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Package Bio
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<!-- ==================== 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>
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<td align="left"><span class="table-header">Submodules</span></td>
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<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">No version number yet.</em> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.Ais-module.html">Bio.Ais</a></strong>: <em class="summary">Immune system simulation based on ideas from Immunocomputing: a survey.</em> </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.FormatConvert-module.html">Bio.Align.FormatConvert</a></strong>: <em class="summary">Utility for conversion between different formats for representing
alignments.</em> </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.AlignAce-module.html">Bio.AlignAce</a></strong>: <em class="summary">Parser and code for dealing with the standalone version of
AlignAce, a motif search program.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.AlignAce.AlignAceStandalone-module.html">Bio.AlignAce.AlignAceStandalone</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>
<li> <strong class="uidlink"><a href="Bio.AlignAce.Applications-module.html">Bio.AlignAce.Applications</a></strong>: <em class="summary">Definitions for interacting with AlignAce.</em> </li>
<li> <strong class="uidlink"><a href="Bio.AlignAce.CompareAceStandalone-module.html">Bio.AlignAce.CompareAceStandalone</a></strong>: <em class="summary">This module provides code to work with the standalone version of
CompareAce, for motif comparison</em> </li>
<li> <strong class="uidlink"><a href="Bio.AlignAce.Motif-module.html">Bio.AlignAce.Motif</a></strong>: <em class="summary">Implementation of sequence motifs.</em> </li>
<li> <strong class="uidlink"><a href="Bio.AlignAce.Parser-module.html">Bio.AlignAce.Parser</a></strong>: <em class="summary">Classes for pparsing AlignAce and CompareACE files</em> </li>
<li> <strong class="uidlink"><a href="Bio.AlignAce.Scanner-module.html">Bio.AlignAce.Scanner</a></strong>: <em class="summary">Consumers for AlignACE and CompareACE parsers.</em> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.AlignIO-module.html">Bio.AlignIO</a></strong>: <em class="summary">Alignment input/output designed to look similar to Bio.SeqIO.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.AlignIO.ClustalIO-module.html">Bio.AlignIO.ClustalIO</a></strong> </li>
<li> <strong class="uidlink"><a href="Bio.AlignIO.EmbossIO-module.html">Bio.AlignIO.EmbossIO</a></strong> </li>
<li> <strong class="uidlink"><a href="Bio.AlignIO.FastaIO-module.html">Bio.AlignIO.FastaIO</a></strong>: <em class="summary">This module contains a parser for the pairwise alignments produced
by Bill Pearson's FASTA tool, for use from the Bio.AlignIO
interface where it is refered to as the "fasta-m10" file
format (as we only support the machine readable output format
selected with the -m 10 command line option).</em> </li>
<li> <strong class="uidlink"><a href="Bio.AlignIO.Interfaces-module.html">Bio.AlignIO.Interfaces</a></strong> </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">Note
====
In TREE_PUZZLE (Schmidt et al.</em> </li>
<li> <strong class="uidlink"><a href="Bio.AlignIO.StockholmIO-module.html">Bio.AlignIO.StockholmIO</a></strong> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.Alphabet-module.html">Bio.Alphabet</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.Alphabet.IUPAC-module.html">Bio.Alphabet.IUPAC</a></strong> </li>
<li> <strong class="uidlink"><a href="Bio.Alphabet.Reduced-module.html">Bio.Alphabet.Reduced</a></strong> </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">This module provides code to work with the standalone version of
BLAST, either blastall or blastpgp, provided by the NCBI.</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> </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.CDD-module.html">Bio.CDD</a></strong>: <em class="summary">Deal with Conserved Domain Database (CDD) entries from NCBI.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.CDD.Record-module.html">Bio.CDD.Record</a></strong>: <em class="summary">Hold CDD data in a straightforward format.</em> </li>
<li> <strong class="uidlink"><a href="Bio.CDD.cdd_format-module.html">Bio.CDD.cdd_format</a></strong>: <em class="summary">Martel based parser to read CDD formatted files.</em> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.Clustalw-module.html">Bio.Clustalw</a></strong>: <em class="summary">A set of classes to interact with the multiple alignment command
