">This module provides code to work with the enzyme.dat file from
Enzyme.</em> </li>
<li> <strong class="uidlink"><a href="Bio.ExPASy.Prodoc-module.html">Bio.ExPASy.Prodoc</a></strong>: <em class="summary">This module provides code to work with the prosite.doc file from
Prosite.</em> </li>
<li> <strong class="uidlink"><a href="Bio.ExPASy.Prosite-module.html">Bio.ExPASy.Prosite</a></strong>: <em class="summary">This module provides code to work with the prosite dat file from
Prosite.</em> </li>
<li> <strong class="uidlink"><a href="Bio.ExPASy.ScanProsite-module.html">Bio.ExPASy.ScanProsite</a></strong> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.FSSP-module.html">Bio.FSSP</a></strong>: <em class="summary">Parser for FSSP files, used in a database of protein fold
classifications.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.FSSP.FSSPTools-module.html">Bio.FSSP.FSSPTools</a></strong> </li>
<li> <strong class="uidlink"><a href="Bio.FSSP.fssp_rec-module.html">Bio.FSSP.fssp_rec</a></strong> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.File-module.html">Bio.File</a></strong>: <em class="summary">Code for more fancy file handles.</em> </li>
<li> <strong class="uidlink"><a href="Bio.GA-module.html">Bio.GA</a></strong>: <em class="summary">A selection of genetic algorithm code.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.GA.Crossover-module.html">Bio.GA.Crossover</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.GA.Crossover.General-module.html">Bio.GA.Crossover.General</a></strong>: <em class="summary">General functionality for crossover that doesn't apply.</em> </li>
<li> <strong class="uidlink"><a href="Bio.GA.Crossover.GeneralPoint-module.html">Bio.GA.Crossover.GeneralPoint</a></strong>: <em class="summary">Generalized N-Point Crossover.</em> </li>
<li> <strong class="uidlink"><a href="Bio.GA.Crossover.Point-module.html">Bio.GA.Crossover.Point</a></strong>: <em class="summary">Perform two-point crossovers between the genomes of two organisms.</em> </li>
<li> <strong class="uidlink"><a href="Bio.GA.Crossover.TwoPoint-module.html">Bio.GA.Crossover.TwoPoint</a></strong>: <em class="summary">Perform two-point crossovers between the genomes of two organisms.</em> </li>
<li> <strong class="uidlink"><a href="Bio.GA.Crossover.Uniform-module.html">Bio.GA.Crossover.Uniform</a></strong>: <em class="summary">Perform uniform crossovers between the genomes of two organisms.</em> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.GA.Evolver-module.html">Bio.GA.Evolver</a></strong>: <em class="summary">Evolution Strategies for a Population.</em> </li>
<li> <strong class="uidlink"><a href="Bio.GA.Mutation-module.html">Bio.GA.Mutation</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.GA.Mutation.General-module.html">Bio.GA.Mutation.General</a></strong>: <em class="summary">General functionality for mutations.</em> </li>
<li> <strong class="uidlink"><a href="Bio.GA.Mutation.Simple-module.html">Bio.GA.Mutation.Simple</a></strong>: <em class="summary">Perform Simple mutations on an organism's genome.</em> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.GA.Organism-module.html">Bio.GA.Organism</a></strong>: <em class="summary">Deal with an Organism in a Genetic Algorithm population.</em> </li>
<li> <strong class="uidlink"><a href="Bio.GA.Repair-module.html">Bio.GA.Repair</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.GA.Repair.Stabilizing-module.html">Bio.GA.Repair.Stabilizing</a></strong>: <em class="summary">Methods for performing repairs that will Stabilize genomes.</em> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.GA.Selection-module.html">Bio.GA.Selection</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.GA.Selection.Abstract-module.html">Bio.GA.Selection.Abstract</a></strong>: <em class="summary">Base selection class from which all Selectors should derive.</em> </li>
<li> <strong class="uidlink"><a href="Bio.GA.Selection.Diversity-module.html">Bio.GA.Selection.Diversity</a></strong>: <em class="summary">Select individuals into a new population trying to maintain
diversity.</em> </li>
<li> <strong class="uidlink"><a href="Bio.GA.Selection.RouletteWheel-module.html">Bio.GA.Selection.RouletteWheel</a></strong>: <em class="summary">Implement Roulette Wheel selection on a population.</em> </li>
<li> <strong class="uidlink"><a href="Bio.GA.Selection.Tournament-module.html">Bio.GA.Selection.Tournament</a></strong>: <em class="summary">Provide Tournament style selection.</em> </li>
</ul>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.GenBank-module.html">Bio.GenBank</a></strong>: <em class="summary">Code to work with GenBank formatted files.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.GenBank.LocationParser-module.html">Bio.GenBank.LocationParser</a></strong>: <em class="summary">Code used for parsing GenBank/EMBL feature location strings
(DEPRECATED).</em> </li>
<li> <strong class="uidlink"><a href="Bio.GenBank.Record-module.html">Bio.GenBank.Record</a></strong>: <em class="summary">Hold GenBank data in a straightforward format.</em> </li>
<li> <strong class="uidlink"><a href="Bio.GenBank.Scanner-module.html">Bio.GenBank.Scanner</a></strong> </li>