line program clustalw.</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">Hetero, Crystal and Chain exist to represent the NDB Atlas
structure.</em> </li>
<li> <strong class="uidlink"><a href="Bio.DBXRef-module.html">Bio.DBXRef</a></strong> </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> </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.Decode-module.html">Bio.Decode</a></strong> </li>
<li> <strong class="uidlink"><a href="Bio.DocSQL-module.html">Bio.DocSQL</a></strong> </li>
<li> <strong class="uidlink"><a href="Bio.ECell-module.html">Bio.ECell</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.ECell.Record-module.html">Bio.ECell.Record</a></strong>: <em class="summary">Martel based parser to read ECell formatted files.</em> </li>
<li> <strong class="uidlink"><a href="Bio.ECell.ecell_format-module.html">Bio.ECell.ecell_format</a></strong>: <em class="summary">Martel based parser to read ECell formatted files.</em> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils-module.html">Bio.EUtils</a></strong>: <em class="summary">EUtils is a client-side library for the Entrez databases at NCBI.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.EUtils.Config-module.html">Bio.EUtils.Config</a></strong>: <em class="summary">Configuration information about NCBI's databases</em> </li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DBIdsClient-module.html">Bio.EUtils.DBIdsClient</a></strong>: <em class="summary">Search and retrieve information given a set of database
identifiers.</em> </li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs-module.html">Bio.EUtils.DTDs</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.LinkOut-module.html">Bio.EUtils.DTDs.LinkOut</a></strong> </li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.eInfo_020511-module.html">Bio.EUtils.DTDs.eInfo_020511</a></strong> </li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.eLink_020511-module.html">Bio.EUtils.DTDs.eLink_020511</a></strong> </li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.ePost_020511-module.html">Bio.EUtils.DTDs.ePost_020511</a></strong> </li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.eSearch_020511-module.html">Bio.EUtils.DTDs.eSearch_020511</a></strong> </li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.eSummary_020511-module.html">Bio.EUtils.DTDs.eSummary_020511</a></strong> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.Datatypes-module.html">Bio.EUtils.Datatypes</a></strong>: <em class="summary">various EUtils datatypes</em> </li>
<li> <strong class="uidlink"><a href="Bio.EUtils.HistoryClient-module.html">Bio.EUtils.HistoryClient</a></strong>: <em class="summary">Search and retreive information using the EUtils history.</em> </li>
<li> <strong class="uidlink"><a href="Bio.EUtils.Mixins-module.html">Bio.EUtils.Mixins</a></strong>: <em class="summary">implements functionality shared between HistoryClient and
DBIdsClient</em> </li>
<li> <strong class="uidlink"><a href="Bio.EUtils.MultiDict-module.html">Bio.EUtils.MultiDict</a></strong>: <em class="summary">Dictionary-like objects which allow multiple keys</em> </li>
<li> <strong class="uidlink"><a href="Bio.EUtils.POM-module.html">Bio.EUtils.POM</a></strong>: <em class="summary">This module implements the XML POM -- the Python Object Model for
XML.</em> </li>
<li> <strong class="uidlink"><a href="Bio.EUtils.ReseekFile-module.html">Bio.EUtils.ReseekFile</a></strong>: <em class="summary">Wrap a file handle to allow seeks back to the beginning</em> </li>
<li> <strong class="uidlink"><a href="Bio.EUtils.ThinClient-module.html">Bio.EUtils.ThinClient</a></strong>: <em class="summary">Low-level interface to NCBI's EUtils for Entrez search and retrieval.</em> </li>
<li> <strong class="uidlink"><a href="Bio.EUtils.dtd2py-module.html">Bio.EUtils.dtd2py</a></strong>: <em class="summary">Internal class to convert DTDs to python form.</em> </li>
<li> <strong class="uidlink"><a href="Bio.EUtils.parse-module.html">Bio.EUtils.parse</a></strong> </li>
<li> <strong class="uidlink"><a href="Bio.EUtils.setup-module.html">Bio.EUtils.setup</a></strong> </li>
<li> <strong class="uidlink"><a href="Bio.EUtils.sourcegen-module.html">Bio.EUtils.sourcegen</a></strong>: <em class="summary">This module can be used to generate python source code.</em> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.EZRetrieve-module.html">Bio.EZRetrieve</a></strong>: <em class="summary">This module contains code to access EZRetrieve.</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.Primer-module.html">Bio.Emboss.Primer</a></strong>: <em class="summary">Code to interact with various Primer-related programs from EMBOSS.</em> </li>
<li> <strong class="uidlink"><a href="Bio.Emboss.primer3_format-module.html">Bio.Emboss.primer3_format</a></strong>: <em class="summary">Martel definitions for the output files produced by primer3.</em> </li>
<li> <strong class="uidlink"><a href="Bio.Emboss.primersearch_format-module.html">Bio.Emboss.primersearch_format</a></strong>: <em class="summary">Martel format for primersearch output files,</em> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.Encodings-module.html">Bio.Encodings</a></strong>: <em class="summary">Properties for functionality such as transcription and translation.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.Encodings.IUPACEncoding-module.html">Bio.Encodings.IUPACEncoding</a></strong> </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>
<li> <strong class="uidlink"><a href="Bio.Entrez.SerialSet-module.html">Bio.Entrez.SerialSet</a></strong> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.Enzyme-module.html">Bio.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-module.html">Bio.ExPASy</a></strong>: <em class="summary">This module provides code to access resources at ExPASy over the
WWW.</em> </li>
<li> <strong class="uidlink"><a href="Bio.FSSP-module.html">Bio.FSSP</a></strong>
<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.Fasta-module.html">Bio.Fasta</a></strong>: <em class="summary">Utilities for working with FASTA-formatted sequences.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.Fasta.FastaAlign-module.html">Bio.Fasta.FastaAlign</a></strong>: <em class="summary">Code to deal with alignments written in Fasta format.</em> </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.FilteredReader-module.html">Bio.FilteredReader</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>
<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.GFF-module.html">Bio.GFF</a></strong>: <em class="summary">Access to General Feature Format databases created with Bio::DB:GFF</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.GFF.GenericTools-module.html">Bio.GFF.GenericTools</a></strong>: <em class="summary">Docstring</em> </li>
<li> <strong class="uidlink"><a href="Bio.GFF.binning-module.html">Bio.GFF.binning</a></strong>: <em class="summary">Binning support for Bio.GFF</em> </li>
<li> <strong class="uidlink"><a href="Bio.GFF.easy-module.html">Bio.GFF.easy</a></strong>: <em class="summary">Bio.GFF.easy: some functions to ease the use of Biopython</em> </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> </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.Gobase-module.html">Bio.Gobase</a></strong>: <em class="summary">This module provides code to work with files from Gobase.</em> </li>
<li> <strong class="uidlink"><a href="Bio.Graphics-module.html">Bio.Graphics</a></strong>
<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>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.HMM-module.html">Bio.HMM</a></strong>
<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.IntelliGenetics-module.html">Bio.IntelliGenetics</a></strong>: <em class="summary">Parser for the MASE/Intelligenetics alignment file format.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.IntelliGenetics.Record-module.html">Bio.IntelliGenetics.Record</a></strong>: <em class="summary">Martel based parser to read IntelliGenetics formatted files.</em> </li>
<li> <strong class="uidlink"><a href="Bio.IntelliGenetics.intelligenetics_format-module.html">Bio.IntelliGenetics.intelligenetics_format</a></strong>: <em class="summary">Martel regular expression for Intelligenetic format.</em> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.InterPro-module.html">Bio.InterPro</a></strong>: <em class="summary">This module provides code to work with html files from InterPro,
and code to access resources at InterPro over the WWW.</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.CKDTree-module.html">Bio.KDTree.CKDTree</a></strong> </li>
<li> <strong class="uidlink"><a href="Bio.KDTree.KDTree-module.html">Bio.KDTree.KDTree</a></strong>: <em class="summary">The KD tree data structure can be used for all kinds of searches
that involve N-dimensional vectors, e.g.</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.LocusLink-module.html">Bio.LocusLink</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.LocusLink.locus_format-module.html">Bio.LocusLink.locus_format</a></strong>: <em class="summary">Martel based parser to read LocusLink flat files.</em> </li>