<li> <strong class="uidlink"><a href="Bio.GenBank.utils-module.html">Bio.GenBank.utils</a></strong>: <em class="summary">Useful utilities for helping in parsing GenBank files.</em> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.Geo-module.html">Bio.Geo</a></strong>: <em class="summary">Parser for files from NCBI's Gene Expression Omnibus (GEO).</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.Geo.Record-module.html">Bio.Geo.Record</a></strong>: <em class="summary">Hold GEO data in a straightforward format.</em> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.Graphics-module.html">Bio.Graphics</a></strong>: <em class="summary">Bio.Graphics offsers several graphical ouputs, all using ReportLab.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.Graphics.BasicChromosome-module.html">Bio.Graphics.BasicChromosome</a></strong>: <em class="summary">Draw representations of organism chromosomes with added
information.</em> </li>
<li> <strong class="uidlink"><a href="Bio.Graphics.Comparative-module.html">Bio.Graphics.Comparative</a></strong>: <em class="summary">Plots to compare information between different sources.</em> </li>
<li> <strong class="uidlink"><a href="Bio.Graphics.DisplayRepresentation-module.html">Bio.Graphics.DisplayRepresentation</a></strong>: <em class="summary">Represent information for graphical display.</em> </li>
<li> <strong class="uidlink"><a href="Bio.Graphics.Distribution-module.html">Bio.Graphics.Distribution</a></strong>: <em class="summary">Display information distributed across a Chromosome-like object.</em> </li>
<li> <strong class="uidlink"><a href="Bio.Graphics.GenomeDiagram-module.html">Bio.Graphics.GenomeDiagram</a></strong>
<ul>
<li class="private"> <strong class="uidlink"><a href="Bio.Graphics.GenomeDiagram._AbstractDrawer-module.html" onclick="show_private();">Bio.Graphics.GenomeDiagram._AbstractDrawer</a></strong>: <em class="summary">AbstractDrawer module (considered to be a private module, the API may change!)</em> </li>
<li class="private"> <strong class="uidlink"><a href="Bio.Graphics.GenomeDiagram._CircularDrawer-module.html" onclick="show_private();">Bio.Graphics.GenomeDiagram._CircularDrawer</a></strong>: <em class="summary">CircularDrawer module</em> </li>
<li class="private"> <strong class="uidlink"><a href="Bio.Graphics.GenomeDiagram._Colors-module.html" onclick="show_private();">Bio.Graphics.GenomeDiagram._Colors</a></strong>: <em class="summary">Colors module</em> </li>
<li class="private"> <strong class="uidlink"><a href="Bio.Graphics.GenomeDiagram._Diagram-module.html" onclick="show_private();">Bio.Graphics.GenomeDiagram._Diagram</a></strong>: <em class="summary">Diagram module</em> </li>
<li class="private"> <strong class="uidlink"><a href="Bio.Graphics.GenomeDiagram._Feature-module.html" onclick="show_private();">Bio.Graphics.GenomeDiagram._Feature</a></strong>: <em class="summary">Feature module</em> </li>
<li class="private"> <strong class="uidlink"><a href="Bio.Graphics.GenomeDiagram._FeatureSet-module.html" onclick="show_private();">Bio.Graphics.GenomeDiagram._FeatureSet</a></strong>: <em class="summary">FeatureSet module</em> </li>
<li class="private"> <strong class="uidlink"><a href="Bio.Graphics.GenomeDiagram._Graph-module.html" onclick="show_private();">Bio.Graphics.GenomeDiagram._Graph</a></strong>: <em class="summary">Graph module</em> </li>
<li class="private"> <strong class="uidlink"><a href="Bio.Graphics.GenomeDiagram._GraphSet-module.html" onclick="show_private();">Bio.Graphics.GenomeDiagram._GraphSet</a></strong>: <em class="summary">GraphSet module</em> </li>
<li class="private"> <strong class="uidlink"><a href="Bio.Graphics.GenomeDiagram._LinearDrawer-module.html" onclick="show_private();">Bio.Graphics.GenomeDiagram._LinearDrawer</a></strong>: <em class="summary">LinearDrawer module</em> </li>
<li class="private"> <strong class="uidlink"><a href="Bio.Graphics.GenomeDiagram._Track-module.html" onclick="show_private();">Bio.Graphics.GenomeDiagram._Track</a></strong>: <em class="summary">Track module</em> </li>
</ul>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.HMM-module.html">Bio.HMM</a></strong>: <em class="summary">A selection of Hidden Markov Model code.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.HMM.DynamicProgramming-module.html">Bio.HMM.DynamicProgramming</a></strong>: <em class="summary">Dynamic Programming algorithms for general usage.</em> </li>
<li> <strong class="uidlink"><a href="Bio.HMM.MarkovModel-module.html">Bio.HMM.MarkovModel</a></strong>: <em class="summary">Deal with representations of Markov Models.</em> </li>
<li> <strong class="uidlink"><a href="Bio.HMM.Trainer-module.html">Bio.HMM.Trainer</a></strong>: <em class="summary">Provide trainers which estimate parameters based on training
sequences.</em> </li>
<li> <strong class="uidlink"><a href="Bio.HMM.Utilities-module.html">Bio.HMM.Utilities</a></strong>: <em class="summary">Generic functions which are useful for working with HMMs.</em> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.HotRand-module.html">Bio.HotRand</a></strong>: <em class="summary">handles true random numbers supplied from the the web server of
fourmilab.</em> </li>
<li> <strong class="uidlink"><a href="Bio.Index-module.html">Bio.Index</a></strong>: <em class="summary">Index.py</em> </li>
<li> <strong class="uidlink"><a href="Bio.KDTree-module.html">Bio.KDTree</a></strong>: <em class="summary">The KD tree data structure can be used for all kinds of searches
that involve N-dimensional vectors.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.KDTree.KDTree-module.html">Bio.KDTree.KDTree</a></strong>: <em class="summary">KD tree data structure for searching N-dimensional vectors.</em> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.KEGG-module.html">Bio.KEGG</a></strong>: <em class="summary">This module provides code to work with data from the KEGG database.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.KEGG.Compound-module.html">Bio.KEGG.Compound</a></strong>: <em class="summary">This module provides code to work with the KEGG Ligand/Compound
database.</em> </li>
<li> <strong class="uidlink"><a href="Bio.KEGG.Enzyme-module.html">Bio.KEGG.Enzyme</a></strong>: <em class="summary">This module provides code to work with the KEGG Enzyme database.</em> </li>
<li> <strong class="uidlink"><a href="Bio.KEGG.Map-module.html">Bio.KEGG.Map</a></strong>: <em class="summary">This module provides code to import KEGG Pathway maps for use with
the Biopython Pathway module.</em> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.LogisticRegression-module.html">Bio.LogisticRegression</a></strong>: <em class="summary">This module provides code for doing logistic regressions.</em> </li>
<li> <strong class="uidlink"><a href="Bio.MarkovModel-module.html">Bio.MarkovModel</a></strong>: <em class="summary">This is an implementation of a state-emitting MarkovModel.</em> </li>
<li> <strong class="uidlink"><a href="Bio.MaxEntropy-module.html">Bio.MaxEntropy</a></strong>: <em class="summary">Maximum Entropy code.</em> </li>
<li> <strong class="uidlink"><a href="Bio.Medline-module.html">Bio.Medline</a></strong>: <em class="summary">This module provides code to work with Medline.</em> </li>
<li> <strong class="uidlink"><a href="Bio.Motif-module.html">Bio.Motif</a></strong>: <em class="summary">Module containing different tools for sequence motif analysis.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.Motif.Applications-module.html">Bio.Motif.Applications</a></strong>: <em class="summary">Motif command line tool wrappers.</em>
<ul>
<li class="private"> <strong class="uidlink"><a href="Bio.Motif.Applications._AlignAce-module.html" onclick="show_private();">Bio.Motif.Applications._AlignAce</a></strong>: <em class="summary">This module provides code to work with the standalone version of
AlignACE, for motif search in DNA sequences.</em> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.Motif.Parsers-module.html">Bio.Motif.Parsers</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.Motif.Parsers.AlignAce-module.html">Bio.Motif.Parsers.AlignAce</a></strong>: <em class="summary">Parsing AlignACE files: AlignAceParser</em> </li>
<li> <strong class="uidlink"><a href="Bio.Motif.Parsers.MAST-module.html">Bio.Motif.Parsers.MAST</a></strong> </li>
<li> <strong class="uidlink"><a href="Bio.Motif.Parsers.MEME-module.html">Bio.Motif.Parsers.MEME</a></strong> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.Motif.Thresholds-module.html">Bio.Motif.Thresholds</a></strong>: <em class="summary">Approximate calculation of appropriate thresholds for motif finding</em> </li>
<li class="private"> <strong class="uidlink"><a href="Bio.Motif._Motif-module.html" onclick="show_private();">Bio.Motif._Motif</a></strong>: <em class="summary">Implementation of sequence motifs (PRIVATE).</em> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.NMR-module.html">Bio.NMR</a></strong>: <em class="summary">Code for working with NMR data</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.NMR.NOEtools-module.html">Bio.NMR.NOEtools</a></strong> </li>
<li> <strong class="uidlink"><a href="Bio.NMR.xpktools-module.html">Bio.NMR.xpktools</a></strong> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.NaiveBayes-module.html">Bio.NaiveBayes</a></strong>: <em class="summary">This provides code for a general Naive Bayes learner.</em> </li>
<li> <strong class="uidlink"><a href="Bio.NeuralNetwork-module.html">Bio.NeuralNetwork</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.NeuralNetwork.BackPropagation-module.html">Bio.NeuralNetwork.BackPropagation</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.NeuralNetwork.BackPropagation.Layer-module.html">Bio.NeuralNetwork.BackPropagation.Layer</a></strong>: <em class="summary">Model a single layer in a nueral network.</em> </li>
<li> <strong class="uidlink"><a href="Bio.NeuralNetwork.BackPropagation.Network-module.html">Bio.NeuralNetwork.BackPropagation.Network</a></strong>: <em class="summary">Represent Neural Networks.</em> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.NeuralNetwork.Gene-module.html">Bio.NeuralNetwork.Gene</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.NeuralNetwork.Gene.Motif-module.html">Bio.NeuralNetwork.Gene.Motif</a></strong>: <em class="summary">Find and deal with motifs in biological sequence data.</em> </li>
<li> <strong class="uidlink"><a href="Bio.NeuralNetwork.Gene.Pattern-module.html">Bio.NeuralNetwork.Gene.Pattern</a></strong>: <em class="summary">Generic functionality useful for all gene representations.</em> </li>
<li> <strong class="uidlink"><a href="Bio.NeuralNetwork.Gene.Schema-module.html">Bio.NeuralNetwork.Gene.Schema</a></strong>: <em class="summary">Deal with Motifs or Signatures allowing ambiguity in the sequences.</em> </li>
<li> <strong class="uidlink"><a href="Bio.NeuralNetwork.Gene.Signature-module.html">Bio.NeuralNetwork.Gene.Signature</a></strong>: <em class="summary">Find and deal with signatures in biological sequence data.</em> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.NeuralNetwork.StopTraining-module.html">Bio.NeuralNetwork.StopTraining</a></strong>: <em class="summary">Classes to help deal with stopping training a neural network.</em> </li>
<li> <strong class="uidlink"><a href="Bio.NeuralNetwork.Training-module.html">Bio.NeuralNetwork.Training</a></strong>: <em class="summary">Provide classes for dealing with Training Neural Networks.</em> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.Nexus-module.html">Bio.Nexus</a></strong>: <em class="summary">The Bio.Nexus contains a NEXUS file parser and objects to model