<li> <strong class="uidlink"><a href="Bio.LocusLink.web_parse-module.html">Bio.LocusLink.web_parse</a></strong> </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.MEME-module.html">Bio.MEME</a></strong>: <em class="summary">Parser for dealing with text output from the MEME motif search
program</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.MEME.Motif-module.html">Bio.MEME.Motif</a></strong> </li>
<li> <strong class="uidlink"><a href="Bio.MEME.Parser-module.html">Bio.MEME.Parser</a></strong> </li>
</ul>
</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.MetaTool-module.html">Bio.MetaTool</a></strong>: <em class="summary">Parser for output from MetaTool, a program which defines metabolic
routes within networks.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.MetaTool.Input-module.html">Bio.MetaTool.Input</a></strong>: <em class="summary">This module provides code to convert Bio.Pathway.System objects
into a text file that can be used as input for the MetaTool
program.</em> </li>
<li> <strong class="uidlink"><a href="Bio.MetaTool.Record-module.html">Bio.MetaTool.Record</a></strong>: <em class="summary">Hold MetaTool data in a straightforward format.</em> </li>
<li> <strong class="uidlink"><a href="Bio.MetaTool.metatool_format-module.html">Bio.MetaTool.metatool_format</a></strong>: <em class="summary">Martel based parser to read MetaTool output files.</em> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.Mindy-module.html">Bio.Mindy</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.Mindy.BaseDB-module.html">Bio.Mindy.BaseDB</a></strong> </li>
<li> <strong class="uidlink"><a href="Bio.Mindy.BerkeleyDB-module.html">Bio.Mindy.BerkeleyDB</a></strong> </li>
<li> <strong class="uidlink"><a href="Bio.Mindy.FlatDB-module.html">Bio.Mindy.FlatDB</a></strong> </li>
<li> <strong class="uidlink"><a href="Bio.Mindy.Location-module.html">Bio.Mindy.Location</a></strong> </li>
<li> <strong class="uidlink"><a href="Bio.Mindy.SimpleSeqRecord-module.html">Bio.Mindy.SimpleSeqRecord</a></strong>: <em class="summary">Index a file based on information in a SeqRecord object.</em> </li>
<li> <strong class="uidlink"><a href="Bio.Mindy.XPath-module.html">Bio.Mindy.XPath</a></strong> </li>
<li> <strong class="uidlink"><a href="Bio.Mindy.compression-module.html">Bio.Mindy.compression</a></strong> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.NBRF-module.html">Bio.NBRF</a></strong>: <em class="summary">Parser for the NBRF/PIR file format.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.NBRF.Record-module.html">Bio.NBRF.Record</a></strong>: <em class="summary">Martel based parser to read NBRF formatted files.</em> </li>
<li> <strong class="uidlink"><a href="Bio.NBRF.ValSeq-module.html">Bio.NBRF.ValSeq</a></strong> </li>
<li> <strong class="uidlink"><a href="Bio.NBRF.nbrf_format-module.html">Bio.NBRF.nbrf_format</a></strong>: <em class="summary">Martel based parser to read NBRF formatted files.</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.Ndb-module.html">Bio.Ndb</a></strong>: <em class="summary">This module provides code to work with html files from NDB.</em> </li>
<li> <strong class="uidlink"><a href="Bio.NetCatch-module.html">Bio.NetCatch</a></strong>: <em class="summary">NetCatch enables the user to scan a list of labelled urls and
select a subset to read into a file.</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> </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>: <em class="summary">Base class for Residue, Chain, Model and Structure classes.</em> </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> </li>
<li> <strong class="uidlink"><a href="Bio.PDB.MMCIFParser-module.html">Bio.PDB.MMCIFParser</a></strong> </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>: <em class="summary">Interface for the program NACCESS - http://wolf.bms.umist.ac.uk/naccess/</em> </li>
<li> <strong class="uidlink"><a href="Bio.PDB.NeighborSearch-module.html">Bio.PDB.NeighborSearch</a></strong> </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> </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>: <em class="summary">Residue class, used by Structure objects.</em> </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 Michel Sanner's MSMS program for the
surface calculation).</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.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.Parsers.spark-module.html">Bio.Parsers.spark</a></strong> </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.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.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 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.PropertyManager-module.html">Bio.PropertyManager</a></strong> </li>
<li> <strong class="uidlink"><a href="Bio.Prosite-module.html">Bio.Prosite</a></strong>: <em class="summary">This module provides code to work with the prosite dat file from
Prosite.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.Prosite.Pattern-module.html">Bio.Prosite.Pattern</a></strong> </li>
<li> <strong class="uidlink"><a href="Bio.Prosite.Prodoc-module.html">Bio.Prosite.Prodoc</a></strong>: <em class="summary">This module provides code to work with the prosite.doc file from
Prosite.</em> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.PubMed-module.html">Bio.PubMed</a></strong>: <em class="summary">This module provides code to work with PubMed from the NCBI.</em> </li>
<li> <strong class="uidlink"><a href="Bio.Rebase-module.html">Bio.Rebase</a></strong>: <em class="summary">This module provides code to work with files from Rebase.</em> </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.FileIndex-module.html">Bio.SCOP.FileIndex</a></strong> </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.SGMLExtractor-module.html">Bio.SGMLExtractor</a></strong>: <em class="summary">Code for more fancy file handles.</em> </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.Saf-module.html">Bio.Saf</a></strong>: <em class="summary">Parser for SAF (Simple Alignment Format).</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.Saf.Record-module.html">Bio.Saf.Record</a></strong>: <em class="summary">Martel based parser to read SAF formatted files.</em> </li>
<li> <strong class="uidlink"><a href="Bio.Saf.saf_format-module.html">Bio.Saf.saf_format</a></strong>: <em class="summary">Martel based parser to read SAF formatted files.</em> </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> </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.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.ClustalIO-module.html">Bio.SeqIO.ClustalIO</a></strong>: <em class="summary">Bio.SeqIO support for the "clustal" (aka ClustalW) 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> </li>
<li> <strong class="uidlink"><a href="Bio.SeqIO.NexusIO-module.html">Bio.SeqIO.NexusIO</a></strong>: <em class="summary">Bio.SeqIO support for the "nexus" file format.</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.PhylipIO-module.html">Bio.SeqIO.PhylipIO</a></strong>: <em class="summary">Bio.SeqIO support for the "phylip" (PHYLIP) file format.</em> </li>
<li> <strong class="uidlink"><a href="Bio.SeqIO.StockholmIO-module.html">Bio.SeqIO.StockholmIO</a></strong>: <em class="summary">Bio.SeqIO support for the "stockholm" (aka PFAM) 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>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.SeqRecord-module.html">Bio.SeqRecord</a></strong> </li>
<li> <strong class="uidlink"><a href="Bio.SeqUtils-module.html">Bio.SeqUtils</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.SeqUtils.CheckSum-module.html">Bio.SeqUtils.CheckSum</a></strong> </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> </li>
<li> <strong class="uidlink"><a href="Bio.SeqUtils.ProtParam-module.html">Bio.SeqUtils.ProtParam</a></strong> </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 (new) ACE files output by PHRAP.</em> </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.Std-module.html">Bio.Std</a></strong> </li>
<li> <strong class="uidlink"><a href="Bio.StdHandler-module.html">Bio.StdHandler</a></strong> </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">Parsers for file formats from the SwissProt database.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.SwissProt.KeyWList-module.html">Bio.SwissProt.KeyWList</a></strong>: <em class="summary">This module provides code to work with the keywlist.txt file from
SwissProt.</em> </li>
<li> <strong class="uidlink"><a href="Bio.SwissProt.SProt-module.html">Bio.SwissProt.SProt</a></strong>: <em class="summary">This module provides code to work with the sprotXX.dat file from
SwissProt.</em> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.Transcribe-module.html">Bio.Transcribe</a></strong> </li>
<li> <strong class="uidlink"><a href="Bio.Translate-module.html">Bio.Translate</a></strong> </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> </li>