this data.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.Nexus.Nexus-module.html">Bio.Nexus.Nexus</a></strong>: <em class="summary">Nexus class.</em> </li>
<li> <strong class="uidlink"><a href="Bio.Nexus.Nodes-module.html">Bio.Nexus.Nodes</a></strong> </li>
<li> <strong class="uidlink"><a href="Bio.Nexus.Trees-module.html">Bio.Nexus.Trees</a></strong>: <em class="summary">Tree class to handle phylogenetic trees.</em> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.PDB-module.html">Bio.PDB</a></strong>: <em class="summary">Classes that deal with macromolecular crystal structures.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.PDB.AbstractPropertyMap-module.html">Bio.PDB.AbstractPropertyMap</a></strong>: <em class="summary">Class that maps (chain_id, residue_id) to a residue property.</em> </li>
<li> <strong class="uidlink"><a href="Bio.PDB.Atom-module.html">Bio.PDB.Atom</a></strong>: <em class="summary">Atom class, used in Structure objects.</em> </li>
<li> <strong class="uidlink"><a href="Bio.PDB.Chain-module.html">Bio.PDB.Chain</a></strong>: <em class="summary">Chain class, used in Structure objects.</em> </li>
<li> <strong class="uidlink">Bio.PDB.DSSP</strong> </li>
<li> <strong class="uidlink"><a href="Bio.PDB.DSSP%27-module.html">Bio.PDB.DSSP'</a></strong>: <em class="summary">Use the DSSP program to calculate secondary structure and
accessibility.</em> </li>
<li> <strong class="uidlink"><a href="Bio.PDB.Dice-module.html">Bio.PDB.Dice</a></strong> </li>
<li> <strong class="uidlink"><a href="Bio.PDB.Entity-module.html">Bio.PDB.Entity</a></strong> </li>
<li> <strong class="uidlink">Bio.PDB.FragmentMapper</strong> </li>
<li> <strong class="uidlink"><a href="Bio.PDB.FragmentMapper%27-module.html">Bio.PDB.FragmentMapper'</a></strong>: <em class="summary">Classify protein backbone structure according to Kolodny et al's
fragment libraries.</em> </li>
<li> <strong class="uidlink"><a href="Bio.PDB.HSExposure-module.html">Bio.PDB.HSExposure</a></strong>: <em class="summary">Half-sphere exposure and coordination number calculation.</em> </li>
<li> <strong class="uidlink"><a href="Bio.PDB.MMCIF2Dict-module.html">Bio.PDB.MMCIF2Dict</a></strong>: <em class="summary">Turn an mmCIF file into a dictionary.</em> </li>
<li> <strong class="uidlink"><a href="Bio.PDB.MMCIFParser-module.html">Bio.PDB.MMCIFParser</a></strong>: <em class="summary">mmCIF parser (partly implemented in C).</em> </li>
<li> <strong class="uidlink"><a href="Bio.PDB.Model-module.html">Bio.PDB.Model</a></strong>: <em class="summary">Model class, used in Structure objects.</em> </li>
<li> <strong class="uidlink"><a href="Bio.PDB.NACCESS-module.html">Bio.PDB.NACCESS</a></strong> </li>
<li> <strong class="uidlink"><a href="Bio.PDB.NeighborSearch-module.html">Bio.PDB.NeighborSearch</a></strong>: <em class="summary">Fast atom neighbor lookup using a KD tree (implemented in C++).</em> </li>
<li> <strong class="uidlink"><a href="Bio.PDB.PDBExceptions-module.html">Bio.PDB.PDBExceptions</a></strong>: <em class="summary">Some Bio.PDB-specific exceptions.</em> </li>
<li> <strong class="uidlink">Bio.PDB.PDBIO</strong> </li>
<li> <strong class="uidlink"><a href="Bio.PDB.PDBIO%27-module.html">Bio.PDB.PDBIO'</a></strong>: <em class="summary">Output of PDB files.</em> </li>
<li> <strong class="uidlink">Bio.PDB.PDBList</strong> </li>
<li> <strong class="uidlink"><a href="Bio.PDB.PDBList%27-module.html">Bio.PDB.PDBList'</a></strong>: <em class="summary">Access the PDB over the internet (for example to download
structures).</em> </li>
<li> <strong class="uidlink">Bio.PDB.PDBParser</strong> </li>
<li> <strong class="uidlink"><a href="Bio.PDB.PDBParser%27-module.html">Bio.PDB.PDBParser'</a></strong>: <em class="summary">Parser for PDB files.</em> </li>
<li> <strong class="uidlink"><a href="Bio.PDB.PSEA-module.html">Bio.PDB.PSEA</a></strong>: <em class="summary">Wrappers for PSEA, a program for secondary structure assignment.</em> </li>
<li> <strong class="uidlink"><a href="Bio.PDB.Polypeptide-module.html">Bio.PDB.Polypeptide</a></strong>: <em class="summary">Polypeptide-related classes (construction and representation).</em> </li>
<li> <strong class="uidlink"><a href="Bio.PDB.Residue-module.html">Bio.PDB.Residue</a></strong> </li>
<li> <strong class="uidlink">Bio.PDB.ResidueDepth</strong> </li>
<li> <strong class="uidlink"><a href="Bio.PDB.ResidueDepth%27-module.html">Bio.PDB.ResidueDepth'</a></strong>: <em class="summary">Calculation of residue depth using command line tool MSMS.</em> </li>
<li> <strong class="uidlink"><a href="Bio.PDB.Selection-module.html">Bio.PDB.Selection</a></strong>: <em class="summary">Selection of atoms, residues, etc.</em> </li>
<li> <strong class="uidlink"><a href="Bio.PDB.Structure-module.html">Bio.PDB.Structure</a></strong>: <em class="summary">The structure class, representing a macromolecular structure.</em> </li>
<li> <strong class="uidlink">Bio.PDB.StructureAlignment</strong> </li>
<li> <strong class="uidlink"><a href="Bio.PDB.StructureAlignment%27-module.html">Bio.PDB.StructureAlignment'</a></strong>: <em class="summary">Map the residues of two structures to each other based on a FASTA
alignment file.</em> </li>
<li> <strong class="uidlink"><a href="Bio.PDB.StructureBuilder-module.html">Bio.PDB.StructureBuilder</a></strong>: <em class="summary">Consumer class that builds a Structure object.</em> </li>
<li> <strong class="uidlink">Bio.PDB.Superimposer</strong> </li>