<li> <strong class="uidlink"><a href="Bio.WWW-module.html">Bio.WWW</a></strong>: <em class="summary">Deal with various biological databases and services on the web.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.WWW.ExPASy-module.html">Bio.WWW.ExPASy</a></strong>: <em class="summary">This module provides code to access resources at ExPASy over the
WWW.</em> </li>
<li> <strong class="uidlink"><a href="Bio.WWW.InterPro-module.html">Bio.WWW.InterPro</a></strong>: <em class="summary">This module is deprecated; its functions are now available from
Bio.InterPro.</em> </li>
<li> <strong class="uidlink"><a href="Bio.WWW.NCBI-module.html">Bio.WWW.NCBI</a></strong>: <em class="summary">Provides code to access NCBI over the WWW.</em> </li>
<li> <strong class="uidlink"><a href="Bio.WWW.SCOP-module.html">Bio.WWW.SCOP</a></strong>: <em class="summary">This module is deprecated; its functions are now available from
Bio.SCOP.</em> </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> <strong class="uidlink"><a href="Bio.Writer-module.html">Bio.Writer</a></strong> </li>
<li> <strong class="uidlink"><a href="Bio.biblio-module.html">Bio.biblio</a></strong>: <em class="summary">This file implements a SOAP interface into the Bibliographic
database of the European Bioinformatics Institute.</em> </li>
<li> <strong class="uidlink"><a href="Bio.builders-module.html">Bio.builders</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.builders.Search-module.html">Bio.builders.Search</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.builders.Search.search-module.html">Bio.builders.Search.search</a></strong> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.builders.SeqRecord-module.html">Bio.builders.SeqRecord</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.builders.SeqRecord.sequence-module.html">Bio.builders.SeqRecord.sequence</a></strong> </li>
</ul>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.config-module.html">Bio.config</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.config.DBRegistry-module.html">Bio.config.DBRegistry</a></strong>: <em class="summary">Implements Registry to access databases.</em> </li>
<li> <strong class="uidlink"><a href="Bio.config.FormatRegistry-module.html">Bio.config.FormatRegistry</a></strong>: <em class="summary">Implements a Registry to store Martel-type format expressions.</em> </li>
<li> <strong class="uidlink"><a href="Bio.config.Registry-module.html">Bio.config.Registry</a></strong>: <em class="summary">This module implements some base classes used in the Registry
system for Biopython.</em> </li>
<li> <strong class="uidlink"><a href="Bio.config.SeqDBRegistry-module.html">Bio.config.SeqDBRegistry</a></strong>: <em class="summary">This module handles seqdatabase.INI file.</em> </li>
<li class="private"> <strong class="uidlink"><a href="Bio.config._stanzaformat-module.html">Bio.config._stanzaformat</a></strong>: <em class="summary">This module reads and writes (actually, write not implemented yet)
files in the OBF stanza format.</em> </li>
<li class="private"> <strong class="uidlink"><a href="Bio.config._support-module.html">Bio.config._support</a></strong>: <em class="summary">Support code for dealing with registries.</em> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.dbdefs-module.html">Bio.dbdefs</a></strong>
<ul>
<li class="private"> <strong class="uidlink"><a href="Bio.dbdefs._support-module.html">Bio.dbdefs._support</a></strong> </li>
<li> <strong class="uidlink"><a href="Bio.dbdefs.embl-module.html">Bio.dbdefs.embl</a></strong> </li>
<li> <strong class="uidlink"><a href="Bio.dbdefs.fasta-module.html">Bio.dbdefs.fasta</a></strong>: <em class="summary">Database definitions for retrieval of FASTA formatted sequences.</em> </li>
<li> <strong class="uidlink"><a href="Bio.dbdefs.genbank-module.html">Bio.dbdefs.genbank</a></strong> </li>
<li> <strong class="uidlink"><a href="Bio.dbdefs.interpro-module.html">Bio.dbdefs.interpro</a></strong> </li>
<li> <strong class="uidlink"><a href="Bio.dbdefs.medline-module.html">Bio.dbdefs.medline</a></strong>: <em class="summary">Database definitions for retrieval of Medline information.</em> </li>
<li> <strong class="uidlink"><a href="Bio.dbdefs.pdb-module.html">Bio.dbdefs.pdb</a></strong> </li>
<li> <strong class="uidlink"><a href="Bio.dbdefs.prodoc-module.html">Bio.dbdefs.prodoc</a></strong> </li>
<li> <strong class="uidlink"><a href="Bio.dbdefs.prosite-module.html">Bio.dbdefs.prosite</a></strong> </li>
<li> <strong class="uidlink"><a href="Bio.dbdefs.swissprot-module.html">Bio.dbdefs.swissprot</a></strong> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.distance-module.html">Bio.distance</a></strong>: <em class="summary">This module provides code for various distance measures.</em> </li>