<li> <strong class="uidlink"><a href="Bio.PDB.Superimposer%27-module.html">Bio.PDB.Superimposer'</a></strong>: <em class="summary">Superimpose two structures.</em> </li>
<li> <strong class="uidlink">Bio.PDB.Vector</strong> </li>
<li> <strong class="uidlink"><a href="Bio.PDB.Vector%27-module.html">Bio.PDB.Vector'</a></strong>: <em class="summary">Vector class, including rotation-related functions.</em> </li>
<li> <strong class="uidlink"><a href="Bio.PDB.mmCIF-module.html">Bio.PDB.mmCIF</a></strong> </li>
<li> <strong class="uidlink">Bio.PDB.parse_pdb_header</strong> </li>
<li> <strong class="uidlink"><a href="Bio.PDB.parse_pdb_header%27-module.html">Bio.PDB.parse_pdb_header'</a></strong>: <em class="summary">Parse the header of a PDB file.</em> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.ParserSupport-module.html">Bio.ParserSupport</a></strong>: <em class="summary">Code to support writing parsers.</em> </li>
<li> <strong class="uidlink"><a href="Bio.Parsers-module.html">Bio.Parsers</a></strong>: <em class="summary">Third party and other parsers useful internally to Biopython
(DEPRECATED).</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.Parsers.spark-module.html">Bio.Parsers.spark</a></strong>: <em class="summary">Copy of John Aycock's SPARK parser included with Biopython
(DEPRECATED).</em> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.Pathway-module.html">Bio.Pathway</a></strong>: <em class="summary">BioPython Pathway module.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.Pathway.Rep-module.html">Bio.Pathway.Rep</a></strong>: <em class="summary">BioPython Pathway support module.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.Pathway.Rep.Graph-module.html">Bio.Pathway.Rep.Graph</a></strong> </li>
<li> <strong class="uidlink"><a href="Bio.Pathway.Rep.HashSet-module.html">Bio.Pathway.Rep.HashSet</a></strong> </li>
<li> <strong class="uidlink"><a href="Bio.Pathway.Rep.MultiGraph-module.html">Bio.Pathway.Rep.MultiGraph</a></strong> </li>
</ul>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.Phylo-module.html">Bio.Phylo</a></strong>: <em class="summary">Package for working with phylogenetic trees.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.Phylo.Applications-module.html">Bio.Phylo.Applications</a></strong>: <em class="summary">Phylogenetics command line tool wrappers.</em>
<ul>
<li class="private"> <strong class="uidlink"><a href="Bio.Phylo.Applications._Phyml-module.html" onclick="show_private();">Bio.Phylo.Applications._Phyml</a></strong>: <em class="summary">Command-line wrapper for the tree inference program PhyML.</em> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.Phylo.BaseTree-module.html">Bio.Phylo.BaseTree</a></strong>: <em class="summary">Base classes for Bio.Phylo objects.</em> </li>
<li> <strong class="uidlink"><a href="Bio.Phylo.Newick-module.html">Bio.Phylo.Newick</a></strong>: <em class="summary">Classes corresponding to Newick trees, also used for Nexus trees.</em> </li>
<li> <strong class="uidlink"><a href="Bio.Phylo.NewickIO-module.html">Bio.Phylo.NewickIO</a></strong>: <em class="summary">I/O function wrappers for the Newick file format.</em> </li>
<li> <strong class="uidlink"><a href="Bio.Phylo.NexusIO-module.html">Bio.Phylo.NexusIO</a></strong>: <em class="summary">I/O function wrappers for <a href="Bio.Nexus-module.html" class="link">Bio.Nexus</a> trees.</em> </li>
<li> <strong class="uidlink"><a href="Bio.Phylo.PAML-module.html">Bio.Phylo.PAML</a></strong>
<ul>
<li class="private"> <strong class="uidlink"><a href="Bio.Phylo.PAML._paml-module.html">Bio.Phylo.PAML._paml</a></strong> </li>
<li class="private"> <strong class="uidlink"><a href="Bio.Phylo.PAML._parse_baseml-module.html">Bio.Phylo.PAML._parse_baseml</a></strong> </li>
<li class="private"> <strong class="uidlink"><a href="Bio.Phylo.PAML._parse_codeml-module.html">Bio.Phylo.PAML._parse_codeml</a></strong> </li>
<li class="private"> <strong class="uidlink"><a href="Bio.Phylo.PAML._parse_yn00-module.html">Bio.Phylo.PAML._parse_yn00</a></strong> </li>
<li> <strong class="uidlink"><a href="Bio.Phylo.PAML.baseml-module.html">Bio.Phylo.PAML.baseml</a></strong> </li>
<li> <strong class="uidlink"><a href="Bio.Phylo.PAML.chi2-module.html">Bio.Phylo.PAML.chi2</a></strong> </li>
<li> <strong class="uidlink"><a href="Bio.Phylo.PAML.codeml-module.html">Bio.Phylo.PAML.codeml</a></strong> </li>
<li> <strong class="uidlink"><a href="Bio.Phylo.PAML.yn00-module.html">Bio.Phylo.PAML.yn00</a></strong> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.Phylo.PhyloXML-module.html">Bio.Phylo.PhyloXML</a></strong>: <em class="summary">Classes corresponding to phyloXML elements.</em> </li>
<li> <strong class="uidlink"><a href="Bio.Phylo.PhyloXMLIO-module.html">Bio.Phylo.PhyloXMLIO</a></strong>: <em class="summary">PhyloXML reader/parser, writer, and associated functions.</em> </li>
<li class="private"> <strong class="uidlink"><a href="Bio.Phylo._io-module.html" onclick="show_private();">Bio.Phylo._io</a></strong>: <em class="summary">I/O function wrappers for phylogenetic tree formats.</em> </li>
<li class="private"> <strong class="uidlink"><a href="Bio.Phylo._sugar-module.html" onclick="show_private();">Bio.Phylo._sugar</a></strong>: <em class="summary">Short helper functions (syntax sugar) used in Bio.Phylo.</em> </li>
<li class="private"> <strong class="uidlink"><a href="Bio.Phylo._utils-module.html" onclick="show_private();">Bio.Phylo._utils</a></strong>: <em class="summary">Utilities for handling, displaying and exporting Phylo trees.</em> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.PopGen-module.html">Bio.PopGen</a></strong>: <em class="summary">PopGen: Population Genetics and Genomics library in Python</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.PopGen.Async-module.html">Bio.PopGen.Async</a></strong>: <em class="summary">Support for asynchronous execution.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.PopGen.Async.Local-module.html">Bio.PopGen.Async.Local</a></strong>: <em class="summary">Asynchronous local execution.</em> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.PopGen.FDist-module.html">Bio.PopGen.FDist</a></strong>: <em class="summary">This module provides code to work with FDist.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.PopGen.FDist.Async-module.html">Bio.PopGen.FDist.Async</a></strong>: <em class="summary">This modules allows for asynchronous execution of Fdist and
spliting of loads.</em> </li>
<li> <strong class="uidlink"><a href="Bio.PopGen.FDist.Controller-module.html">Bio.PopGen.FDist.Controller</a></strong>: <em class="summary">This module allows to control fdist.</em> </li>
<li> <strong class="uidlink"><a href="Bio.PopGen.FDist.Utils-module.html">Bio.PopGen.FDist.Utils</a></strong> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.PopGen.GenePop-module.html">Bio.PopGen.GenePop</a></strong>: <em class="summary">This module provides code to work with GenePop.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.PopGen.GenePop.Controller-module.html">Bio.PopGen.GenePop.Controller</a></strong>: <em class="summary">This module allows to control GenePop.</em> </li>
<li> <strong class="uidlink"><a href="Bio.PopGen.GenePop.EasyController-module.html">Bio.PopGen.GenePop.EasyController</a></strong>: <em class="summary">This module allows to control GenePop through an easier interface.</em> </li>
<li> <strong class="uidlink"><a href="Bio.PopGen.GenePop.FileParser-module.html">Bio.PopGen.GenePop.FileParser</a></strong>: <em class="summary">This class provides code to parse BIG GenePop files.</em> </li>
<li> <strong class="uidlink"><a href="Bio.PopGen.GenePop.LargeFileParser-module.html">Bio.PopGen.GenePop.LargeFileParser</a></strong>: <em class="summary">Large file parsing of Genepop files</em> </li>
<li> <strong class="uidlink"><a href="Bio.PopGen.GenePop.Utils-module.html">Bio.PopGen.GenePop.Utils</a></strong> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.PopGen.SimCoal-module.html">Bio.PopGen.SimCoal</a></strong>: <em class="summary">SimCoal2 execution module and support functions.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.PopGen.SimCoal.Async-module.html">Bio.PopGen.SimCoal.Async</a></strong>: <em class="summary">This module allows to cache Simcoal2 results, and return on the fly
in case the calculation was done.</em> </li>
<li> <strong class="uidlink"><a href="Bio.PopGen.SimCoal.Cache-module.html">Bio.PopGen.SimCoal.Cache</a></strong>: <em class="summary">This module allows to cache Simcoal2 results, and return on the fly
in case the calculation was done.</em> </li>
<li> <strong class="uidlink"><a href="Bio.PopGen.SimCoal.Controller-module.html">Bio.PopGen.SimCoal.Controller</a></strong>: <em class="summary">This module allows you to control Simcoal2.</em> </li>
<li> <strong class="uidlink"><a href="Bio.PopGen.SimCoal.Template-module.html">Bio.PopGen.SimCoal.Template</a></strong> </li>
</ul>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.Restriction-module.html">Bio.Restriction</a></strong>: <em class="summary">Usage:
=====</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.Restriction.PrintFormat-module.html">Bio.Restriction.PrintFormat</a></strong> </li>
<li> <strong class="uidlink"><a href="Bio.Restriction.RanaConfig-module.html">Bio.Restriction.RanaConfig</a></strong> </li>
<li> <strong class="uidlink"><a href="Bio.Restriction.Restriction-module.html">Bio.Restriction.Restriction</a></strong>: <em class="summary">Notes about the diverses class of the restriction enzyme implementation.</em> </li>
<li> <strong class="uidlink"><a href="Bio.Restriction.Restriction_Dictionary-module.html">Bio.Restriction.Restriction_Dictionary</a></strong> </li>
<li class="private"> <strong class="uidlink"><a href="Bio.Restriction._Update-module.html">Bio.Restriction._Update</a></strong>
<ul class="private">
<li> <strong class="uidlink"><a href="Bio.Restriction._Update.RestrictionCompiler-module.html">Bio.Restriction._Update.RestrictionCompiler</a></strong>: <em class="summary">Convert a serie of Rebase files into a Restriction_Dictionary.py module.</em> </li>
<li> <strong class="uidlink"><a href="Bio.Restriction._Update.Update-module.html">Bio.Restriction._Update.Update</a></strong>: <em class="summary">Update the Rebase emboss files used by Restriction to build the
Restriction_Dictionary.py module.</em> </li>
</ul>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.SCOP-module.html">Bio.SCOP</a></strong>: <em class="summary">SCOP: Structural Classification of Proteins.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.SCOP.Cla-module.html">Bio.SCOP.Cla</a></strong>: <em class="summary">Handle the SCOP CLAssification file, which describes SCOP domains.</em> </li>
<li> <strong class="uidlink"><a href="Bio.SCOP.Des-module.html">Bio.SCOP.Des</a></strong>: <em class="summary">Handle the SCOP DEScription file.</em> </li>
<li> <strong class="uidlink"><a href="Bio.SCOP.Dom-module.html">Bio.SCOP.Dom</a></strong>: <em class="summary">Handle the SCOP DOMain file.</em> </li>