<li> <strong class="uidlink"><a href="Bio.expressions-module.html">Bio.expressions</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.expressions.blast-module.html">Bio.expressions.blast</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.expressions.blast.ncbiblast-module.html">Bio.expressions.blast.ncbiblast</a></strong> </li>
<li> <strong class="uidlink"><a href="Bio.expressions.blast.wublast-module.html">Bio.expressions.blast.wublast</a></strong> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.expressions.blocks-module.html">Bio.expressions.blocks</a></strong> </li>
<li> <strong class="uidlink"><a href="Bio.expressions.embl-module.html">Bio.expressions.embl</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.expressions.embl.embl65-module.html">Bio.expressions.embl.embl65</a></strong>: <em class="summary">Format from EMBL Nucleotide Sequence Database Release 65, December
2000</em> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.expressions.fasta-module.html">Bio.expressions.fasta</a></strong> </li>
<li> <strong class="uidlink"><a href="Bio.expressions.genbank-module.html">Bio.expressions.genbank</a></strong>: <em class="summary">Martel based parser to read GenBank formatted files.</em> </li>
<li> <strong class="uidlink"><a href="Bio.expressions.hmmpfam-module.html">Bio.expressions.hmmpfam</a></strong>: <em class="summary">Martel expression for the hmmpfam database search program in hmmer.</em> </li>
<li> <strong class="uidlink"><a href="Bio.expressions.swissprot-module.html">Bio.expressions.swissprot</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.expressions.swissprot.ipi-module.html">Bio.expressions.swissprot.ipi</a></strong>: <em class="summary">Expression for IPI format.</em> </li>
<li> <strong class="uidlink"><a href="Bio.expressions.swissprot.speclist-module.html">Bio.expressions.swissprot.speclist</a></strong>: <em class="summary">Parser for the SPECLIST.TXT file in SWISS-PROT.</em> </li>
<li> <strong class="uidlink"><a href="Bio.expressions.swissprot.sprot38-module.html">Bio.expressions.swissprot.sprot38</a></strong>: <em class="summary">Parser for the SWISS-PROT 38 format.</em> </li>
<li> <strong class="uidlink"><a href="Bio.expressions.swissprot.sprot40-module.html">Bio.expressions.swissprot.sprot40</a></strong> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.expressions.transfac-module.html">Bio.expressions.transfac</a></strong>: <em class="summary">A Martel format to parse the output from transfac.</em> </li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.formatdefs-module.html">Bio.formatdefs</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.formatdefs.embl-module.html">Bio.formatdefs.embl</a></strong> </li>
<li> <strong class="uidlink"><a href="Bio.formatdefs.genbank-module.html">Bio.formatdefs.genbank</a></strong> </li>
<li> <strong class="uidlink"><a href="Bio.formatdefs.search-module.html">Bio.formatdefs.search</a></strong> </li>
<li> <strong class="uidlink"><a href="Bio.formatdefs.sequence-module.html">Bio.formatdefs.sequence</a></strong> </li>
<li> <strong class="uidlink"><a href="Bio.formatdefs.swissprot-module.html">Bio.formatdefs.swissprot</a></strong> </li>
</ul>
</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.listfns-module.html">Bio.listfns</a></strong>: <em class="summary">This provides useful general functions for working with lists.</em> </li>
<li> <strong class="uidlink"><a href="Bio.mathfns-module.html">Bio.mathfns</a></strong>: <em class="summary">This provides useful general math tools.</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.stringfns-module.html">Bio.stringfns</a></strong>: <em class="summary">This provides useful general functions for working with strings.</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>
<li> <strong class="uidlink"><a href="Bio.utils-module.html">Bio.utils</a></strong> </li>
<li> <strong class="uidlink"><a href="Bio.writers-module.html">Bio.writers</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.writers.SeqRecord-module.html">Bio.writers.SeqRecord</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.writers.SeqRecord.embl-module.html">Bio.writers.SeqRecord.embl</a></strong> </li>
<li> <strong class="uidlink"><a href="Bio.writers.SeqRecord.empty-module.html">Bio.writers.SeqRecord.empty</a></strong> </li>
<li> <strong class="uidlink"><a href="Bio.writers.SeqRecord.fasta-module.html">Bio.writers.SeqRecord.fasta</a></strong> </li>
</ul>
</li>
</ul>
</li>
</ul></td></tr>
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