<li> <strong class="uidlink"><a href="Bio.SCOP.Hie-module.html">Bio.SCOP.Hie</a></strong>: <em class="summary">Handle the SCOP HIErarchy files, which describe the SCOP hierarchy
in terms of SCOP unique identifiers (sunid).</em> </li>
<li> <strong class="uidlink"><a href="Bio.SCOP.Raf-module.html">Bio.SCOP.Raf</a></strong>: <em class="summary">ASTRAL RAF (Rapid Access Format) Sequence Maps.</em> </li>
<li> <strong class="uidlink">Bio.SCOP.Residues</strong> </li>
<li> <strong class="uidlink"><a href="Bio.SCOP.Residues%27-module.html">Bio.SCOP.Residues'</a></strong> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.SVDSuperimposer-module.html">Bio.SVDSuperimposer</a></strong>: <em class="summary">SVDSuperimposer finds the best rotation and translation to put two
point sets on top of each other (minimizing the RMSD).</em>
<ul>
<li> <strong class="uidlink">Bio.SVDSuperimposer.SVDSuperimposer</strong> </li>
<li> <strong class="uidlink"><a href="Bio.SVDSuperimposer.SVDSuperimposer%27-module.html">Bio.SVDSuperimposer.SVDSuperimposer'</a></strong> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.Search-module.html">Bio.Search</a></strong> </li>
<li> <strong class="uidlink"><a href="Bio.Seq-module.html">Bio.Seq</a></strong>: <em class="summary">Provides objects to represent biological sequences with alphabets.</em> </li>
<li> <strong class="uidlink"><a href="Bio.SeqFeature-module.html">Bio.SeqFeature</a></strong>: <em class="summary">Represent a Sequence Feature holding info about a part of a sequence.</em> </li>
<li> <strong class="uidlink"><a href="Bio.SeqIO-module.html">Bio.SeqIO</a></strong>: <em class="summary">Sequence input/output as SeqRecord objects.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.SeqIO.AbiIO-module.html">Bio.SeqIO.AbiIO</a></strong>: <em class="summary">Bio.SeqIO parser for the ABI format.</em> </li>
<li> <strong class="uidlink"><a href="Bio.SeqIO.AceIO-module.html">Bio.SeqIO.AceIO</a></strong>: <em class="summary">Bio.SeqIO support for the "ace" file format.</em> </li>
<li> <strong class="uidlink"><a href="Bio.SeqIO.FastaIO-module.html">Bio.SeqIO.FastaIO</a></strong>: <em class="summary">Bio.SeqIO support for the "fasta" (aka FastA or Pearson)
file format.</em> </li>
<li> <strong class="uidlink"><a href="Bio.SeqIO.IgIO-module.html">Bio.SeqIO.IgIO</a></strong>: <em class="summary">Bio.SeqIO support for the "ig" (IntelliGenetics or MASE)
file format.</em> </li>
<li> <strong class="uidlink"><a href="Bio.SeqIO.InsdcIO-module.html">Bio.SeqIO.InsdcIO</a></strong>: <em class="summary">Bio.SeqIO support for the "genbank" and "embl"
file formats.</em> </li>
<li> <strong class="uidlink"><a href="Bio.SeqIO.Interfaces-module.html">Bio.SeqIO.Interfaces</a></strong>: <em class="summary">Bio.SeqIO support module (not for general use).</em> </li>
<li> <strong class="uidlink"><a href="Bio.SeqIO.PhdIO-module.html">Bio.SeqIO.PhdIO</a></strong>: <em class="summary">Bio.SeqIO support for the "phd" file format.</em> </li>
<li> <strong class="uidlink"><a href="Bio.SeqIO.PirIO-module.html">Bio.SeqIO.PirIO</a></strong>: <em class="summary">Bio.SeqIO support for the "pir" (aka PIR or NBRF) file format.</em> </li>
<li> <strong class="uidlink"><a href="Bio.SeqIO.QualityIO-module.html">Bio.SeqIO.QualityIO</a></strong>: <em class="summary">Bio.SeqIO support for the FASTQ and QUAL file formats.</em> </li>
<li> <strong class="uidlink"><a href="Bio.SeqIO.SeqXmlIO-module.html">Bio.SeqIO.SeqXmlIO</a></strong>: <em class="summary">Bio.SeqIO support for the "seqxml" file format, SeqXML.</em> </li>
<li> <strong class="uidlink"><a href="Bio.SeqIO.SffIO-module.html">Bio.SeqIO.SffIO</a></strong>: <em class="summary">Bio.SeqIO support for the binary Standard Flowgram Format (SFF)
file format.</em> </li>
<li> <strong class="uidlink"><a href="Bio.SeqIO.SwissIO-module.html">Bio.SeqIO.SwissIO</a></strong>: <em class="summary">Bio.SeqIO support for the "swiss" (aka SwissProt/UniProt)
file format.</em> </li>
<li> <strong class="uidlink"><a href="Bio.SeqIO.TabIO-module.html">Bio.SeqIO.TabIO</a></strong>: <em class="summary">Bio.SeqIO support for the "tab" (simple tab separated)
file format.</em> </li>
<li> <strong class="uidlink"><a href="Bio.SeqIO.UniprotIO-module.html">Bio.SeqIO.UniprotIO</a></strong>: <em class="summary">Bio.SeqIO support for the "uniprot-xml" file format.</em> </li>
<li class="private"> <strong class="uidlink"><a href="Bio.SeqIO._convert-module.html">Bio.SeqIO._convert</a></strong>: <em class="summary">Optimised sequence conversion code (PRIVATE).</em> </li>
<li class="private"> <strong class="uidlink"><a href="Bio.SeqIO._index-module.html">Bio.SeqIO._index</a></strong>: <em class="summary">Dictionary like indexing of sequence files (PRIVATE).</em> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.SeqRecord-module.html">Bio.SeqRecord</a></strong>: <em class="summary">Represent a Sequence Record, a sequence with annotation.</em> </li>
<li> <strong class="uidlink"><a href="Bio.SeqUtils-module.html">Bio.SeqUtils</a></strong>: <em class="summary">Miscellaneous functions for dealing with sequences.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.SeqUtils.CheckSum-module.html">Bio.SeqUtils.CheckSum</a></strong>: <em class="summary">Functions to calculate assorted sequence checksums.</em> </li>
<li> <strong class="uidlink"><a href="Bio.SeqUtils.CodonUsage-module.html">Bio.SeqUtils.CodonUsage</a></strong> </li>
<li> <strong class="uidlink"><a href="Bio.SeqUtils.CodonUsageIndices-module.html">Bio.SeqUtils.CodonUsageIndices</a></strong> </li>
<li> <strong class="uidlink"><a href="Bio.SeqUtils.IsoelectricPoint-module.html">Bio.SeqUtils.IsoelectricPoint</a></strong>: <em class="summary">Calculate isoelectric points of polypeptides using methods of
Bjellqvist.</em> </li>
<li> <strong class="uidlink"><a href="Bio.SeqUtils.MeltingTemp-module.html">Bio.SeqUtils.MeltingTemp</a></strong>: <em class="summary">Calculate the thermodynamic melting temperatures of nucleotide
sequences.</em> </li>
<li> <strong class="uidlink"><a href="Bio.SeqUtils.ProtParam-module.html">Bio.SeqUtils.ProtParam</a></strong>: <em class="summary">Simple protein analysis.</em> </li>
<li> <strong class="uidlink"><a href="Bio.SeqUtils.ProtParamData-module.html">Bio.SeqUtils.ProtParamData</a></strong> </li>
<li> <strong class="uidlink"><a href="Bio.SeqUtils.lcc-module.html">Bio.SeqUtils.lcc</a></strong> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.Sequencing-module.html">Bio.Sequencing</a></strong>: <em class="summary">Code to deal with various programs for sequencing and assembly.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.Sequencing.Ace-module.html">Bio.Sequencing.Ace</a></strong>: <em class="summary">Parser for ACE files output by PHRAP.</em> </li>
<li> <strong class="uidlink"><a href="Bio.Sequencing.Applications-module.html">Bio.Sequencing.Applications</a></strong>: <em class="summary">Main entry point for application command line wrappers related to
sequencing.</em>
<ul>
<li class="private"> <strong class="uidlink"><a href="Bio.Sequencing.Applications._Novoalign-module.html" onclick="show_private();">Bio.Sequencing.Applications._Novoalign</a></strong>: <em class="summary">Command line wrapper for the short read aligner Novoalign by
Novocraft.</em> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.Sequencing.Phd-module.html">Bio.Sequencing.Phd</a></strong>: <em class="summary">Parser for PHD files output by PHRED and used by PHRAP and CONSED.</em> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.Statistics-module.html">Bio.Statistics</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.Statistics.lowess-module.html">Bio.Statistics.lowess</a></strong>: <em class="summary">This module implements the Lowess function for nonparametric
regression.</em> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.SubsMat-module.html">Bio.SubsMat</a></strong>: <em class="summary">Substitution matrices, log odds matrices, and operations on them.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.SubsMat.FreqTable-module.html">Bio.SubsMat.FreqTable</a></strong> </li>
<li> <strong class="uidlink"><a href="Bio.SubsMat.MatrixInfo-module.html">Bio.SubsMat.MatrixInfo</a></strong>: <em class="summary">A whole bunch of substitution matrices for use in alignments, etc.</em> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.SwissProt-module.html">Bio.SwissProt</a></strong>: <em class="summary">This module provides code to work with the sprotXX.dat file from
SwissProt.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.SwissProt.KeyWList-module.html">Bio.SwissProt.KeyWList</a></strong>: <em class="summary">Code to parse the keywlist.txt file from SwissProt/UniProt</em> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.UniGene-module.html">Bio.UniGene</a></strong>: <em class="summary">Parse Unigene flat file format files such as the Hs.data file.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.UniGene.UniGene-module.html">Bio.UniGene.UniGene</a></strong> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.Wise-module.html">Bio.Wise</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.Wise.dnal-module.html">Bio.Wise.dnal</a></strong> </li>
<li> <strong class="uidlink"><a href="Bio.Wise.psw-module.html">Bio.Wise.psw</a></strong> </li>
</ul>
</li>
<li class="private"> <strong class="uidlink"><a href="Bio._py3k-module.html">Bio._py3k</a></strong>: <em class="summary">Python 3 compatibility tools (PRIVATE).</em> </li>
<li> <strong class="uidlink"><a href="Bio.kNN-module.html">Bio.kNN</a></strong>: <em class="summary">This module provides code for doing k-nearest-neighbors classification.</em> </li>
<li> <strong class="uidlink"><a href="Bio.pairwise2-module.html">Bio.pairwise2</a></strong>: <em class="summary">This package implements pairwise sequence alignment using a dynamic
programming algorithm.</em> </li>
<li> <strong class="uidlink"><a href="Bio.triefind-module.html">Bio.triefind</a></strong>: <em class="summary">Given a trie, find all occurrences of a word in the trie in a
string.</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.BiopythonDeprecationWarning-class.html" class="summary-name">BiopythonDeprecationWarning</a><br />
Biopython deprecation warning.
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.BiopythonParserWarning-class.html" class="summary-name">BiopythonParserWarning</a><br />
Biopython parser warning.
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.BiopythonWarning-class.html" class="summary-name">BiopythonWarning</a><br />
Biopython warning.
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.MissingExternalDependencyError-class.html" class="summary-name">MissingExternalDependencyError</a><br />
Missing an external dependency.
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.MissingPythonDependencyError-class.html" class="summary-name">MissingPythonDependencyError</a><br />
Missing an external python dependency (subclass of ImportError).
</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="None">None</code><br />
hash(x)
</td>
</tr>
</table>
<!-- ==================== 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 18:19:19 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>
