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<center><b>
[ <a href="module-tree.html">Module Hierarchy</a>
| <a href="class-tree.html">Class Hierarchy</a> ]
</b></center><br />
<h1 class="epydoc">Class Hierarchy</h1>
<ul class="nomargin-top">
<li> <strong class="uidlink"><a href="Bio.Sequencing.Ace.ACEFileRecord-class.html">Bio.Sequencing.Ace.ACEFileRecord</a></strong>:
<em class="summary">Holds data of an ACE file.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.GenBank.LocationParser.AbsoluteLocation-class.html">Bio.GenBank.LocationParser.AbsoluteLocation</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.Application.AbstractCommandline-class.html">Bio.Application.AbstractCommandline</a></strong>:
<em class="summary">Generic interface for running applications from biopython.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.AlignAce.Applications.AlignAceCommandline-class.html">Bio.AlignAce.Applications.AlignAceCommandline</a></strong>:
<em class="summary">Create a commandline for the AlignAce program.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Blast.Applications.BlastallCommandline-class.html">Bio.Blast.Applications.BlastallCommandline</a></strong>:
<em class="summary">Create a commandline for the blastall program from NCBI.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.AlignAce.Applications.CompareAceCommandline-class.html">Bio.AlignAce.Applications.CompareAceCommandline</a></strong>:
<em class="summary">Create a commandline for the CompareAce program.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Emboss.Applications.EConsenseCommandline-class.html">Bio.Emboss.Applications.EConsenseCommandline</a></strong>:
<em class="summary">Commandline object for the econsense program from EMBOSS.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Emboss.Applications.EInvertedCommandline-class.html">Bio.Emboss.Applications.EInvertedCommandline</a></strong>:
<em class="summary">Commandline object for the einverted program from EMBOSS.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Emboss.Applications.ENeighborCommandline-class.html">Bio.Emboss.Applications.ENeighborCommandline</a></strong>:
<em class="summary">Commandline object for the eneighbor program from EMBOSS.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Emboss.Applications.EProtDistCommandline-class.html">Bio.Emboss.Applications.EProtDistCommandline</a></strong>:
<em class="summary">Commandline object for the eprotdist program from EMBOSS.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Emboss.Applications.EProtParsCommandline-class.html">Bio.Emboss.Applications.EProtParsCommandline</a></strong>:
<em class="summary">Commandline object for the eprotpars program from EMBOSS.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Emboss.Applications.ESeqBootCommandline-class.html">Bio.Emboss.Applications.ESeqBootCommandline</a></strong>:
<em class="summary">Commandline object for the eseqboot program from EMBOSS.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Emboss.Applications.ETandemCommandline-class.html">Bio.Emboss.Applications.ETandemCommandline</a></strong>:
<em class="summary">Commandline object for the etandem program from EMBOSS.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Emboss.Applications.Est2GenomeCommandline-class.html">Bio.Emboss.Applications.Est2GenomeCommandline</a></strong>:
<em class="summary">Commandline object for the est2genome program from EMBOSS.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Blast.Applications.FastacmdCommandline-class.html">Bio.Blast.Applications.FastacmdCommandline</a></strong>:
<em class="summary">Create a commandline for the fasta program from NCBI.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Emboss.Applications.FuzznucCommandline-class.html">Bio.Emboss.Applications.FuzznucCommandline</a></strong>:
<em class="summary">Commandline object for the fuzznuc program from EMBOSS.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Emboss.Applications.PalindromeCommandline-class.html">Bio.Emboss.Applications.PalindromeCommandline</a></strong>:
<em class="summary">Commandline object for the palindrome program from EMBOSS.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Emboss.Applications.Primer3Commandline-class.html">Bio.Emboss.Applications.Primer3Commandline</a></strong>:
<em class="summary">Commandline object for the Primer3 interface from EMBOSS.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Emboss.Applications.PrimerSearchCommandline-class.html">Bio.Emboss.Applications.PrimerSearchCommandline</a></strong>:
<em class="summary">Commandline object for the primersearch program from EMBOSS.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Emboss.Applications.TranalignCommandline-class.html">Bio.Emboss.Applications.TranalignCommandline</a></strong>:
<em class="summary">Commandline object for the tranalign program from EMBOSS.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Emboss.Applications.WaterCommandline-class.html">Bio.Emboss.Applications.WaterCommandline</a></strong>:
<em class="summary">Commandline object for the water program from EMBOSS.</em>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.ParserSupport.AbstractConsumer-class.html">Bio.ParserSupport.AbstractConsumer</a></strong>:
<em class="summary">Base class for other Consumers.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.Affy.CelFile.CelConsumer-class.html">Bio.Affy.CelFile.CelConsumer</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.ParserSupport.TaggingConsumer-class.html">Bio.ParserSupport.TaggingConsumer</a></strong>:
<em class="summary">A Consumer that tags the data stream with the event and prints it
to a handle.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.GenBank._BaseGenBankConsumer-class.html">Bio.GenBank._BaseGenBankConsumer</a></strong>:
<em class="summary">Abstract GenBank consumer providing useful general functions.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.GenBank._FeatureConsumer-class.html">Bio.GenBank._FeatureConsumer</a></strong>:
<em class="summary">Create a SeqRecord object with Features to return.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.GenBank._RecordConsumer-class.html">Bio.GenBank._RecordConsumer</a></strong>:
<em class="summary">Create a GenBank Record object from scanner generated information.</em>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.Blast.NCBIStandalone._BlastConsumer-class.html" onclick="show_private();">Bio.Blast.NCBIStandalone._BlastConsumer</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.Blast.NCBIStandalone._BlastErrorConsumer-class.html" onclick="show_private();">Bio.Blast.NCBIStandalone._BlastErrorConsumer</a></strong>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.SwissProt.KeyWList._ListConsumer-class.html" onclick="show_private();">Bio.SwissProt.KeyWList._ListConsumer</a></strong>:
<em class="summary">Consumer that converts a keywlist.txt file into a list of keywords.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Blast.NCBIStandalone._PSIBlastConsumer-class.html" onclick="show_private();">Bio.Blast.NCBIStandalone._PSIBlastConsumer</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.Emboss.Primer._Primer3RecordConsumer-class.html" onclick="show_private();">Bio.Emboss.Primer._Primer3RecordConsumer</a></strong>:
<em class="summary">Get output from prime3 into a Primer3Record</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Emboss.Primer._PrimerSearchRecordConsumer-class.html" onclick="show_private();">Bio.Emboss.Primer._PrimerSearchRecordConsumer</a></strong>:
<em class="summary">Get output from primersearch into a PrimerSearchOutputRecord</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Medline._RecordConsumer-class.html" onclick="show_private();">Bio.Medline._RecordConsumer</a></strong>:
<em class="summary">Consumer that converts a Medline record to a Record object.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Gobase._RecordConsumer-class.html" onclick="show_private();">Bio.Gobase._RecordConsumer</a></strong>:
<em class="summary">Consumer that converts a gobase record to a Record object.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.UniGene._RecordConsumer-class.html" onclick="show_private();">Bio.UniGene._RecordConsumer</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.Prosite.Prodoc._RecordConsumer-class.html" onclick="show_private();">Bio.Prosite.Prodoc._RecordConsumer</a></strong>:
<em class="summary">Consumer that converts a Prodoc record to a Record object.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Enzyme._RecordConsumer-class.html" onclick="show_private();">Bio.Enzyme._RecordConsumer</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.PopGen.FDist._RecordConsumer-class.html">Bio.PopGen.FDist._RecordConsumer</a></strong>:
<em class="summary">Consumer that converts a FDist record to a Record object.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.SwissProt.SProt._RecordConsumer-class.html" onclick="show_private();">Bio.SwissProt.SProt._RecordConsumer</a></strong>:
<em class="summary">Consumer that converts a SwissProt record to a Record object.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Sequencing.Phd._RecordConsumer-class.html" onclick="show_private();">Bio.Sequencing.Phd._RecordConsumer</a></strong>:
<em class="summary">Consumer that converts a PHD record to a Record object.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Rebase._RecordConsumer-class.html" onclick="show_private();">Bio.Rebase._RecordConsumer</a></strong>:
<em class="summary">Consumer that converts a rebase record to a Record object.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Prosite._RecordConsumer-class.html" onclick="show_private();">Bio.Prosite._RecordConsumer</a></strong>:
<em class="summary">Consumer that converts a Prosite record to a Record object.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Sequencing.Ace._RecordConsumer-class.html" onclick="show_private();">Bio.Sequencing.Ace._RecordConsumer</a></strong>:
<em class="summary">Reads the ace tags into data records.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.PopGen.GenePop._RecordConsumer-class.html" onclick="show_private();">Bio.PopGen.GenePop._RecordConsumer</a></strong>:
<em class="summary">Consumer that converts a GenePop record to a Record object.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.SwissProt.SProt._SequenceConsumer-class.html" onclick="show_private();">Bio.SwissProt.SProt._SequenceConsumer</a></strong>:
<em class="summary">Consumer that converts a SwissProt record to a SeqRecord object.</em>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.HMM.DynamicProgramming.AbstractDPAlgorithms-class.html">Bio.HMM.DynamicProgramming.AbstractDPAlgorithms</a></strong>:
<em class="summary">An abstract class to calculate forward and backward probabiliies.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.HMM.DynamicProgramming.LogDPAlgorithms-class.html">Bio.HMM.DynamicProgramming.LogDPAlgorithms</a></strong>:
<em class="summary">Implement forward and backward algorithms using a log approach.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.HMM.DynamicProgramming.ScaledDPAlgorithms-class.html">Bio.HMM.DynamicProgramming.ScaledDPAlgorithms</a></strong>:
<em class="summary">Implement forward and backward algorithms using a rescaling
approach.</em>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.NeuralNetwork.BackPropagation.Layer.AbstractLayer-class.html">Bio.NeuralNetwork.BackPropagation.Layer.AbstractLayer</a></strong>:
<em class="summary">Abstract base class for all layers.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer-class.html">Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.NeuralNetwork.BackPropagation.Layer.InputLayer-class.html">Bio.NeuralNetwork.BackPropagation.Layer.InputLayer</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer-class.html">Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer</a></strong>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.ParserSupport.AbstractParser-class.html">Bio.ParserSupport.AbstractParser</a></strong>:
<em class="summary">Base class for other parsers.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.Sequencing.Ace.ACEParser-class.html">Bio.Sequencing.Ace.ACEParser</a></strong>:
<em class="summary">Parses full ACE file in list of contigs.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.AlignAce.Parser.AlignAceParser-class.html">Bio.AlignAce.Parser.AlignAceParser</a></strong>:
<em class="summary">Parses AlignAce data into a sequence of Motifs.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Blast.NCBIStandalone.BlastErrorParser-class.html">Bio.Blast.NCBIStandalone.BlastErrorParser</a></strong>:
<em class="summary">Attempt to catch and diagnose BLAST errors while parsing.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Blast.NCBIStandalone.BlastParser-class.html">Bio.Blast.NCBIStandalone.BlastParser</a></strong>:
<em class="summary">Parses BLAST data into a Record.Blast object.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Blast.NCBIWWW.BlastParser-class.html">Bio.Blast.NCBIWWW.BlastParser</a></strong>:
<em class="summary">Parses WWW BLAST data into a Record.Blast object.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.AlignAce.Parser.CompareAceParser-class.html">Bio.AlignAce.Parser.CompareAceParser</a></strong>:
<em class="summary">Parses CompareAce output to usable form</em>
</li>
<li> <strong class="uidlink"><a href="Bio.SwissProt.KeyWList.ListParser-class.html">Bio.SwissProt.KeyWList.ListParser</a></strong>:
<em class="summary">Parses keywlist.txt data into a list of keywords.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.MEME.Parser.MASTParser-class.html">Bio.MEME.Parser.MASTParser</a></strong>:
<em class="summary">Parser for MAST text output.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.MEME.Parser.MEMEParser-class.html">Bio.MEME.Parser.MEMEParser</a></strong>:
<em class="summary">A parser for the text output of the MEME program.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Blast.NCBIStandalone.PSIBlastParser-class.html">Bio.Blast.NCBIStandalone.PSIBlastParser</a></strong>:
<em class="summary">Parses BLAST data into a Record.PSIBlast object.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.SwissProt.SProt.RecordParser-class.html">Bio.SwissProt.SProt.RecordParser</a></strong>:
<em class="summary">Parses SwissProt data into a Record object.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.UniGene.RecordParser-class.html">Bio.UniGene.RecordParser</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.Sequencing.Phd.RecordParser-class.html">Bio.Sequencing.Phd.RecordParser</a></strong>:
<em class="summary">Parses PHD file data into a Record object.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Prosite.RecordParser-class.html">Bio.Prosite.RecordParser</a></strong>:
<em class="summary">Parses Prosite data into a Record object.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Compass.RecordParser-class.html">Bio.Compass.RecordParser</a></strong>:
<em class="summary">Parses compass results into a Record object.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Sequencing.Ace.RecordParser-class.html">Bio.Sequencing.Ace.RecordParser</a></strong>:
<em class="summary">Parses ACE file data into a Record object.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.PopGen.FDist.RecordParser-class.html">Bio.PopGen.FDist.RecordParser</a></strong>:
<em class="summary">Parses FDist data into a Record object.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.PopGen.GenePop.RecordParser-class.html">Bio.PopGen.GenePop.RecordParser</a></strong>:
<em class="summary">Parses GenePop data into a Record object.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Prosite.Prodoc.RecordParser-class.html">Bio.Prosite.Prodoc.RecordParser</a></strong>:
<em class="summary">Parses Prodoc data into a Record object.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Enzyme.RecordParser-class.html">Bio.Enzyme.RecordParser</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.Medline.RecordParser-class.html">Bio.Medline.RecordParser</a></strong>:
<em class="summary">Parses Medline data into a Record object.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.SwissProt.SProt.SequenceParser-class.html">Bio.SwissProt.SProt.SequenceParser</a></strong>:
<em class="summary">Parses SwissProt data into a standard SeqRecord object.</em>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.SeqFeature.AbstractPosition-class.html">Bio.SeqFeature.AbstractPosition</a></strong>:
<em class="summary">Abstract base class representing a position.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.SeqFeature.AfterPosition-class.html">Bio.SeqFeature.AfterPosition</a></strong>:
<em class="summary">Specify a position where the actual location is found after it.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.SeqFeature.BeforePosition-class.html">Bio.SeqFeature.BeforePosition</a></strong>:
<em class="summary">Specify a position where the actual location occurs before it.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.SeqFeature.BetweenPosition-class.html">Bio.SeqFeature.BetweenPosition</a></strong>:
<em class="summary">Specify the position of a boundary between two coordinates.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.SeqFeature.ExactPosition-class.html">Bio.SeqFeature.ExactPosition</a></strong>:
<em class="summary">Specify the specific position of a boundary.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.SeqFeature.OneOfPosition-class.html">Bio.SeqFeature.OneOfPosition</a></strong>:
<em class="summary">Specify a position where the location can be multiple positions.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.SeqFeature.WithinPosition-class.html">Bio.SeqFeature.WithinPosition</a></strong>:
<em class="summary">Specify the position of a boundary within some coordinates.</em>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.PDB.AbstractPropertyMap.AbstractPropertyMap-class.html">Bio.PDB.AbstractPropertyMap.AbstractPropertyMap</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.PDB.AbstractPropertyMap.AbstractAtomPropertyMap-class.html">Bio.PDB.AbstractPropertyMap.AbstractAtomPropertyMap</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.PDB.NACCESS.NACCESS_atomic-class.html">Bio.PDB.NACCESS.NACCESS_atomic</a></strong>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.PDB.AbstractPropertyMap.AbstractResiduePropertyMap-class.html">Bio.PDB.AbstractPropertyMap.AbstractResiduePropertyMap</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.PDB.DSSP%27.DSSP-class.html">Bio.PDB.DSSP'.DSSP</a></strong>:
<em class="summary">Run DSSP on a pdb file, and provide a handle to the DSSP secondary
structure and accessibility.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.PDB.NACCESS.NACCESS-class.html">Bio.PDB.NACCESS.NACCESS</a></strong>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.PDB.HSExposure.ExposureCN-class.html">Bio.PDB.HSExposure.ExposureCN</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.PDB.ResidueDepth%27.ResidueDepth-class.html">Bio.PDB.ResidueDepth'.ResidueDepth</a></strong>:
<em class="summary">Calculate residue and CA depth for all residues.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.PDB.HSExposure._AbstractHSExposure-class.html" onclick="show_private();">Bio.PDB.HSExposure._AbstractHSExposure</a></strong>:
<em class="summary">Abstract class to calculate Half-Sphere Exposure (HSE).</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.PDB.HSExposure.HSExposureCA-class.html">Bio.PDB.HSExposure.HSExposureCA</a></strong>:
<em class="summary">Class to calculate HSE based on the approximate CA-CB vectors,
using three consecutive CA positions.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.PDB.HSExposure.HSExposureCB-class.html">Bio.PDB.HSExposure.HSExposureCB</a></strong>:
<em class="summary">Class to calculate HSE based on the real CA-CB vectors.</em>
</li>
</ul>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.GA.Selection.Abstract.AbstractSelection-class.html">Bio.GA.Selection.Abstract.AbstractSelection</a></strong>:
<em class="summary">Base class for Selector classes.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.GA.Selection.Diversity.DiversitySelection-class.html">Bio.GA.Selection.Diversity.DiversitySelection</a></strong>:
<em class="summary">Implement diversity selection.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.GA.Selection.RouletteWheel.RouletteWheelSelection-class.html">Bio.GA.Selection.RouletteWheel.RouletteWheelSelection</a></strong>:
<em class="summary">Roulette wheel selection proportional to individuals fitness.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.GA.Selection.Tournament.TournamentSelection-class.html">Bio.GA.Selection.Tournament.TournamentSelection</a></strong>:
<em class="summary">Implement tournament style selection.</em>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.HMM.Trainer.AbstractTrainer-class.html">Bio.HMM.Trainer.AbstractTrainer</a></strong>:
<em class="summary">Provide generic functionality needed in all trainers.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.HMM.Trainer.BaumWelchTrainer-class.html">Bio.HMM.Trainer.BaumWelchTrainer</a></strong>:
<em class="summary">Trainer that uses the Baum-Welch algorithm to estimate parameters.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.HMM.Trainer.KnownStateTrainer-class.html">Bio.HMM.Trainer.KnownStateTrainer</a></strong>:
<em class="summary">Estimate probabilities with known state sequences.</em>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="BioSQL.BioSeqDatabase.Adaptor-class.html">BioSQL.BioSeqDatabase.Adaptor</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.Search.Algorithm-class.html">Bio.Search.Algorithm</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.AlignAce.Parser.AlignAceConsumer-class.html">Bio.AlignAce.Parser.AlignAceConsumer</a></strong>:
<em class="summary">The general purpose consumer for the AlignAceScanner.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.AlignAce.Scanner.AlignAceScanner-class.html">Bio.AlignAce.Scanner.AlignAceScanner</a></strong>:
<em class="summary">Scannner for AlignACE output</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Align.Generic.Alignment-class.html">Bio.Align.Generic.Alignment</a></strong>:
<em class="summary">Represent a set of alignments.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.Clustalw.ClustalAlignment-class.html">Bio.Clustalw.ClustalAlignment</a></strong>:
<em class="summary">Work with the clustal aligment format.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.FSSP.FSSPTools.FSSPAlign-class.html">Bio.FSSP.FSSPTools.FSSPAlign</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.Fasta.FastaAlign.FastaAlignment-class.html">Bio.Fasta.FastaAlign.FastaAlignment</a></strong>:
<em class="summary">Work with the Fasta Alignment format.</em>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.Blast.Record.Alignment-class.html">Bio.Blast.Record.Alignment</a></strong>:
<em class="summary">Stores information about one hit in the alignments section.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.AlignIO.Interfaces.AlignmentIterator-class.html">Bio.AlignIO.Interfaces.AlignmentIterator</a></strong>:
<em class="summary">Base class for building Alignment iterators.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.AlignIO.ClustalIO.ClustalIterator-class.html">Bio.AlignIO.ClustalIO.ClustalIterator</a></strong>:
<em class="summary">Clustalw alignment iterator.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.AlignIO.EmbossIO.EmbossIterator-class.html">Bio.AlignIO.EmbossIO.EmbossIterator</a></strong>:
<em class="summary">Emboss alignment iterator</em>
</li>
<li> <strong class="uidlink"><a href="Bio.AlignIO.FastaIO.FastaM10Iterator-class.html">Bio.AlignIO.FastaIO.FastaM10Iterator</a></strong>:
<em class="summary">Alignment iterator for the FASTA tool's pairwise alignment output.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.AlignIO.PhylipIO.PhylipIterator-class.html">Bio.AlignIO.PhylipIO.PhylipIterator</a></strong>:
<em class="summary">Reads a Phylip alignment file returning an Alignment object
iterator.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.AlignIO.StockholmIO.StockholmIterator-class.html">Bio.AlignIO.StockholmIO.StockholmIterator</a></strong>:
<em class="summary">Loads a Stockholm file from PFAM into Alignment objects.</em>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.AlignIO.Interfaces.AlignmentWriter-class.html">Bio.AlignIO.Interfaces.AlignmentWriter</a></strong>:
<em class="summary">Base class for building Alignment writers.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.AlignIO.Interfaces.SequentialAlignmentWriter-class.html">Bio.AlignIO.Interfaces.SequentialAlignmentWriter</a></strong>:
<em class="summary">Base class for building Alignment writers.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.AlignIO.ClustalIO.ClustalWriter-class.html">Bio.AlignIO.ClustalIO.ClustalWriter</a></strong>:
<em class="summary">Clustalw alignment writer.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.AlignIO.EmbossIO.EmbossWriter-class.html">Bio.AlignIO.EmbossIO.EmbossWriter</a></strong>:
<em class="summary">Emboss alignment writer</em>
</li>
<li> <strong class="uidlink"><a href="Bio.AlignIO.PhylipIO.PhylipWriter-class.html">Bio.AlignIO.PhylipIO.PhylipWriter</a></strong>:
<em class="summary">Phylip alignment writer.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.AlignIO.StockholmIO.StockholmWriter-class.html">Bio.AlignIO.StockholmIO.StockholmWriter</a></strong>:
<em class="summary">Stockholm/PFAM alignment writer.</em>
</li>
</ul>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.Alphabet.Alphabet-class.html">Bio.Alphabet.Alphabet</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.Prosite.Pattern.PrositeAlphabet-class.html">Bio.Prosite.Pattern.PrositeAlphabet</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet-class.html">Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet</a></strong>:
<em class="summary">Alphabet of a simple Schema for DNA sequences.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Alphabet.SingleLetterAlphabet-class.html">Bio.Alphabet.SingleLetterAlphabet</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.Alphabet.NucleotideAlphabet-class.html">Bio.Alphabet.NucleotideAlphabet</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.Alphabet.DNAAlphabet-class.html">Bio.Alphabet.DNAAlphabet</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.Alphabet.IUPAC.ExtendedIUPACDNA-class.html">Bio.Alphabet.IUPAC.ExtendedIUPACDNA</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.Alphabet.IUPAC.IUPACAmbiguousDNA-class.html">Bio.Alphabet.IUPAC.IUPACAmbiguousDNA</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.Alphabet.IUPAC.IUPACUnambiguousDNA-class.html">Bio.Alphabet.IUPAC.IUPACUnambiguousDNA</a></strong>
</li>
</ul>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.Alphabet.RNAAlphabet-class.html">Bio.Alphabet.RNAAlphabet</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.Alphabet.IUPAC.IUPACAmbiguousRNA-class.html">Bio.Alphabet.IUPAC.IUPACAmbiguousRNA</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.Alphabet.IUPAC.IUPACUnambiguousRNA-class.html">Bio.Alphabet.IUPAC.IUPACUnambiguousRNA</a></strong>
</li>
</ul>
</li>
</ul>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.Alphabet.ProteinAlphabet-class.html">Bio.Alphabet.ProteinAlphabet</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.Alphabet.IUPAC.ExtendedIUPACProtein-class.html">Bio.Alphabet.IUPAC.ExtendedIUPACProtein</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.Alphabet.Reduced.HPModel-class.html">Bio.Alphabet.Reduced.HPModel</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.Alphabet.IUPAC.IUPACProtein-class.html">Bio.Alphabet.IUPAC.IUPACProtein</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.Alphabet.Reduced.Murphy10-class.html">Bio.Alphabet.Reduced.Murphy10</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.Alphabet.Reduced.Murphy15-class.html">Bio.Alphabet.Reduced.Murphy15</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.Alphabet.Reduced.Murphy4-class.html">Bio.Alphabet.Reduced.Murphy4</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.Alphabet.Reduced.Murphy8-class.html">Bio.Alphabet.Reduced.Murphy8</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.Alphabet.Reduced.PC5-class.html">Bio.Alphabet.Reduced.PC5</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.SeqUtils.ProteinX-class.html">Bio.SeqUtils.ProteinX</a></strong>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.Alphabet.SecondaryStructure-class.html">Bio.Alphabet.SecondaryStructure</a></strong>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.Alphabet.ThreeLetterProtein-class.html">Bio.Alphabet.ThreeLetterProtein</a></strong>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.Alphabet.AlphabetEncoder-class.html">Bio.Alphabet.AlphabetEncoder</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.Alphabet.Gapped-class.html">Bio.Alphabet.Gapped</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.Alphabet.HasStopCodon-class.html">Bio.Alphabet.HasStopCodon</a></strong>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.Data.CodonTable.AmbiguousForwardTable-class.html">Bio.Data.CodonTable.AmbiguousForwardTable</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.GA.Repair.Stabilizing.AmbiguousRepair-class.html">Bio.GA.Repair.Stabilizing.AmbiguousRepair</a></strong>:
<em class="summary">Perform repair to reduce the number of Ambiguous genes in a genome.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Application.ApplicationResult-class.html">Bio.Application.ApplicationResult</a></strong>:
<em class="summary">Make results of a program available through a standard interface.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.SCOP.Astral-class.html">Bio.SCOP.Astral</a></strong>:
<em class="summary">Abstraction of the ASTRAL database, which has sequences for all the
SCOP domains, as well as clusterings by percent id or evalue.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.PopGen.Async.Async-class.html">Bio.PopGen.Async.Async</a></strong>:
<em class="summary">Abstract Asynchronous execution class.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.PopGen.Async.Local.Local-class.html">Bio.PopGen.Async.Local.Local</a></strong>:
<em class="summary">Execution on Local machine.</em>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.PDB.Atom.Atom-class.html">Bio.PDB.Atom.Atom</a></strong>
</li>
<li> <strong class="uidlink">exceptions.AttributeError</strong>
</li>
<li> <strong class="uidlink">xml.sax.xmlreader.AttributesImpl</strong>
<ul>
<li> <strong class="uidlink"><a href="Martel.Parser.MartelAttributeList-class.html">Martel.Parser.MartelAttributeList</a></strong>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.Graphics.Distribution.BarChartDistribution-class.html">Bio.Graphics.Distribution.BarChartDistribution</a></strong>:
<em class="summary">Display the distribution of values as a bunch of bars.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Mindy.SimpleSeqRecord.BaseSeqRecordIndexer-class.html">Bio.Mindy.SimpleSeqRecord.BaseSeqRecordIndexer</a></strong>:
<em class="summary">Base class for indexing using SeqRecord information.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.Mindy.SimpleSeqRecord.FunctionIndexer-class.html">Bio.Mindy.SimpleSeqRecord.FunctionIndexer</a></strong>:
<em class="summary">Indexer to index based on values returned by a function.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Mindy.SimpleSeqRecord.SimpleIndexer-class.html">Bio.Mindy.SimpleSeqRecord.SimpleIndexer</a></strong>:
<em class="summary">Index a file based on .id and .name attributes of a SeqRecord.</em>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.NeuralNetwork.BackPropagation.Network.BasicNetwork-class.html">Bio.NeuralNetwork.BackPropagation.Network.BasicNetwork</a></strong>:
<em class="summary">Represent a Basic Neural Network with three layers.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.GenBank.LocationParser.Between-class.html">Bio.GenBank.LocationParser.Between</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.biblio.Biblio-class.html">Bio.biblio.Biblio</a></strong>:
<em class="summary">this class provides low-level access to the EBI Bibliographics
services exported through SOAP.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.biblio.BiblioCollection-class.html">Bio.biblio.BiblioCollection</a></strong>:
<em class="summary">this class attempts to hide the concept of a collection id from
users.</em>
</li>
<li> <strong class="uidlink"><a href="BioSQL.BioSeqDatabase.BioSeqDatabase-class.html">BioSQL.BioSeqDatabase.BioSeqDatabase</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.DBXRef.BioformatDBName-class.html">Bio.DBXRef.BioformatDBName</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.Mindy.FlatDB.BisectFile-class.html">Bio.Mindy.FlatDB.BisectFile</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.Blast.ParseBlastTable.BlastTableEntry-class.html">Bio.Blast.ParseBlastTable.BlastTableEntry</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.Blast.ParseBlastTable.BlastTableReader-class.html">Bio.Blast.ParseBlastTable.BlastTableReader</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.Blast.ParseBlastTable.BlastTableRec-class.html">Bio.Blast.ParseBlastTable.BlastTableRec</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.Nexus.Nexus.Block-class.html">Bio.Nexus.Nexus.Block</a></strong>:
<em class="summary">Represent a NEXUS block with block name and list of commandlines .</em>
</li>
<li> <strong class="uidlink"><a href="Bio.CAPS.CAPSMap-class.html">Bio.CAPS.CAPSMap</a></strong>:
<em class="summary">A map of an alignment showing all possible dcuts.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Affy.CelFile.CelParser-class.html">Bio.Affy.CelFile.CelParser</a></strong>:
<em class="summary">Takes a handle to an Affymetrix cel file, parses the file and
returns an instance of a CelRecord</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Affy.CelFile.CelRecord-class.html">Bio.Affy.CelFile.CelRecord</a></strong>:
<em class="summary">Stores the information in a cel file</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Affy.CelFile.CelScanner-class.html">Bio.Affy.CelFile.CelScanner</a></strong>:
<em class="summary">Scannner for Affymetrix CEL files.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Nexus.Nodes.Chain-class.html">Bio.Nexus.Nodes.Chain</a></strong>:
<em class="summary">Stores a list of nodes that are linked together.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.Nexus.Trees.Tree-class.html">Bio.Nexus.Trees.Tree</a></strong>:
<em class="summary">Represents a tree using a chain of nodes with on predecessor
(=ancestor) and multiple successors (=subclades).</em>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.Crystal.Chain-class.html">Bio.Crystal.Chain</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.PDB.Dice.ChainSelector-class.html">Bio.PDB.Dice.ChainSelector</a></strong>:
<em class="summary">Only accepts residues with right chainid and between start and end.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Nexus.Nexus.CharBuffer-class.html">Bio.Nexus.Nexus.CharBuffer</a></strong>:
<em class="summary">Helps reading NEXUS-words and characters from a buffer.</em>
</li>
<li> <strong class="uidlink"><a href="Martel.Generate.CheckAssert-class.html">Martel.Generate.CheckAssert</a></strong>
</li>
<li> <strong class="uidlink"><a href="Martel.Generate.CheckAssertNot-class.html">Martel.Generate.CheckAssertNot</a></strong>
</li>
<li> <strong class="uidlink"><a href="Martel.Generate.CheckGroupRef-class.html">Martel.Generate.CheckGroupRef</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.Graphics.DisplayRepresentation.ChromosomeCounts-class.html">Bio.Graphics.DisplayRepresentation.ChromosomeCounts</a></strong>:
<em class="summary">Represent a chromosome with count information.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.sourcegen.ClassHolder-class.html">Bio.EUtils.sourcegen.ClassHolder</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.SeqUtils.CodonUsage.CodonAdaptationIndex-class.html">Bio.SeqUtils.CodonUsage.CodonAdaptationIndex</a></strong>:
<em class="summary">This class implements the codon adaptaion index (CAI) described by
Sharp and Li (Nucleic Acids Res.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Data.CodonTable.CodonTable-class.html">Bio.Data.CodonTable.CodonTable</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.Data.CodonTable.AmbiguousCodonTable-class.html">Bio.Data.CodonTable.AmbiguousCodonTable</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.Data.CodonTable.NCBICodonTable-class.html">Bio.Data.CodonTable.NCBICodonTable</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.Data.CodonTable.NCBICodonTableDNA-class.html">Bio.Data.CodonTable.NCBICodonTableDNA</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.Data.CodonTable.NCBICodonTableRNA-class.html">Bio.Data.CodonTable.NCBICodonTableRNA</a></strong>
</li>
</ul>
</li>
</ul>
</li>
<li> <strong class="uidlink">distutils.core.Command</strong>
</li>
<li> <strong class="uidlink"><a href="Bio.Nexus.Nexus.Commandline-class.html">Bio.Nexus.Nexus.Commandline</a></strong>:
<em class="summary">Represent a commandline as command and options.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Graphics.Comparative.ComparativeScatterPlot-class.html">Bio.Graphics.Comparative.ComparativeScatterPlot</a></strong>:
<em class="summary">Display a scatter-type plot comparing two different kinds of info.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.AlignAce.Parser.CompareAceConsumer-class.html">Bio.AlignAce.Parser.CompareAceConsumer</a></strong>:
<em class="summary">The general purpose consumer for the CompareAceScanner.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.AlignAce.Scanner.CompareAceScanner-class.html">Bio.AlignAce.Scanner.CompareAceScanner</a></strong>:
<em class="summary">Scannner for CompareACE output</em>
</li>
<li> <strong class="uidlink">xml.sax.handler.ContentHandler</strong>:
<em class="summary">Interface for receiving logical document content events.</em>
<ul>
<li> <strong class="uidlink"><a href="Martel.test.test_macros.Capture-class.html">Martel.test.test_macros.Capture</a></strong>
</li>
<li> <strong class="uidlink"><a href="Martel.test.test_delimiter.CatchFields-class.html">Martel.test.test_delimiter.CatchFields</a></strong>
</li>
<li> <strong class="uidlink"><a href="Martel.test.support.CheckGood-class.html">Martel.test.support.CheckGood</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.StdHandler.ConvertHandler-class.html">Bio.StdHandler.ConvertHandler</a></strong>:
<em class="summary">Used to read records and produce output</em>
</li>
<li> <strong class="uidlink"><a href="Martel.test.test_Parser.CountRecords-class.html">Martel.test.test_Parser.CountRecords</a></strong>
</li>
<li> <strong class="uidlink"><a href="Martel.Dispatch.Dispatcher-class.html">Martel.Dispatch.Dispatcher</a></strong>:
<em class="summary">Adapter from the standard SAX events</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.builders.Search.search.BuildSearch-class.html">Bio.builders.Search.search.BuildSearch</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.builders.SeqRecord.sequence.BuildSeqRecord-class.html">Bio.builders.SeqRecord.sequence.BuildSeqRecord</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.Mindy.SimpleSeqRecord.FixDocumentBuilder-class.html">Bio.Mindy.SimpleSeqRecord.FixDocumentBuilder</a></strong>:
<em class="summary">A SAX builder-style class to make a parsed SeqRecord available.</em>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.StdHandler.ConvertDispatchHandler-class.html">Bio.StdHandler.ConvertDispatchHandler</a></strong>:
<em class="summary">Used to read records and produce output through a Dispatcher</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Saf._RecordConsumer-class.html" onclick="show_private();">Bio.Saf._RecordConsumer</a></strong>:
<em class="summary">Create a Saf Record object from scanner generated information.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.LocusLink._RecordConsumer-class.html" onclick="show_private();">Bio.LocusLink._RecordConsumer</a></strong>:
<em class="summary">Create a LocusLink Record object from scanner generated
information.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.CDD._RecordConsumer-class.html" onclick="show_private();">Bio.CDD._RecordConsumer</a></strong>:
<em class="summary">Create a CDD Record object from scanner generated information.</em>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Martel.test.support.Dump-class.html">Martel.test.support.Dump</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.ParserSupport.EventGenerator-class.html">Bio.ParserSupport.EventGenerator</a></strong>:
<em class="summary">Handler to generate events associated with a Martel parsed file.</em>
</li>
<li> <strong class="uidlink"><a href="Martel.test.test_optimize.GetErrorPos-class.html">Martel.test.test_optimize.GetErrorPos</a></strong>
</li>
<li> <strong class="uidlink"><a href="Martel.test.test_attrs.GrabElements-class.html">Martel.test.test_attrs.GrabElements</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.Mindy.XPath.GrabXPathNodes-class.html">Bio.Mindy.XPath.GrabXPathNodes</a></strong>
</li>
<li> <strong class="uidlink"><a href="Martel.LAX.LAX-class.html">Martel.LAX.LAX</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Martel.LAX.LAXAttrs-class.html">Martel.LAX.LAXAttrs</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Martel.LAX.LAXPositions-class.html">Martel.LAX.LAXPositions</a></strong>
</li>
</ul>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.StdHandler.RecognizeHandler-class.html">Bio.StdHandler.RecognizeHandler</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.Blast.NCBIXML._XMLparser-class.html" onclick="show_private();">Bio.Blast.NCBIXML._XMLparser</a></strong>:
<em class="summary">Generic SAX Parser</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.Blast.NCBIXML.BlastParser-class.html">Bio.Blast.NCBIXML.BlastParser</a></strong>:
<em class="summary">Parse XML BLAST data into a Record.Blast object</em>
</li>
</ul>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.POM.ContentModel-class.html">Bio.EUtils.POM.ContentModel</a></strong>:
<em class="summary">Represents and validates a content model.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Sequencing.Ace.Contig-class.html">Bio.Sequencing.Ace.Contig</a></strong>:
<em class="summary">Holds information about a contig from an ACE record.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.GA.Mutation.Simple.ConversionMutation-class.html">Bio.GA.Mutation.Simple.ConversionMutation</a></strong>:
<em class="summary">Potentially mutate any item to another in the alphabet.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Crystal.Crystal-class.html">Bio.Crystal.Crystal</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.Datatypes.DBIds-class.html">Bio.EUtils.Datatypes.DBIds</a></strong>:
<em class="summary">Store a list of identifiers for a database</em>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DBIdsClient.DBIdsClient-class.html">Bio.EUtils.DBIdsClient.DBIdsClient</a></strong>:
<em class="summary">Create a RecordSet either from a search or a set of dbids</em>
</li>
<li> <strong class="uidlink"><a href="BioSQL.BioSeqDatabase.DBServer-class.html">BioSQL.BioSeqDatabase.DBServer</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.DBXRef.DBXRef-class.html">Bio.DBXRef.DBXRef</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.POM.DTDConsumerForSourceGeneration-class.html">Bio.EUtils.POM.DTDConsumerForSourceGeneration</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.Entrez.Parser.DataHandler-class.html">Bio.Entrez.Parser.DataHandler</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.Enzyme.DataRecord-class.html">Bio.Enzyme.DataRecord</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.Search.Database-class.html">Bio.Search.Database</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.Config.DatabaseInfo-class.html">Bio.EUtils.Config.DatabaseInfo</a></strong>:
<em class="summary">stores NCBI's name for the database and its type</em>
</li>
<li> <strong class="uidlink"><a href="BioSQL.Loader.DatabaseLoader-class.html">BioSQL.Loader.DatabaseLoader</a></strong>:
<em class="summary">Load a database with biopython objects.</em>
</li>
<li> <strong class="uidlink"><a href="BioSQL.Loader.DatabaseRemover-class.html">BioSQL.Loader.DatabaseRemover</a></strong>:
<em class="summary">Complement the Loader functionality by fully removing a database.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Blast.Record.DatabaseReport-class.html">Bio.Blast.Record.DatabaseReport</a></strong>:
<em class="summary">Holds information about a database report.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.Blast.Record.Blast-class.html">Bio.Blast.Record.Blast</a></strong>:
<em class="summary">Saves the results from a blast search.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Blast.Record.PSIBlast-class.html">Bio.Blast.Record.PSIBlast</a></strong>:
<em class="summary">Saves the results from a blastpgp search.</em>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.Datatypes.Date-class.html">Bio.EUtils.Datatypes.Date</a></strong>:
<em class="summary">Allow simple Date storage</em>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.Datatypes.DateRange-class.html">Bio.EUtils.Datatypes.DateRange</a></strong>:
<em class="summary">Restrict a search to matches within a date range</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Blast.Record.Description-class.html">Bio.Blast.Record.Description</a></strong>:
<em class="summary">Stores information about one hit in the descriptions section.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Mindy.BaseDB.DictLookup-class.html">Bio.Mindy.BaseDB.DictLookup</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.Mindy.BaseDB.OpenDB-class.html">Bio.Mindy.BaseDB.OpenDB</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.Mindy.FlatDB.BaseFlatDB-class.html">Bio.Mindy.FlatDB.BaseFlatDB</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.Mindy.FlatDB.DiskFlatDB-class.html">Bio.Mindy.FlatDB.DiskFlatDB</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.Mindy.FlatDB.MemoryFlatDB-class.html">Bio.Mindy.FlatDB.MemoryFlatDB</a></strong>
</li>
</ul>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.Mindy.FlatDB.PrimaryNamespace-class.html">Bio.Mindy.FlatDB.PrimaryNamespace</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.Mindy.FlatDB.PrimaryTable-class.html">Bio.Mindy.FlatDB.PrimaryTable</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.Mindy.FlatDB.SecondaryNamespace-class.html">Bio.Mindy.FlatDB.SecondaryNamespace</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.Mindy.FlatDB.SecondaryTable-class.html">Bio.Mindy.FlatDB.SecondaryTable</a></strong>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.Prosite.Prodoc.Dictionary-class.html">Bio.Prosite.Prodoc.Dictionary</a></strong>:
<em class="summary">Accesses a Prodoc file using a dictionary interface.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.SwissProt.SProt.Dictionary-class.html">Bio.SwissProt.SProt.Dictionary</a></strong>:
<em class="summary">Accesses a SwissProt file using a dictionary interface.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Prosite.Dictionary-class.html">Bio.Prosite.Dictionary</a></strong>:
<em class="summary">Accesses a Prosite file using a dictionary interface.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Gobase.Dictionary-class.html">Bio.Gobase.Dictionary</a></strong>:
<em class="summary">Accesses a gobase file using a dictionary interface.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.PubMed.Dictionary-class.html">Bio.PubMed.Dictionary</a></strong>:
<em class="summary">Access PubMed using a read-only dictionary interface.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Rebase.Dictionary-class.html">Bio.Rebase.Dictionary</a></strong>:
<em class="summary">Accesses a rebase file using a dictionary interface.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.CAPS.DifferentialCutsite-class.html">Bio.CAPS.DifferentialCutsite</a></strong>:
<em class="summary">A differential cutsite is a location in an alignment where an enzyme cuts
at least one sequence and also cannot cut at least one other sequence.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.NeuralNetwork.Gene.Schema.DifferentialSchemaFitness-class.html">Bio.NeuralNetwork.Gene.Schema.DifferentialSchemaFitness</a></strong>:
<em class="summary">Calculate fitness for schemas that differentiate between sequences.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.PDB.Entity.DisorderedEntityWrapper-class.html">Bio.PDB.Entity.DisorderedEntityWrapper</a></strong>:
<em class="summary">This class is a simple wrapper class that groups a number of
equivalent Entities and forwards all method calls to one of them
(the currently selected object).</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.PDB.Atom.DisorderedAtom-class.html">Bio.PDB.Atom.DisorderedAtom</a></strong>:
<em class="summary">This class contains all Atom objects that represent the same
disordered atom.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.PDB.Residue.DisorderedResidue-class.html">Bio.PDB.Residue.DisorderedResidue</a></strong>:
<em class="summary">DisorderedResidue is a wrapper around two or more Residue objects.</em>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Martel.Dispatch.DispatchHandler-class.html">Martel.Dispatch.DispatchHandler</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Martel.Dispatch.Callback-class.html">Martel.Dispatch.Callback</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.StdHandler.Handle_dbid-class.html">Bio.StdHandler.Handle_dbid</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.StdHandler.Handle_dbxref-class.html">Bio.StdHandler.Handle_dbxref</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.StdHandler.Handle_description-class.html">Bio.StdHandler.Handle_description</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.StdHandler.Handle_feature_location-class.html">Bio.StdHandler.Handle_feature_location</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.StdHandler.Handle_feature_qualifier-class.html">Bio.StdHandler.Handle_feature_qualifier</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.StdHandler.Handle_features-class.html">Bio.StdHandler.Handle_features</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.StdHandler.Handle_hsp-class.html">Bio.StdHandler.Handle_hsp</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.StdHandler.Handle_hsp_seqalign-class.html">Bio.StdHandler.Handle_hsp_seqalign</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.StdHandler.Handle_search_header-class.html">Bio.StdHandler.Handle_search_header</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.StdHandler.Handle_search_info-class.html">Bio.StdHandler.Handle_search_info</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.StdHandler.Handle_search_table-class.html">Bio.StdHandler.Handle_search_table</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.StdHandler.Handle_sequence-class.html">Bio.StdHandler.Handle_sequence</a></strong>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Martel.Dispatch.Dispatcher-class.html">Martel.Dispatch.Dispatcher</a></strong>:
<em class="summary">Adapter from the standard SAX events</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.builders.Search.search.BuildSearch-class.html">Bio.builders.Search.search.BuildSearch</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.builders.SeqRecord.sequence.BuildSeqRecord-class.html">Bio.builders.SeqRecord.sequence.BuildSeqRecord</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.Mindy.SimpleSeqRecord.FixDocumentBuilder-class.html">Bio.Mindy.SimpleSeqRecord.FixDocumentBuilder</a></strong>:
<em class="summary">A SAX builder-style class to make a parsed SeqRecord available.</em>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.StdHandler.ConvertDispatchHandler-class.html">Bio.StdHandler.ConvertDispatchHandler</a></strong>:
<em class="summary">Used to read records and produce output through a Dispatcher</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Saf._RecordConsumer-class.html" onclick="show_private();">Bio.Saf._RecordConsumer</a></strong>:
<em class="summary">Create a Saf Record object from scanner generated information.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.LocusLink._RecordConsumer-class.html" onclick="show_private();">Bio.LocusLink._RecordConsumer</a></strong>:
<em class="summary">Create a LocusLink Record object from scanner generated
information.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.CDD._RecordConsumer-class.html" onclick="show_private();">Bio.CDD._RecordConsumer</a></strong>:
<em class="summary">Create a CDD Record object from scanner generated information.</em>
</li>
</ul>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.Graphics.Distribution.DistributionPage-class.html">Bio.Graphics.Distribution.DistributionPage</a></strong>:
<em class="summary">Display a grouping of distributions on a page.</em>
</li>
<li> <strong class="uidlink"><a href="Martel.LAX.ElementInfo-class.html">Martel.LAX.ElementInfo</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.POM.ElementNode-class.html">Bio.EUtils.POM.ElementNode</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.eLink_020511.Attribute-class.html">Bio.EUtils.DTDs.eLink_020511.Attribute</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.LinkOut.Attribute-class.html">Bio.EUtils.DTDs.LinkOut.Attribute</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.LinkOut.Base-class.html">Bio.EUtils.DTDs.LinkOut.Base</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.LinkOut.Brief-class.html">Bio.EUtils.DTDs.LinkOut.Brief</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.eInfo_020511.Count-class.html">Bio.EUtils.DTDs.eInfo_020511.Count</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.eSearch_020511.Count-class.html">Bio.EUtils.DTDs.eSearch_020511.Count</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.LinkOut.Database-class.html">Bio.EUtils.DTDs.LinkOut.Database</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.eLink_020511.DbFrom-class.html">Bio.EUtils.DTDs.eLink_020511.DbFrom</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.eInfo_020511.DbInfo-class.html">Bio.EUtils.DTDs.eInfo_020511.DbInfo</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.eInfo_020511.DbList-class.html">Bio.EUtils.DTDs.eInfo_020511.DbList</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.eInfo_020511.DbName-class.html">Bio.EUtils.DTDs.eInfo_020511.DbName</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.eInfo_020511.DbTo-class.html">Bio.EUtils.DTDs.eInfo_020511.DbTo</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.eLink_020511.DbTo-class.html">Bio.EUtils.DTDs.eLink_020511.DbTo</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.eInfo_020511.Descriptor-class.html">Bio.EUtils.DTDs.eInfo_020511.Descriptor</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.eSummary_020511.DocSum-class.html">Bio.EUtils.DTDs.eSummary_020511.DocSum</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.eSearch_020511.ERROR-class.html">Bio.EUtils.DTDs.eSearch_020511.ERROR</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.eLink_020511.ERROR-class.html">Bio.EUtils.DTDs.eLink_020511.ERROR</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.eInfo_020511.ERROR-class.html">Bio.EUtils.DTDs.eInfo_020511.ERROR</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.eSummary_020511.ERROR-class.html">Bio.EUtils.DTDs.eSummary_020511.ERROR</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.ePost_020511.ERROR-class.html">Bio.EUtils.DTDs.ePost_020511.ERROR</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.eSearch_020511.ErrorList-class.html">Bio.EUtils.DTDs.eSearch_020511.ErrorList</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.LinkOut.ExclQuery-class.html">Bio.EUtils.DTDs.LinkOut.ExclQuery</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.eSearch_020511.Explode-class.html">Bio.EUtils.DTDs.eSearch_020511.Explode</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.eInfo_020511.Field-class.html">Bio.EUtils.DTDs.eInfo_020511.Field</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.eSearch_020511.Field-class.html">Bio.EUtils.DTDs.eSearch_020511.Field</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.eSearch_020511.FieldNotFound-class.html">Bio.EUtils.DTDs.eSearch_020511.FieldNotFound</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.eInfo_020511.FiledList-class.html">Bio.EUtils.DTDs.eInfo_020511.FiledList</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.POM.Fragments-class.html">Bio.EUtils.POM.Fragments</a></strong>:
<em class="summary">Fragments is a special holder class to hold 'loose' markup
fragments.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.eSearch_020511.From-class.html">Bio.EUtils.DTDs.eSearch_020511.From</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.eInfo_020511.Hierarchy-class.html">Bio.EUtils.DTDs.eInfo_020511.Hierarchy</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.LinkOut.IconUrl-class.html">Bio.EUtils.DTDs.LinkOut.IconUrl</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.eLink_020511.IconUrl-class.html">Bio.EUtils.DTDs.eLink_020511.IconUrl</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.eSearch_020511.Id-class.html">Bio.EUtils.DTDs.eSearch_020511.Id</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.ePost_020511.Id-class.html">Bio.EUtils.DTDs.ePost_020511.Id</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.eLink_020511.Id-class.html">Bio.EUtils.DTDs.eLink_020511.Id</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.eSummary_020511.Id-class.html">Bio.EUtils.DTDs.eSummary_020511.Id</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.eLink_020511.IdCheckList-class.html">Bio.EUtils.DTDs.eLink_020511.IdCheckList</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.eSearch_020511.IdList-class.html">Bio.EUtils.DTDs.eSearch_020511.IdList</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.eLink_020511.IdList-class.html">Bio.EUtils.DTDs.eLink_020511.IdList</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.eLink_020511.IdUrlList-class.html">Bio.EUtils.DTDs.eLink_020511.IdUrlList</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.eLink_020511.IdUrlSet-class.html">Bio.EUtils.DTDs.eLink_020511.IdUrlSet</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.LinkOut.InclQuery-class.html">Bio.EUtils.DTDs.LinkOut.InclQuery</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.eLink_020511.Info-class.html">Bio.EUtils.DTDs.eLink_020511.Info</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.ePost_020511.InvalidIdList-class.html">Bio.EUtils.DTDs.ePost_020511.InvalidIdList</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.eInfo_020511.IsDate-class.html">Bio.EUtils.DTDs.eInfo_020511.IsDate</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.eInfo_020511.IsNumerical-class.html">Bio.EUtils.DTDs.eInfo_020511.IsNumerical</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.eSummary_020511.Item-class.html">Bio.EUtils.DTDs.eSummary_020511.Item</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.LinkOut.Link-class.html">Bio.EUtils.DTDs.LinkOut.Link</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.eLink_020511.Link-class.html">Bio.EUtils.DTDs.eLink_020511.Link</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.eInfo_020511.Link-class.html">Bio.EUtils.DTDs.eInfo_020511.Link</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.LinkOut.LinkId-class.html">Bio.EUtils.DTDs.LinkOut.LinkId</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.eInfo_020511.LinkList-class.html">Bio.EUtils.DTDs.eInfo_020511.LinkList</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.eLink_020511.LinkName-class.html">Bio.EUtils.DTDs.eLink_020511.LinkName</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.LinkOut.LinkSet-class.html">Bio.EUtils.DTDs.LinkOut.LinkSet</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.eLink_020511.LinkSet-class.html">Bio.EUtils.DTDs.eLink_020511.LinkSet</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.eLink_020511.LinkSetDb-class.html">Bio.EUtils.DTDs.eLink_020511.LinkSetDb</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.eInfo_020511.Menu-class.html">Bio.EUtils.DTDs.eInfo_020511.Menu</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.eInfo_020511.MenuName-class.html">Bio.EUtils.DTDs.eInfo_020511.MenuName</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.LinkOut.Name-class.html">Bio.EUtils.DTDs.LinkOut.Name</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.eLink_020511.Name-class.html">Bio.EUtils.DTDs.eLink_020511.Name</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.eInfo_020511.Name-class.html">Bio.EUtils.DTDs.eInfo_020511.Name</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.eLink_020511.NameAbbr-class.html">Bio.EUtils.DTDs.eLink_020511.NameAbbr</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.LinkOut.NameAbbr-class.html">Bio.EUtils.DTDs.LinkOut.NameAbbr</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.eSearch_020511.OP-class.html">Bio.EUtils.DTDs.eSearch_020511.OP</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.LinkOut.ObjId-class.html">Bio.EUtils.DTDs.LinkOut.ObjId</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.eLink_020511.ObjUrl-class.html">Bio.EUtils.DTDs.eLink_020511.ObjUrl</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.LinkOut.ObjectList-class.html">Bio.EUtils.DTDs.LinkOut.ObjectList</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.LinkOut.ObjectSelector-class.html">Bio.EUtils.DTDs.LinkOut.ObjectSelector</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.LinkOut.ObjectUrl-class.html">Bio.EUtils.DTDs.LinkOut.ObjectUrl</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.eSearch_020511.OutputMessage-class.html">Bio.EUtils.DTDs.eSearch_020511.OutputMessage</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.eSearch_020511.PhraseIgnored-class.html">Bio.EUtils.DTDs.eSearch_020511.PhraseIgnored</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.eSearch_020511.PhraseNotFound-class.html">Bio.EUtils.DTDs.eSearch_020511.PhraseNotFound</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.LinkOut.Provider-class.html">Bio.EUtils.DTDs.LinkOut.Provider</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.eLink_020511.Provider-class.html">Bio.EUtils.DTDs.eLink_020511.Provider</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.LinkOut.ProviderId-class.html">Bio.EUtils.DTDs.LinkOut.ProviderId</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.LinkOut.Query-class.html">Bio.EUtils.DTDs.LinkOut.Query</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.ePost_020511.QueryKey-class.html">Bio.EUtils.DTDs.ePost_020511.QueryKey</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.eSearch_020511.QueryKey-class.html">Bio.EUtils.DTDs.eSearch_020511.QueryKey</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.eSearch_020511.QueryTranslation-class.html">Bio.EUtils.DTDs.eSearch_020511.QueryTranslation</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.eSearch_020511.QuotedPhraseNotFound-class.html">Bio.EUtils.DTDs.eSearch_020511.QuotedPhraseNotFound</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.eSearch_020511.RetMax-class.html">Bio.EUtils.DTDs.eSearch_020511.RetMax</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.eSearch_020511.RetStart-class.html">Bio.EUtils.DTDs.eSearch_020511.RetStart</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.LinkOut.Rule-class.html">Bio.EUtils.DTDs.LinkOut.Rule</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.LinkOut.RuleToMany-class.html">Bio.EUtils.DTDs.LinkOut.RuleToMany</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.eLink_020511.Score-class.html">Bio.EUtils.DTDs.eLink_020511.Score</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.LinkOut.Separator-class.html">Bio.EUtils.DTDs.LinkOut.Separator</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.eInfo_020511.SingleToken-class.html">Bio.EUtils.DTDs.eInfo_020511.SingleToken</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.LinkOut.SubObjectSelector-class.html">Bio.EUtils.DTDs.LinkOut.SubObjectSelector</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.LinkOut.SubProvider-class.html">Bio.EUtils.DTDs.LinkOut.SubProvider</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.LinkOut.SubjectType-class.html">Bio.EUtils.DTDs.LinkOut.SubjectType</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.eLink_020511.SubjectType-class.html">Bio.EUtils.DTDs.eLink_020511.SubjectType</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.eSearch_020511.Term-class.html">Bio.EUtils.DTDs.eSearch_020511.Term</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.eInfo_020511.TermCount-class.html">Bio.EUtils.DTDs.eInfo_020511.TermCount</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.eSearch_020511.TermSet-class.html">Bio.EUtils.DTDs.eSearch_020511.TermSet</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.eSearch_020511.To-class.html">Bio.EUtils.DTDs.eSearch_020511.To</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.eSearch_020511.Translation-class.html">Bio.EUtils.DTDs.eSearch_020511.Translation</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.eSearch_020511.TranslationSet-class.html">Bio.EUtils.DTDs.eSearch_020511.TranslationSet</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.eSearch_020511.TranslationStack-class.html">Bio.EUtils.DTDs.eSearch_020511.TranslationStack</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.eLink_020511.Url-class.html">Bio.EUtils.DTDs.eLink_020511.Url</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.LinkOut.Url-class.html">Bio.EUtils.DTDs.LinkOut.Url</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.LinkOut.UrlName-class.html">Bio.EUtils.DTDs.LinkOut.UrlName</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.eSearch_020511.WarningList-class.html">Bio.EUtils.DTDs.eSearch_020511.WarningList</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.eSearch_020511.WebEnv-class.html">Bio.EUtils.DTDs.eSearch_020511.WebEnv</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.ePost_020511.WebEnv-class.html">Bio.EUtils.DTDs.ePost_020511.WebEnv</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.LinkOut.apad-class.html">Bio.EUtils.DTDs.LinkOut.apad</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.eInfo_020511.eInfoResult-class.html">Bio.EUtils.DTDs.eInfo_020511.eInfoResult</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.eLink_020511.eLinkResult-class.html">Bio.EUtils.DTDs.eLink_020511.eLinkResult</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.ePost_020511.ePostResult-class.html">Bio.EUtils.DTDs.ePost_020511.ePostResult</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.eSearch_020511.eSearchResult-class.html">Bio.EUtils.DTDs.eSearch_020511.eSearchResult</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.eSummary_020511.eSummaryResult-class.html">Bio.EUtils.DTDs.eSummary_020511.eSummaryResult</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.LinkOut.normalize-class.html">Bio.EUtils.DTDs.LinkOut.normalize</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.LinkOut.pad-class.html">Bio.EUtils.DTDs.LinkOut.pad</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.LinkOut.strip-class.html">Bio.EUtils.DTDs.LinkOut.strip</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.LinkOut.subs-class.html">Bio.EUtils.DTDs.LinkOut.subs</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.LinkOut.tolower-class.html">Bio.EUtils.DTDs.LinkOut.tolower</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DTDs.LinkOut.toupper-class.html">Bio.EUtils.DTDs.LinkOut.toupper</a></strong>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.PDB.Entity.Entity-class.html">Bio.PDB.Entity.Entity</a></strong>:
<em class="summary">Basic container object.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.PDB.Chain.Chain-class.html">Bio.PDB.Chain.Chain</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.PDB.Model.Model-class.html">Bio.PDB.Model.Model</a></strong>:
<em class="summary">The object representing a model in a structure.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.PDB.Residue.Residue-class.html">Bio.PDB.Residue.Residue</a></strong>:
<em class="summary">Represents a residue.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.PDB.Structure.Structure-class.html">Bio.PDB.Structure.Structure</a></strong>:
<em class="summary">The Structure class contains a collection of Model instances.</em>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.Enzyme.EnzymeRecord-class.html">Bio.Enzyme.EnzymeRecord</a></strong>
</li>
<li> <strong class="uidlink">xml.sax.handler.ErrorHandler</strong>:
<em class="summary">Basic interface for SAX error handlers.</em>
<ul>
<li> <strong class="uidlink"><a href="Martel.test.support.CheckGood-class.html">Martel.test.support.CheckGood</a></strong>
</li>
<li> <strong class="uidlink"><a href="Martel.test.test_Parser.CountErrors-class.html">Martel.test.test_Parser.CountErrors</a></strong>
</li>
<li> <strong class="uidlink"><a href="Martel.test.support.Dump-class.html">Martel.test.support.Dump</a></strong>
</li>
<li> <strong class="uidlink"><a href="Martel.test.test_optimize.GetErrorPos-class.html">Martel.test.test_optimize.GetErrorPos</a></strong>
</li>
<li> <strong class="uidlink"><a href="Martel.test.test_attrs.GrabElements-class.html">Martel.test.test_attrs.GrabElements</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.StdHandler.RecognizeHandler-class.html">Bio.StdHandler.RecognizeHandler</a></strong>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Martel.Iterator.EventStream-class.html">Martel.Iterator.EventStream</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.SwissProt.SProt.ExPASyDictionary-class.html">Bio.SwissProt.SProt.ExPASyDictionary</a></strong>:
<em class="summary">Access SwissProt at ExPASy using a read-only dictionary interface.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Prosite.ExPASyDictionary-class.html">Bio.Prosite.ExPASyDictionary</a></strong>:
<em class="summary">Access PROSITE at ExPASy using a read-only dictionary interface.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Prosite.Prodoc.ExPASyDictionary-class.html">Bio.Prosite.Prodoc.ExPASyDictionary</a></strong>:
<em class="summary">Access PRODOC at ExPASy using a read-only dictionary interface.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.NeuralNetwork.Training.ExampleManager-class.html">Bio.NeuralNetwork.Training.ExampleManager</a></strong>:
<em class="summary">Manage a grouping of Training Examples.</em>
</li>
<li> <strong class="uidlink">exceptions.Exception</strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.Datatypes.Expression-class.html">Bio.EUtils.Datatypes.Expression</a></strong>:
<em class="summary">Base class for the Expression given in the eSearch output</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.EUtils.Datatypes.BinaryOp-class.html">Bio.EUtils.Datatypes.BinaryOp</a></strong>:
<em class="summary">Base class for binary expressions.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.EUtils.Datatypes.And-class.html">Bio.EUtils.Datatypes.And</a></strong>:
<em class="summary">intersection of two subexpressions</em>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.Datatypes.Not-class.html">Bio.EUtils.Datatypes.Not</a></strong>:
<em class="summary">the set of the left child without elements from the right child</em>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.Datatypes.Or-class.html">Bio.EUtils.Datatypes.Or</a></strong>:
<em class="summary">union two subexpressions</em>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.Datatypes.Range-class.html">Bio.EUtils.Datatypes.Range</a></strong>:
<em class="summary">Used to store a date range</em>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.Datatypes.Term-class.html">Bio.EUtils.Datatypes.Term</a></strong>:
<em class="summary">Information about an Expression Term, which is the leaf node</em>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Martel.Expression.Expression-class.html">Martel.Expression.Expression</a></strong>:
<em class="summary">Base class for nodes in the Expression tree</em>
<ul>
<li> <strong class="uidlink"><a href="Martel.Expression.Any-class.html">Martel.Expression.Any</a></strong>
</li>
<li> <strong class="uidlink"><a href="Martel.Expression.AnyEol-class.html">Martel.Expression.AnyEol</a></strong>:
<em class="summary">Match a newline (" ", "
" or " ")</em>
</li>
<li> <strong class="uidlink"><a href="Martel.Expression.Assert-class.html">Martel.Expression.Assert</a></strong>
</li>
<li> <strong class="uidlink"><a href="Martel.Expression.AtBeginning-class.html">Martel.Expression.AtBeginning</a></strong>:
<em class="summary">Match the beginning of a line</em>
</li>
<li> <strong class="uidlink"><a href="Martel.Expression.AtEnd-class.html">Martel.Expression.AtEnd</a></strong>:
<em class="summary">Match the end of a line</em>
</li>
<li> <strong class="uidlink"><a href="Martel.Expression.Debug-class.html">Martel.Expression.Debug</a></strong>
</li>
<li> <strong class="uidlink"><a href="Martel.Expression.Dot-class.html">Martel.Expression.Dot</a></strong>:
<em class="summary">Match any character except newline</em>
</li>
<li> <strong class="uidlink"><a href="Martel.Expression.ExpressionList-class.html">Martel.Expression.ExpressionList</a></strong>:
<em class="summary">shares implementation used by 'Expressions with subexpressions'</em>
<ul>
<li> <strong class="uidlink"><a href="Martel.Expression.Alt-class.html">Martel.Expression.Alt</a></strong>:
<em class="summary">An Expression tree with a list of alternate matches.</em>
</li>
<li> <strong class="uidlink"><a href="Martel.Expression.Seq-class.html">Martel.Expression.Seq</a></strong>:
<em class="summary">An Expression matching a set of subexpressions, in sequential order</em>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Martel.Expression.Group-class.html">Martel.Expression.Group</a></strong>
</li>
<li> <strong class="uidlink"><a href="Martel.Expression.GroupRef-class.html">Martel.Expression.GroupRef</a></strong>
</li>
<li> <strong class="uidlink"><a href="Martel.Expression.Literal-class.html">Martel.Expression.Literal</a></strong>
</li>
<li> <strong class="uidlink"><a href="Martel.Expression.MaxRepeat-class.html">Martel.Expression.MaxRepeat</a></strong>
</li>
<li> <strong class="uidlink"><a href="Martel.Expression.NullOp-class.html">Martel.Expression.NullOp</a></strong>
</li>
<li> <strong class="uidlink"><a href="Martel.Expression.PassThrough-class.html">Martel.Expression.PassThrough</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Martel.Expression.FastFeature-class.html">Martel.Expression.FastFeature</a></strong>
</li>
<li> <strong class="uidlink"><a href="Martel.Expression.HeaderFooter-class.html">Martel.Expression.HeaderFooter</a></strong>
</li>
<li> <strong class="uidlink"><a href="Martel.Expression.ParseRecords-class.html">Martel.Expression.ParseRecords</a></strong>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Martel.Expression.Str-class.html">Martel.Expression.Str</a></strong>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.PopGen.FDist.Controller.FDistController-class.html">Bio.PopGen.FDist.Controller.FDistController</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.PopGen.FDist.Async.FDistAsync-class.html">Bio.PopGen.FDist.Async.FDistAsync</a></strong>:
<em class="summary">Asynchronous FDist execution.</em>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.FSSP.FSSPAlignRec-class.html">Bio.FSSP.FSSPAlignRec</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.FSSP.FSSPHeader-class.html">Bio.FSSP.FSSPHeader</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.FSSP.FSSPSumRec-class.html">Bio.FSSP.FSSPSumRec</a></strong>:
<em class="summary">Contains info from an FSSP summary record</em>
</li>
<li> <strong class="uidlink"><a href="Bio.StdHandler.Feature-class.html">Bio.StdHandler.Feature</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.GenBank.Record.Feature-class.html">Bio.GenBank.Record.Feature</a></strong>:
<em class="summary">Hold information about a Feature in the Feature Table of GenBank
record.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.SeqFeature.FeatureLocation-class.html">Bio.SeqFeature.FeatureLocation</a></strong>:
<em class="summary">Specify the location of a feature along a sequence.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.GenBank.LocationParser.FeatureName-class.html">Bio.GenBank.LocationParser.FeatureName</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.GenBank.FeatureParser-class.html">Bio.GenBank.FeatureParser</a></strong>:
<em class="summary">Parse GenBank files into Seq + Feature objects.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.GenBank.utils.FeatureValueCleaner-class.html">Bio.GenBank.utils.FeatureValueCleaner</a></strong>:
<em class="summary">Provide specialized capabilities for cleaning up values in features.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.PopGen.Async.FileRetriever-class.html">Bio.PopGen.Async.FileRetriever</a></strong>:
<em class="summary">A Abstract Support class to retrieve files.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.PopGen.Async.DirectoryRetriever-class.html">Bio.PopGen.Async.DirectoryRetriever</a></strong>:
<em class="summary">Retrieves a directory content.</em>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.FilteredReader.FilteredReader-class.html">Bio.FilteredReader.FilteredReader</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.Align.FormatConvert.FormatConverter-class.html">Bio.Align.FormatConvert.FormatConverter</a></strong>:
<em class="summary">Convert between different alignment representation formats.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.PDB.FragmentMapper%27.Fragment-class.html">Bio.PDB.FragmentMapper'.Fragment</a></strong>:
<em class="summary">Represent a polypeptide C-alpha fragment.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.PDB.FragmentMapper%27.FragmentMapper-class.html">Bio.PDB.FragmentMapper'.FragmentMapper</a></strong>:
<em class="summary">Map polypeptides in a model to lists of representative fragments.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.GenBank.LocationParser.Function-class.html">Bio.GenBank.LocationParser.Function</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.Decode.Function-class.html">Bio.Decode.Function</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.Decode.FunctionCall-class.html">Bio.Decode.FunctionCall</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.Decode.FunctionCallChain-class.html">Bio.Decode.FunctionCallChain</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.sourcegen.FunctionHolder-class.html">Bio.EUtils.sourcegen.FunctionHolder</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.GA.Crossover.GeneralPoint.GeneralPointCrossover-class.html">Bio.GA.Crossover.GeneralPoint.GeneralPointCrossover</a></strong>:
<em class="summary">Perform n-point crossover between genomes at some defined rates.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.GA.Crossover.GeneralPoint.InterleaveCrossover-class.html">Bio.GA.Crossover.GeneralPoint.InterleaveCrossover</a></strong>:
<em class="summary">Demonstration class for Interleaving crossover</em>
</li>
<li> <strong class="uidlink"><a href="Bio.GA.Crossover.GeneralPoint.TwoCrossover-class.html">Bio.GA.Crossover.GeneralPoint.TwoCrossover</a></strong>:
<em class="summary">Helper class for Two Point crossovers</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.GA.Crossover.Point.SinglePointCrossover-class.html">Bio.GA.Crossover.Point.SinglePointCrossover</a></strong>:
<em class="summary">Perform point crossover between genomes at some defined rate.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.GA.Crossover.TwoPoint.TwoPointCrossover-class.html">Bio.GA.Crossover.TwoPoint.TwoPointCrossover</a></strong>:
<em class="summary">Perform two point crossover between genomes at some defined rate.</em>
</li>
</ul>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.GA.Evolver.GenerationEvolver-class.html">Bio.GA.Evolver.GenerationEvolver</a></strong>:
<em class="summary">Evolve a population from generation to generation.</em>
</li>
<li> <strong class="uidlink"><a href="Martel.Generate.GeneratorState-class.html">Martel.Generate.GeneratorState</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.Parsers.spark.GenericASTTraversal-class.html">Bio.Parsers.spark.GenericASTTraversal</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.Parsers.spark.GenericASTTraversalPruningException-class.html">Bio.Parsers.spark.GenericASTTraversalPruningException</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.Parsers.spark.GenericParser-class.html">Bio.Parsers.spark.GenericParser</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.Decode.DecodeParser-class.html">Bio.Decode.DecodeParser</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.Parsers.spark.GenericASTBuilder-class.html">Bio.Parsers.spark.GenericASTBuilder</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.Parsers.spark.GenericASTMatcher-class.html">Bio.Parsers.spark.GenericASTMatcher</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.GenBank.LocationParser.LocationParser-class.html">Bio.GenBank.LocationParser.LocationParser</a></strong>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.Parsers.spark.GenericScanner-class.html">Bio.Parsers.spark.GenericScanner</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.Decode.DecodeScanner-class.html">Bio.Decode.DecodeScanner</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.GenBank.LocationParser.LocationScanner-class.html">Bio.GenBank.LocationParser.LocationScanner</a></strong>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="BioSQL.DBUtils.Generic_dbutils-class.html">BioSQL.DBUtils.Generic_dbutils</a></strong>
<ul>
<li> <strong class="uidlink"><a href="BioSQL.DBUtils.Mysql_dbutils-class.html">BioSQL.DBUtils.Mysql_dbutils</a></strong>
</li>
<li> <strong class="uidlink"><a href="BioSQL.DBUtils.Pgdb_dbutils-class.html">BioSQL.DBUtils.Pgdb_dbutils</a></strong>:
<em class="summary">Add support for pgdb in the PyGreSQL database connectivity package.</em>
</li>
<li> <strong class="uidlink"><a href="BioSQL.DBUtils.Psycopg_dbutils-class.html">BioSQL.DBUtils.Psycopg_dbutils</a></strong>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.NeuralNetwork.Gene.Schema.GeneticAlgorithmFinder-class.html">Bio.NeuralNetwork.Gene.Schema.GeneticAlgorithmFinder</a></strong>:
<em class="summary">Find schemas using a genetic algorithm approach.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.parse.GetObject-class.html">Bio.EUtils.parse.GetObject</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.Pathway.Rep.Graph.Graph-class.html">Bio.Pathway.Rep.Graph.Graph</a></strong>:
<em class="summary">A directed graph abstraction with labeled edges.</em>
</li>
<li> <strong class="uidlink"><a href="Martel.convert_re.GroupNames-class.html">Martel.convert_re.GroupNames</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.Blast.Record.HSP-class.html">Bio.Blast.Record.HSP</a></strong>:
<em class="summary">Stores information about one hsp in an alignment hit.</em>
</li>
<li> <strong class="uidlink"><a href="Martel.Generate.HandleRepeatCount-class.html">Martel.Generate.HandleRepeatCount</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.Pathway.Rep.HashSet.HashSet-class.html">Bio.Pathway.Rep.HashSet.HashSet</a></strong>:
<em class="summary">A set abstraction supporting the basic set operations.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Blast.Record.Header-class.html">Bio.Blast.Record.Header</a></strong>:
<em class="summary">Saves information from a blast header.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.Blast.Record.Blast-class.html">Bio.Blast.Record.Blast</a></strong>:
<em class="summary">Saves the results from a blast search.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Blast.Record.PSIBlast-class.html">Bio.Blast.Record.PSIBlast</a></strong>:
<em class="summary">Saves the results from a blastpgp search.</em>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Martel.Iterator.HeaderFooterEventStream-class.html">Martel.Iterator.HeaderFooterEventStream</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.Crystal.Hetero-class.html">Bio.Crystal.Hetero</a></strong>:
<em class="summary">This class exists to support the PDB hetero codes.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.HMM.MarkovModel.HiddenMarkovModel-class.html">Bio.HMM.MarkovModel.HiddenMarkovModel</a></strong>:
<em class="summary">Represent a hidden markov model that can be used for state
estimation.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.GenBank.LocationParser.HighBound-class.html">Bio.GenBank.LocationParser.HighBound</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.HistoryClient.HistoryClient-class.html">Bio.EUtils.HistoryClient.HistoryClient</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.HistoryClient.HistoryCookie-class.html">Bio.EUtils.HistoryClient.HistoryCookie</a></strong>:
<em class="summary">Data needed to get back to the history</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Search.Hit-class.html">Bio.Search.Hit</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.HotRand.HotCache-class.html">Bio.HotRand.HotCache</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.HotRand.HotRandom-class.html">Bio.HotRand.HotRandom</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.Datatypes.IdCheck-class.html">Bio.EUtils.Datatypes.IdCheck</a></strong>:
<em class="summary">Store results from an lcheck link</em>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.Datatypes.IdUrlSet-class.html">Bio.EUtils.Datatypes.IdUrlSet</a></strong>:
<em class="summary">Set of ObjUrls for the record with the given 'id'</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Ais.Immune-class.html">Bio.Ais.Immune</a></strong>:
<em class="summary">friendly should be an instance of Align.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.GenBank.Scanner.InsdcScanner-class.html">Bio.GenBank.Scanner.InsdcScanner</a></strong>:
<em class="summary">Basic functions for breaking up a GenBank/EMBL file into sub
sections.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.GenBank.Scanner.EmblScanner-class.html">Bio.GenBank.Scanner.EmblScanner</a></strong>:
<em class="summary">For extracting chunks of information in EMBL files</em>
</li>
<li> <strong class="uidlink"><a href="Bio.GenBank.Scanner.GenBankScanner-class.html">Bio.GenBank.Scanner.GenBankScanner</a></strong>:
<em class="summary">For extracting chunks of information in GenBank files</em>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.MEME.Motif.Instance-class.html">Bio.MEME.Motif.Instance</a></strong>:
<em class="summary">A class describing the instances of a motif, and the data thereof.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.GenBank.LocationParser.Integer-class.html">Bio.GenBank.LocationParser.Integer</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.GenBank.LocationParser.UnsignedInteger-class.html">Bio.GenBank.LocationParser.UnsignedInteger</a></strong>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.Pathway.Interaction-class.html">Bio.Pathway.Interaction</a></strong>:
<em class="summary">An arbitrary interaction between any number of species.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint-class.html">Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint</a></strong>
</li>
<li> <strong class="uidlink"><a href="Martel.IterParser.IterHeaderFooter-class.html">Martel.IterParser.IterHeaderFooter</a></strong>
</li>
<li> <strong class="uidlink"><a href="Martel.IterParser.IterRecords-class.html">Martel.IterParser.IterRecords</a></strong>
</li>
<li> <strong class="uidlink"><a href="Martel.Iterator.Iterate-class.html">Martel.Iterator.Iterate</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.NBRF.Iterator-class.html">Bio.NBRF.Iterator</a></strong>:
<em class="summary">Iterator interface to move over a file of NBRF entries one at a
time.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Blast.NCBIStandalone.Iterator-class.html">Bio.Blast.NCBIStandalone.Iterator</a></strong>:
<em class="summary">Iterates over a file of multiple BLAST results.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.SwissProt.SProt.Iterator-class.html">Bio.SwissProt.SProt.Iterator</a></strong>:
<em class="summary">Returns one record at a time from a SwissProt file.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Sequencing.Ace.Iterator-class.html">Bio.Sequencing.Ace.Iterator</a></strong>:
<em class="summary">Iterates over an ACE-file with multiple contigs.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.SCOP.Hie.Iterator-class.html">Bio.SCOP.Hie.Iterator</a></strong>:
<em class="summary">Iterates over a HIE file.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Gobase.Iterator-class.html">Bio.Gobase.Iterator</a></strong>:
<em class="summary">Returns one record at a time from a Gobase file.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.ECell.Iterator-class.html">Bio.ECell.Iterator</a></strong>:
<em class="summary">Iterator interface to move over a file of ecell entries one at a
time.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.UniGene.Iterator-class.html">Bio.UniGene.Iterator</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.Enzyme.Iterator-class.html">Bio.Enzyme.Iterator</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.Medline.Iterator-class.html">Bio.Medline.Iterator</a></strong>:
<em class="summary">Returns one record at a time from a file of Medline records.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.MetaTool.Iterator-class.html">Bio.MetaTool.Iterator</a></strong>:
<em class="summary">Iterator interface to move over a file of MetaTool entries one at a
time.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.CDD.Iterator-class.html">Bio.CDD.Iterator</a></strong>:
<em class="summary">Iterator interface to move over a file of CDD entries one at a
time.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Compass.Iterator-class.html">Bio.Compass.Iterator</a></strong>:
<em class="summary">Iterate through a file of compass results</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Prosite.Prodoc.Iterator-class.html">Bio.Prosite.Prodoc.Iterator</a></strong>:
<em class="summary">Returns one record at a time from a Prodoc file.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.IntelliGenetics.Iterator-class.html">Bio.IntelliGenetics.Iterator</a></strong>:
<em class="summary">Iterator interface to move over a file of IntelliGenetics entries
one at a time.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Sequencing.Phd.Iterator-class.html">Bio.Sequencing.Phd.Iterator</a></strong>:
<em class="summary">Iterates over a file of multiple PHD records.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Saf.Iterator-class.html">Bio.Saf.Iterator</a></strong>:
<em class="summary">Iterator interface to move over a file of Saf entries one at a
time.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Fasta.Iterator-class.html">Bio.Fasta.Iterator</a></strong>:
<em class="summary">Returns one record at a time from a FASTA file.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.SCOP.Dom.Iterator-class.html">Bio.SCOP.Dom.Iterator</a></strong>:
<em class="summary">Iterates over a DOM file.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.SCOP.Des.Iterator-class.html">Bio.SCOP.Des.Iterator</a></strong>:
<em class="summary">Iterates over a DES file.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.SCOP.Cla.Iterator-class.html">Bio.SCOP.Cla.Iterator</a></strong>:
<em class="summary">Iterates over a CLA file.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Prosite.Iterator-class.html">Bio.Prosite.Iterator</a></strong>:
<em class="summary">Returns one record at a time from a Prosite file.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.GenBank.Iterator-class.html">Bio.GenBank.Iterator</a></strong>:
<em class="summary">Iterator interface to move over a file of GenBank entries one at a
time.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Rebase.Iterator-class.html">Bio.Rebase.Iterator</a></strong>:
<em class="summary">Returns one record at a time from a Rebase file.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.SCOP.Raf.Iterator-class.html">Bio.SCOP.Raf.Iterator</a></strong>:
<em class="summary">Iterates over a RAF file.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.LocusLink.Iterator-class.html">Bio.LocusLink.Iterator</a></strong>:
<em class="summary">Iterator interface to move over a file of LocusLink entries one at
a time.</em>
</li>
<li> <strong class="uidlink"><a href="Martel.Iterator.Iterator-class.html">Martel.Iterator.Iterator</a></strong>
</li>
<li> <strong class="uidlink"><a href="Martel.Iterator.IteratorHeaderFooter-class.html">Martel.Iterator.IteratorHeaderFooter</a></strong>
</li>
<li> <strong class="uidlink"><a href="Martel.Iterator.IteratorRecords-class.html">Martel.Iterator.IteratorRecords</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.KDTree.KDTree.KDTree-class.html">Bio.KDTree.KDTree.KDTree</a></strong>:
<em class="summary">KD tree implementation (C++, SWIG python wrapper)</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Graphics.Distribution.LineDistribution-class.html">Bio.Graphics.Distribution.LineDistribution</a></strong>:
<em class="summary">Display the distribution of values as connected lines.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.Datatypes.Link-class.html">Bio.EUtils.Datatypes.Link</a></strong>:
<em class="summary">Store neighbor Link information for a given record</em>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.Mixins.LinkMixin-class.html">Bio.EUtils.Mixins.LinkMixin</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.EUtils.Mixins.PublicationFetchMixin-class.html">Bio.EUtils.Mixins.PublicationFetchMixin</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.EUtils.DBIdsClient.PublicationDBIdsRecord-class.html">Bio.EUtils.DBIdsClient.PublicationDBIdsRecord</a></strong>:
<em class="summary">a single publication record, referenced by database identifier</em>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DBIdsClient.PublicationDBIdsRecordSet-class.html">Bio.EUtils.DBIdsClient.PublicationDBIdsRecordSet</a></strong>:
<em class="summary">a set of publication records, referenced by database identifier</em>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.HistoryClient.PublicationHistoryRecord-class.html">Bio.EUtils.HistoryClient.PublicationHistoryRecord</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.HistoryClient.PublicationHistoryRecordSet-class.html">Bio.EUtils.HistoryClient.PublicationHistoryRecordSet</a></strong>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.Mixins.SequenceFetchMixin-class.html">Bio.EUtils.Mixins.SequenceFetchMixin</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.EUtils.DBIdsClient.SequenceDBIdsRecord-class.html">Bio.EUtils.DBIdsClient.SequenceDBIdsRecord</a></strong>:
<em class="summary">a single sequence record, referenced by database identifier</em>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DBIdsClient.SequenceDBIdsRecordSet-class.html">Bio.EUtils.DBIdsClient.SequenceDBIdsRecordSet</a></strong>:
<em class="summary">a set of sequence records, referenced by database identifier</em>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.HistoryClient.SequenceHistoryRecord-class.html">Bio.EUtils.HistoryClient.SequenceHistoryRecord</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.HistoryClient.SequenceHistoryRecordSet-class.html">Bio.EUtils.HistoryClient.SequenceHistoryRecordSet</a></strong>
</li>
</ul>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.Datatypes.LinksLinkSet-class.html">Bio.EUtils.Datatypes.LinksLinkSet</a></strong>:
<em class="summary">Results of an 'llink' (LinkOut) search</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Mindy.Location.Location-class.html">Bio.Mindy.Location.Location</a></strong>:
<em class="summary">Handle for a record (use 'text' to get the record's text)</em>
</li>
<li> <strong class="uidlink"><a href="Bio.LogisticRegression.LogisticRegression-class.html">Bio.LogisticRegression.LogisticRegression</a></strong>:
<em class="summary">Holds information necessary to do logistic regression
classification.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.GenBank.LocationParser.LowBound-class.html">Bio.GenBank.LocationParser.LowBound</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.Ais.Lymphocyte-class.html">Bio.Ais.Lymphocyte</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.MEME.Parser.MASTRecord-class.html">Bio.MEME.Parser.MASTRecord</a></strong>:
<em class="summary">The class for holding the results from a MAST run.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.MEME.Parser.MEMERecord-class.html">Bio.MEME.Parser.MEMERecord</a></strong>:
<em class="summary">A class for holding the results of a MEME run.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.PDB.MMCIFParser.MMCIFParser-class.html">Bio.PDB.MMCIFParser.MMCIFParser</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.MarkovModel.MarkovModel-class.html">Bio.MarkovModel.MarkovModel</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.HMM.MarkovModel.MarkovModelBuilder-class.html">Bio.HMM.MarkovModel.MarkovModelBuilder</a></strong>:
<em class="summary">Interface to build up a Markov Model.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.MaxEntropy.MaxEntropy-class.html">Bio.MaxEntropy.MaxEntropy</a></strong>:
<em class="summary">Holds information for a Maximum Entropy classifier.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.sourcegen.MethodHolder-class.html">Bio.EUtils.sourcegen.MethodHolder</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.SeqUtils.MissingTable-class.html">Bio.SeqUtils.MissingTable</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.NeuralNetwork.Gene.Schema.MostCountSchemaFitness-class.html">Bio.NeuralNetwork.Gene.Schema.MostCountSchemaFitness</a></strong>:
<em class="summary">Calculate a fitness giving weight to schemas that match many times.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.MEME.Motif.Motif-class.html">Bio.MEME.Motif.Motif</a></strong>:
<em class="summary">A generic motif class.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.MEME.Motif.MEMEMotif-class.html">Bio.MEME.Motif.MEMEMotif</a></strong>:
<em class="summary">A subclass of Motif used in parsing MEME (and MAST) output.</em>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.NeuralNetwork.Gene.Motif.MotifCoder-class.html">Bio.NeuralNetwork.Gene.Motif.MotifCoder</a></strong>:
<em class="summary">Convert motifs and a sequence into neural network representations.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.NeuralNetwork.Gene.Motif.MotifFinder-class.html">Bio.NeuralNetwork.Gene.Motif.MotifFinder</a></strong>:
<em class="summary">Find motifs in a set of Sequence Records.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Pathway.Rep.MultiGraph.MultiGraph-class.html">Bio.Pathway.Rep.MultiGraph.MultiGraph</a></strong>:
<em class="summary">A directed multigraph abstraction with labeled edges.</em>
</li>
<li> <strong class="uidlink"><a href="Martel.Dispatch.Multicall-class.html">Martel.Dispatch.Multicall</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Martel.Dispatch.MulticallEnd-class.html">Martel.Dispatch.MulticallEnd</a></strong>
</li>
<li> <strong class="uidlink"><a href="Martel.Dispatch.MulticallStart-class.html">Martel.Dispatch.MulticallStart</a></strong>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.Clustalw.MultipleAlignCL-class.html">Bio.Clustalw.MultipleAlignCL</a></strong>:
<em class="summary">Represent a clustalw multiple alignment command line.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Blast.Record.MultipleAlignment-class.html">Bio.Blast.Record.MultipleAlignment</a></strong>:
<em class="summary">Holds information about a multiple alignment.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Seq.MutableSeq-class.html">Bio.Seq.MutableSeq</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.GenBank.NCBIDictionary-class.html">Bio.GenBank.NCBIDictionary</a></strong>:
<em class="summary">Access GenBank using a read-only dictionary interface.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.NaiveBayes.NaiveBayes-class.html">Bio.NaiveBayes.NaiveBayes</a></strong>:
<em class="summary">Holds information for a NaiveBayes classifier.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.Datatypes.NeighborLinkSet-class.html">Bio.EUtils.Datatypes.NeighborLinkSet</a></strong>:
<em class="summary">Results from an eLink neighbor search</em>
</li>
<li> <strong class="uidlink"><a href="Bio.PDB.NeighborSearch.NeighborSearch-class.html">Bio.PDB.NeighborSearch.NeighborSearch</a></strong>:
<em class="summary">This class can be used for two related purposes:</em>
</li>
<li> <strong class="uidlink"><a href="Bio.NetCatch.NetCatch-class.html">Bio.NetCatch.NetCatch</a></strong>:
<em class="summary">Decorator for a dictionary of links.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Pathway.Network-class.html">Bio.Pathway.Network</a></strong>:
<em class="summary">A set of species that are explicitly linked by interactions.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Nexus.Nodes.Node-class.html">Bio.Nexus.Nodes.Node</a></strong>:
<em class="summary">A single node.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.SCOP.Node-class.html">Bio.SCOP.Node</a></strong>:
<em class="summary">A node in the Scop hierarchy</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.SCOP.Domain-class.html">Bio.SCOP.Domain</a></strong>:
<em class="summary">A SCOP domain.</em>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.Nexus.Trees.NodeData-class.html">Bio.Nexus.Trees.NodeData</a></strong>:
<em class="summary">Stores tree-relevant data associated with nodes (e.g.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.Datatypes.ObjUrl-class.html">Bio.EUtils.Datatypes.ObjUrl</a></strong>:
<em class="summary">The ObjUrl containing LinkOut information for a record</em>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.POM.ObjectParserHandler-class.html">Bio.EUtils.POM.ObjectParserHandler</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.GA.Organism.Organism-class.html">Bio.GA.Organism.Organism</a></strong>:
<em class="summary">Represent a single individual in a population.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.PDB.PDBIO%27.PDBIO-class.html">Bio.PDB.PDBIO'.PDBIO</a></strong>:
<em class="summary">Write a Structure object (or a subset of a Structure object) as a
PDB file.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.PDB.PDBList%27.PDBList-class.html">Bio.PDB.PDBList'.PDBList</a></strong>:
<em class="summary">This class provides quick access to the structure lists on the PDB
server or its mirrors.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.PDB.PDBParser%27.PDBParser-class.html">Bio.PDB.PDBParser'.PDBParser</a></strong>:
<em class="summary">Parse a PDB file and return a Structure object.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.POM.POMDocument-class.html">Bio.EUtils.POM.POMDocument</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.PDB.PSEA.PSEA-class.html">Bio.PDB.PSEA.PSEA</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.Align.AlignInfo.PSSM-class.html">Bio.Align.AlignInfo.PSSM</a></strong>:
<em class="summary">Represent a position specific score matrix.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Blast.Record.Parameters-class.html">Bio.Blast.Record.Parameters</a></strong>:
<em class="summary">Holds information about the parameters.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.Blast.Record.Blast-class.html">Bio.Blast.Record.Blast</a></strong>:
<em class="summary">Saves the results from a blast search.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Blast.Record.PSIBlast-class.html">Bio.Blast.Record.PSIBlast</a></strong>:
<em class="summary">Saves the results from a blastpgp search.</em>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.SCOP.Dom.Parser-class.html">Bio.SCOP.Dom.Parser</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.SCOP.Cla.Parser-class.html">Bio.SCOP.Cla.Parser</a></strong>:
<em class="summary">Parses tab-deliminated CLA records.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.SCOP.Hie.Parser-class.html">Bio.SCOP.Hie.Parser</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.SCOP.Raf.Parser-class.html">Bio.SCOP.Raf.Parser</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.SCOP.Des.Parser-class.html">Bio.SCOP.Des.Parser</a></strong>
</li>
<li> <strong class="uidlink">markupbase.ParserBase</strong>:
<em class="summary">Parser base class which provides some common support methods used
by the SGML/HTML and XHTML parsers.</em>
<ul>
<li> <strong class="uidlink">sgmllib.SGMLParser</strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.NetCatch.ExtractUrls-class.html">Bio.NetCatch.ExtractUrls</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.InterPro.InterProParser-class.html">Bio.InterPro.InterProParser</a></strong>:
<em class="summary">Parses InterPro sequence data into a Record object.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.SGMLExtractor.SGMLExtractor.LocalParser-class.html">Bio.SGMLExtractor.SGMLExtractor.LocalParser</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.LocusLink.web_parse.LocusLinkParser-class.html">Bio.LocusLink.web_parse.LocusLinkParser</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.File.SGMLStripper.MyParser-class.html">Bio.File.SGMLStripper.MyParser</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.Ndb.NdbParser-class.html">Bio.Ndb.NdbParser</a></strong>:
<em class="summary">Parses Ndb sequence data into a Record object.</em>
</li>
</ul>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.GenBank.LocationParser.Path-class.html">Bio.GenBank.LocationParser.Path</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.MetaTool.Record.PathwayTransform-class.html">Bio.MetaTool.Record.PathwayTransform</a></strong>
</li>
<li> <strong class="uidlink"><a href="Martel.msre_parse.Pattern-class.html">Martel.msre_parse.Pattern</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.Prosite.PatternHit-class.html">Bio.Prosite.PatternHit</a></strong>:
<em class="summary">Holds information from a hit against a Prosite pattern.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.NeuralNetwork.Gene.Pattern.PatternIO-class.html">Bio.NeuralNetwork.Gene.Pattern.PatternIO</a></strong>:
<em class="summary">Allow reading and writing of patterns to files.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.NeuralNetwork.Gene.Pattern.PatternRepository-class.html">Bio.NeuralNetwork.Gene.Pattern.PatternRepository</a></strong>:
<em class="summary">This holds a list of specific patterns found in sequences.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.NMR.xpktools.Peaklist-class.html">Bio.NMR.xpktools.Peaklist</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.FSSP.PosAlign-class.html">Bio.FSSP.PosAlign</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.SeqFeature.PositionGap-class.html">Bio.SeqFeature.PositionGap</a></strong>:
<em class="summary">Simple class to hold information about a gap between positions.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.Datatypes.PostResult-class.html">Bio.EUtils.Datatypes.PostResult</a></strong>:
<em class="summary">Store the results of a Post</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Emboss.Primer.Primer3Parser-class.html">Bio.Emboss.Primer.Primer3Parser</a></strong>:
<em class="summary">Parse primer3 output into a Primer3Record.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Emboss.Primer.Primer3Primers-class.html">Bio.Emboss.Primer.Primer3Primers</a></strong>:
<em class="summary">A primer set designed by Primer3.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Emboss.Primer.Primer3Record-class.html">Bio.Emboss.Primer.Primer3Record</a></strong>:
<em class="summary">Represent information from a primer3 run finding primers.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Emboss.Primer.PrimerSearchAmplifier-class.html">Bio.Emboss.Primer.PrimerSearchAmplifier</a></strong>:
<em class="summary">Represent a single amplification from a primer.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Emboss.Primer.PrimerSearchInputRecord-class.html">Bio.Emboss.Primer.PrimerSearchInputRecord</a></strong>:
<em class="summary">Represent the input file into the primersearch program.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Emboss.Primer.PrimerSearchOutputRecord-class.html">Bio.Emboss.Primer.PrimerSearchOutputRecord</a></strong>:
<em class="summary">Represent the information from a primersearch job.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Emboss.Primer.PrimerSearchParser-class.html">Bio.Emboss.Primer.PrimerSearchParser</a></strong>:
<em class="summary">Parse primersearch output into a PrimerSearchOutputRecord.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.Datatypes.Problem-class.html">Bio.EUtils.Datatypes.Problem</a></strong>:
<em class="summary">Base class for Search Errors or Warnings</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.EUtils.Datatypes.ErrorProblem-class.html">Bio.EUtils.Datatypes.ErrorProblem</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.EUtils.Datatypes.FieldNotFound-class.html">Bio.EUtils.Datatypes.FieldNotFound</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.Datatypes.PhraseNotFound-class.html">Bio.EUtils.Datatypes.PhraseNotFound</a></strong>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.Datatypes.WarningProblem-class.html">Bio.EUtils.Datatypes.WarningProblem</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.EUtils.Datatypes.OutputMessage-class.html">Bio.EUtils.Datatypes.OutputMessage</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.Datatypes.PhraseIgnored-class.html">Bio.EUtils.Datatypes.PhraseIgnored</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.Datatypes.QuotedPhraseNotFound-class.html">Bio.EUtils.Datatypes.QuotedPhraseNotFound</a></strong>
</li>
</ul>
</li>
</ul>
</li>
<li> <strong class="uidlink">reportlab.graphics.widgetbase.PropHolder</strong>:
<em class="summary">Base for property holders</em>
<ul>
<li> <strong class="uidlink">reportlab.graphics.widgetbase.Widget</strong>:
<em class="summary">Base for all user-defined widgets.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.Graphics.BasicChromosome._ChromosomeComponent-class.html" onclick="show_private();">Bio.Graphics.BasicChromosome._ChromosomeComponent</a></strong>:
<em class="summary">Base class specifying the interface for a component of the system.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.Graphics.BasicChromosome.Chromosome-class.html">Bio.Graphics.BasicChromosome.Chromosome</a></strong>:
<em class="summary">Class for drawing a chromosome of an organism.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Graphics.BasicChromosome.ChromosomeSegment-class.html">Bio.Graphics.BasicChromosome.ChromosomeSegment</a></strong>:
<em class="summary">Draw a segment of a chromosome.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.Graphics.BasicChromosome.TelomereSegment-class.html">Bio.Graphics.BasicChromosome.TelomereSegment</a></strong>:
<em class="summary">A segment that is located at the end of a linear chromosome.</em>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.Graphics.BasicChromosome.Organism-class.html">Bio.Graphics.BasicChromosome.Organism</a></strong>:
<em class="summary">Top level class for drawing chromosomes.</em>
</li>
</ul>
</li>
</ul>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.PropertyManager.PropertyManager-class.html">Bio.PropertyManager.PropertyManager</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.Prosite.Pattern.Prosite-class.html">Bio.Prosite.Pattern.Prosite</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.Prosite.Pattern.PrositeMatch-class.html">Bio.Prosite.Pattern.PrositeMatch</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.Prosite.Pattern.PrositeTerm-class.html">Bio.Prosite.Pattern.PrositeTerm</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.SeqUtils.ProtParam.ProteinAnalysis-class.html">Bio.SeqUtils.ProtParam.ProteinAnalysis</a></strong>:
<em class="summary">This class contains methods for protein analysis.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.Datatypes.Provider-class.html">Bio.EUtils.Datatypes.Provider</a></strong>:
<em class="summary">The Provider, as listed in 'llinks' (LinkOut)</em>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DBIdsClient.PublicationDBIdsFetchMixin-class.html">Bio.EUtils.DBIdsClient.PublicationDBIdsFetchMixin</a></strong>:
<em class="summary">Support 'efetch' for publication records</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.EUtils.DBIdsClient.PublicationDBIdsRecord-class.html">Bio.EUtils.DBIdsClient.PublicationDBIdsRecord</a></strong>:
<em class="summary">a single publication record, referenced by database identifier</em>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DBIdsClient.PublicationDBIdsRecordSet-class.html">Bio.EUtils.DBIdsClient.PublicationDBIdsRecordSet</a></strong>:
<em class="summary">a set of publication records, referenced by database identifier</em>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.HistoryClient.PublicationHistoryFetchMixin-class.html">Bio.EUtils.HistoryClient.PublicationHistoryFetchMixin</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.EUtils.HistoryClient.PublicationHistoryRecord-class.html">Bio.EUtils.HistoryClient.PublicationHistoryRecord</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.HistoryClient.PublicationHistoryRecordSet-class.html">Bio.EUtils.HistoryClient.PublicationHistoryRecordSet</a></strong>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.GenBank.Record.Qualifier-class.html">Bio.GenBank.Record.Qualifier</a></strong>:
<em class="summary">Hold information about a qualifier in a GenBank feature.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Search.Query-class.html">Bio.Search.Query</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.NeuralNetwork.Gene.Schema.RandomMotifGenerator-class.html">Bio.NeuralNetwork.Gene.Schema.RandomMotifGenerator</a></strong>:
<em class="summary">Generate a random motif within given parameters.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.GenBank.LocationParser.Range-class.html">Bio.GenBank.LocationParser.Range</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.Pathway.Reaction-class.html">Bio.Pathway.Reaction</a></strong>:
<em class="summary">Abstraction for a biochemical transformation.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Sequencing.Ace.Reads-class.html">Bio.Sequencing.Ace.Reads</a></strong>:
<em class="summary">Holds information about a read supporting an ACE contig.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.IntelliGenetics.Record.Record-class.html">Bio.IntelliGenetics.Record.Record</a></strong>:
<em class="summary">Hold IntelliGenetics information in a format similar to the
original record.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Prosite.Record-class.html">Bio.Prosite.Record</a></strong>:
<em class="summary">Holds information from a Prosite record.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Rebase.Record-class.html">Bio.Rebase.Record</a></strong>:
<em class="summary">Holds information from a FASTA record.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.SCOP.Hie.Record-class.html">Bio.SCOP.Hie.Record</a></strong>:
<em class="summary">Holds information for one node in the SCOP hierarchy.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Medline.Record-class.html">Bio.Medline.Record</a></strong>:
<em class="summary">Holds information from a Medline record.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.KEGG.Enzyme.Record-class.html">Bio.KEGG.Enzyme.Record</a></strong>:
<em class="summary">Holds info from a KEGG Enzyme record.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.KEGG.Compound.Record-class.html">Bio.KEGG.Compound.Record</a></strong>:
<em class="summary">Holds info from a KEGG Ligand/Compound record.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.SCOP.Dom.Record-class.html">Bio.SCOP.Dom.Record</a></strong>:
<em class="summary">Holds information for one SCOP domain.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Geo.Record.Record-class.html">Bio.Geo.Record.Record</a></strong>:
<em class="summary">Hold GEO information in a format similar to the original record.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Compass.Record-class.html">Bio.Compass.Record</a></strong>:
<em class="summary">Hold information from one compass hit.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Cluster.Record-class.html">Bio.Cluster.Record</a></strong>:
<em class="summary">A Record stores the gene expression data and related information
contained in a data file following the file format defined for
Michael Eisen's Cluster/TreeView program.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.PopGen.FDist.Record-class.html">Bio.PopGen.FDist.Record</a></strong>:
<em class="summary">Holds information from a FDist record.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Sequencing.Phd.Record-class.html">Bio.Sequencing.Phd.Record</a></strong>:
<em class="summary">Hold information from a PHD file.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Fasta.Record-class.html">Bio.Fasta.Record</a></strong>:
<em class="summary">Holds information from a FASTA record.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.SwissProt.SProt.Record-class.html">Bio.SwissProt.SProt.Record</a></strong>:
<em class="summary">Holds information from a SwissProt record.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Gobase.Record-class.html">Bio.Gobase.Record</a></strong>:
<em class="summary">Holds information from a Gobase record.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.Gobase.GeneRecord-class.html">Bio.Gobase.GeneRecord</a></strong>:
<em class="summary">Holds information from a Gobase record.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Gobase.ProteinRecord-class.html">Bio.Gobase.ProteinRecord</a></strong>:
<em class="summary">Holds information from a Gobase record.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Gobase.SequenceRecord-class.html">Bio.Gobase.SequenceRecord</a></strong>:
<em class="summary">Holds information from a Gobase record.</em>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.NBRF.Record.Record-class.html">Bio.NBRF.Record.Record</a></strong>:
<em class="summary">Hold NBRF information in a format similar to the original record.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.GenBank.Record.Record-class.html">Bio.GenBank.Record.Record</a></strong>:
<em class="summary">Hold GenBank information in a format similar to the original
record.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Saf.Record.Record-class.html">Bio.Saf.Record.Record</a></strong>:
<em class="summary">Hold Saf information in a format similar to the original record.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.MetaTool.Record.Record-class.html">Bio.MetaTool.Record.Record</a></strong>:
<em class="summary">Hold MetaTool output information.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.PopGen.GenePop.Record-class.html">Bio.PopGen.GenePop.Record</a></strong>:
<em class="summary">Holds information from a GenePop record.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.SCOP.Des.Record-class.html">Bio.SCOP.Des.Record</a></strong>:
<em class="summary">Holds information for one node in the SCOP hierarchy.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.SCOP.Cla.Record-class.html">Bio.SCOP.Cla.Record</a></strong>:
<em class="summary">Holds information for one SCOP domain</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Prosite.Prodoc.Record-class.html">Bio.Prosite.Prodoc.Record</a></strong>:
<em class="summary">Holds information from a Prodoc record.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.ECell.Record.Record-class.html">Bio.ECell.Record.Record</a></strong>:
<em class="summary">Hold ECell information in a format similar to the original record.</em>
</li>
<li> <strong class="uidlink"><a href="Martel.Iterator.RecordEventStream-class.html">Martel.Iterator.RecordEventStream</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.GenBank.RecordParser-class.html">Bio.GenBank.RecordParser</a></strong>:
<em class="summary">Parse GenBank files into Record objects</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Rebase.RecordParser-class.html">Bio.Rebase.RecordParser</a></strong>:
<em class="summary">Parses FASTA sequence data into a Record object.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.MetaTool.RecordParser-class.html">Bio.MetaTool.RecordParser</a></strong>:
<em class="summary">Parse MetaTool files into Record objects</em>
</li>
<li> <strong class="uidlink"><a href="Bio.IntelliGenetics.RecordParser-class.html">Bio.IntelliGenetics.RecordParser</a></strong>:
<em class="summary">Parse IntelliGenetics files into Record objects</em>
</li>
<li> <strong class="uidlink"><a href="Bio.CDD.RecordParser-class.html">Bio.CDD.RecordParser</a></strong>:
<em class="summary">Parse CDD files into Record objects</em>
</li>
<li> <strong class="uidlink"><a href="Bio.ECell.RecordParser-class.html">Bio.ECell.RecordParser</a></strong>:
<em class="summary">Parse ECell files into Record objects</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Fasta.RecordParser-class.html">Bio.Fasta.RecordParser</a></strong>:
<em class="summary">Parses FASTA sequence data into a Fasta.Record object.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Gobase.RecordParser-class.html">Bio.Gobase.RecordParser</a></strong>:
<em class="summary">Parses Gobase sequence data into a Record object.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.LocusLink.RecordParser-class.html">Bio.LocusLink.RecordParser</a></strong>:
<em class="summary">Parse LocusLink files into Record objects</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Saf.RecordParser-class.html">Bio.Saf.RecordParser</a></strong>:
<em class="summary">Parse Saf files into Record objects</em>
</li>
<li> <strong class="uidlink"><a href="Bio.NBRF.RecordParser-class.html">Bio.NBRF.RecordParser</a></strong>:
<em class="summary">Parse NBRF files into Record objects</em>
</li>
<li> <strong class="uidlink"><a href="Martel.RecordReader.RecordReader-class.html">Martel.RecordReader.RecordReader</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Martel.RecordReader.CountLines-class.html">Martel.RecordReader.CountLines</a></strong>:
<em class="summary">Read a specified (fixed) number of lines</em>
</li>
<li> <strong class="uidlink"><a href="Martel.RecordReader.EndsWith-class.html">Martel.RecordReader.EndsWith</a></strong>
</li>
<li> <strong class="uidlink"><a href="Martel.RecordReader.Everything-class.html">Martel.RecordReader.Everything</a></strong>:
<em class="summary">Reads everything</em>
</li>
<li> <strong class="uidlink"><a href="Bio.IntelliGenetics.IntelliGeneticsReader-class.html">Bio.IntelliGenetics.IntelliGeneticsReader</a></strong>
</li>
<li> <strong class="uidlink"><a href="Martel.RecordReader.Nothing-class.html">Martel.RecordReader.Nothing</a></strong>:
<em class="summary">Reads nothing</em>
</li>
<li> <strong class="uidlink"><a href="Martel.RecordReader.StartsWith-class.html">Martel.RecordReader.StartsWith</a></strong>
</li>
<li> <strong class="uidlink"><a href="Martel.RecordReader.Until-class.html">Martel.RecordReader.Until</a></strong>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.Prosite.Prodoc.Reference-class.html">Bio.Prosite.Prodoc.Reference</a></strong>:
<em class="summary">Holds information from a Prodoc citation.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.SeqFeature.Reference-class.html">Bio.SeqFeature.Reference</a></strong>:
<em class="summary">Represent a Generic Reference object.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.SwissProt.SProt.Reference-class.html">Bio.SwissProt.SProt.Reference</a></strong>:
<em class="summary">Holds information from 1 references in a SwissProt entry.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.GenBank.Record.Reference-class.html">Bio.GenBank.Record.Reference</a></strong>:
<em class="summary">Hold information from a GenBank reference.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.config.Registry.RegisterableObject-class.html">Bio.config.Registry.RegisterableObject</a></strong>:
<em class="summary">This is a base class for objects that can be added to a registry.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.config.DBRegistry.DBObject-class.html">Bio.config.DBRegistry.DBObject</a></strong>:
<em class="summary">This is a base class for dictionary-like interfaces to
databases.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.config.DBRegistry.BioCorbaDB-class.html">Bio.config.DBRegistry.BioCorbaDB</a></strong>:
<em class="summary">Represent a BioCorba BioSequenceCollection for SeqRecord objects.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.config.DBRegistry.BioSQLDB-class.html">Bio.config.DBRegistry.BioSQLDB</a></strong>:
<em class="summary">Represent a BioSQL-style database to retrieve SeqRecord objects.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.config.DBRegistry.CGIDB-class.html">Bio.config.DBRegistry.CGIDB</a></strong>:
<em class="summary">This class implements DBObject for accessing CGI databases.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.config.DBRegistry.EUtilsDB-class.html">Bio.config.DBRegistry.EUtilsDB</a></strong>:
<em class="summary">Implement DBObject for accessing EUtils databases at NCBI.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.config.DBRegistry.IndexedFileDB-class.html">Bio.config.DBRegistry.IndexedFileDB</a></strong>:
<em class="summary">Return SeqRecord objects from an indexed file.</em>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.config.FormatRegistry.FormatObject-class.html">Bio.config.FormatRegistry.FormatObject</a></strong>:
<em class="summary">This object stores Biopython file formats and provides methods to
work on them.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.config.Registry.RegisterableGroup-class.html">Bio.config.Registry.RegisterableGroup</a></strong>:
<em class="summary">This is a base class for a RegisterableObject that groups many
objects together.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.config.DBRegistry.DBGroup-class.html">Bio.config.DBRegistry.DBGroup</a></strong>:
<em class="summary">Groups DBObjects that return the same kind of data.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.config.FormatRegistry.FormatGroup-class.html">Bio.config.FormatRegistry.FormatGroup</a></strong>:
<em class="summary">This object holds a group of FormatObjects.</em>
</li>
</ul>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.config.Registry.Registry-class.html">Bio.config.Registry.Registry</a></strong>:
<em class="summary">This is a dictionary-like object for storing and retrieving
objects in a registry.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.config.DBRegistry.DBRegistry-class.html">Bio.config.DBRegistry.DBRegistry</a></strong>:
<em class="summary">This implements a dictionary-like interface to databases.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.config.SeqDBRegistry.SeqDBRegistry-class.html">Bio.config.SeqDBRegistry.SeqDBRegistry</a></strong>:
<em class="summary">This object implements a dictionary-like interface to sequence
databases.</em>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.config.FormatRegistry.FormatRegistry-class.html">Bio.config.FormatRegistry.FormatRegistry</a></strong>:
<em class="summary">This implements a dictionary-like interface to Biopython file
formats.</em>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Martel.Dispatch.RemapEnd-class.html">Martel.Dispatch.RemapEnd</a></strong>
</li>
<li> <strong class="uidlink"><a href="Martel.Dispatch.RemapStart-class.html">Martel.Dispatch.RemapStart</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.WWW.RequestLimiter-class.html">Bio.WWW.RequestLimiter</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.SCOP.Raf.Res-class.html">Bio.SCOP.Raf.Res</a></strong>:
<em class="summary">A single residue mapping from a RAF record.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.ReseekFile.ReseekFile-class.html">Bio.EUtils.ReseekFile.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.SCOP.Residues%27.Residues-class.html">Bio.SCOP.Residues'.Residues</a></strong>:
<em class="summary">A collection of residues from a PDB structure.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Blast.Record.Round-class.html">Bio.Blast.Record.Round</a></strong>:
<em class="summary">Holds information from a PSI-BLAST round.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.SGMLExtractor.SGMLExtractor-class.html">Bio.SGMLExtractor.SGMLExtractor</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.SGMLExtractor.SGMLExtractorHandle-class.html">Bio.SGMLExtractor.SGMLExtractorHandle</a></strong>:
<em class="summary">A Python handle that automatically strips SGML tags and returns
data from specified tag start and end pairs.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.File.SGMLHandle-class.html">Bio.File.SGMLHandle</a></strong>:
<em class="summary">A Python handle that automatically strips SGML tags from data.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.File.SGMLStripper-class.html">Bio.File.SGMLStripper</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.ParserSupport.SGMLStrippingConsumer-class.html">Bio.ParserSupport.SGMLStrippingConsumer</a></strong>:
<em class="summary">A consumer that strips off SGML tags.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.SVDSuperimposer.SVDSuperimposer%27.SVDSuperimposer-class.html">Bio.SVDSuperimposer.SVDSuperimposer'.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>
</li>
<li> <strong class="uidlink"><a href="Bio.GA.Crossover.General.SafeFitnessCrossover-class.html">Bio.GA.Crossover.General.SafeFitnessCrossover</a></strong>:
<em class="summary">Perform crossovers, but do not allow decreases in organism fitness.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.GA.Mutation.General.SafeFitnessMutation-class.html">Bio.GA.Mutation.General.SafeFitnessMutation</a></strong>:
<em class="summary">Perform mutations, but do not allow decreases in organism fitness.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.NeuralNetwork.Gene.Schema.Schema-class.html">Bio.NeuralNetwork.Gene.Schema.Schema</a></strong>:
<em class="summary">Deal with motifs that have ambiguity characters in it.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.NeuralNetwork.Gene.Schema.SchemaCoder-class.html">Bio.NeuralNetwork.Gene.Schema.SchemaCoder</a></strong>:
<em class="summary">Convert a sequence into a representation of ambiguous motifs
(schemas).</em>
</li>
<li> <strong class="uidlink"><a href="Bio.NeuralNetwork.Gene.Schema.SchemaFactory-class.html">Bio.NeuralNetwork.Gene.Schema.SchemaFactory</a></strong>:
<em class="summary">Generate Schema from inputs of Motifs or Signatures.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.NeuralNetwork.Gene.Schema.SchemaFinder-class.html">Bio.NeuralNetwork.Gene.Schema.SchemaFinder</a></strong>:
<em class="summary">Find schema in a set of sequences using a genetic algorithm
approach.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.SCOP.Scop-class.html">Bio.SCOP.Scop</a></strong>:
<em class="summary">The entire SCOP hierarchy.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Search.Search-class.html">Bio.Search.Search</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.Datatypes.SearchResult-class.html">Bio.EUtils.Datatypes.SearchResult</a></strong>:
<em class="summary">Store results from a database search</em>
</li>
<li> <strong class="uidlink"><a href="Bio.PDB.PDBIO%27.Select-class.html">Bio.PDB.PDBIO'.Select</a></strong>:
<em class="summary">Default selection (everything) during writing - can be used as base
class to implement selective output.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Seq.Seq-class.html">Bio.Seq.Seq</a></strong>
<ul>
<li> <strong class="uidlink"><a href="BioSQL.BioSeq.DBSeq-class.html">BioSQL.BioSeq.DBSeq</a></strong>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.SeqFeature.SeqFeature-class.html">Bio.SeqFeature.SeqFeature</a></strong>:
<em class="summary">Represent a Sequence Feature on an object.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.SCOP.Raf.SeqMap-class.html">Bio.SCOP.Raf.SeqMap</a></strong>:
<em class="summary">An ASTRAL RAF (Rapid Access Format) Sequence Map.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.SeqRecord.SeqRecord-class.html">Bio.SeqRecord.SeqRecord</a></strong>:
<em class="summary">A SeqRecord object holds a sequence and information about it.</em>
<ul>
<li> <strong class="uidlink"><a href="BioSQL.BioSeq.DBSeqRecord-class.html">BioSQL.BioSeq.DBSeqRecord</a></strong>:
<em class="summary">BioSQL equivalent of the biopython SeqRecord object.</em>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DBIdsClient.SequenceDBIdsFetchMixin-class.html">Bio.EUtils.DBIdsClient.SequenceDBIdsFetchMixin</a></strong>:
<em class="summary">Support 'efetch' for sequence records</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.EUtils.DBIdsClient.SequenceDBIdsRecord-class.html">Bio.EUtils.DBIdsClient.SequenceDBIdsRecord</a></strong>:
<em class="summary">a single sequence record, referenced by database identifier</em>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DBIdsClient.SequenceDBIdsRecordSet-class.html">Bio.EUtils.DBIdsClient.SequenceDBIdsRecordSet</a></strong>:
<em class="summary">a set of sequence records, referenced by database identifier</em>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.HistoryClient.SequenceHistoryFetchMixin-class.html">Bio.EUtils.HistoryClient.SequenceHistoryFetchMixin</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.EUtils.HistoryClient.SequenceHistoryRecord-class.html">Bio.EUtils.HistoryClient.SequenceHistoryRecord</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.HistoryClient.SequenceHistoryRecordSet-class.html">Bio.EUtils.HistoryClient.SequenceHistoryRecordSet</a></strong>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.SeqIO.Interfaces.SequenceIterator-class.html">Bio.SeqIO.Interfaces.SequenceIterator</a></strong>:
<em class="summary">Base class for building SeqRecord iterators.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.SeqIO.Interfaces.InterlacedSequenceIterator-class.html">Bio.SeqIO.Interfaces.InterlacedSequenceIterator</a></strong>:
<em class="summary">Base class for any iterator of a non-sequential file type.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.SeqIO.StockholmIO.StockholmIterator-class.html">Bio.SeqIO.StockholmIO.StockholmIterator</a></strong>:
<em class="summary">Loads a Stockholm file from PFAM into SeqRecord objects.</em>
</li>
</ul>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.Fasta.SequenceParser-class.html">Bio.Fasta.SequenceParser</a></strong>:
<em class="summary">Parses FASTA sequence data into a SeqRecord object.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.SeqIO.Interfaces.SequenceWriter-class.html">Bio.SeqIO.Interfaces.SequenceWriter</a></strong>:
<em class="summary">This class should be subclassed.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.SeqIO.ClustalIO.ClustalWriter-class.html">Bio.SeqIO.ClustalIO.ClustalWriter</a></strong>:
<em class="summary">Write Clustal sequence alignments.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.SeqIO.PhylipIO.PhylipWriter-class.html">Bio.SeqIO.PhylipIO.PhylipWriter</a></strong>:
<em class="summary">Write interlaced Phylip sequence alignments.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.SeqIO.Interfaces.SequentialSequenceWriter-class.html">Bio.SeqIO.Interfaces.SequentialSequenceWriter</a></strong>:
<em class="summary">This class should be subclassed.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.SeqIO.FastaIO.FastaWriter-class.html">Bio.SeqIO.FastaIO.FastaWriter</a></strong>:
<em class="summary">Class to write Fasta format files.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.SeqIO.StockholmIO.StockholmWriter-class.html">Bio.SeqIO.StockholmIO.StockholmWriter</a></strong>:
<em class="summary">Class to write PFAM style Stockholm format files.</em>
</li>
</ul>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Martel.Generate.SetGroupValue-class.html">Martel.Generate.SetGroupValue</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.NeuralNetwork.Gene.Signature.SignatureCoder-class.html">Bio.NeuralNetwork.Gene.Signature.SignatureCoder</a></strong>:
<em class="summary">Convert a Sequence into its signature representatives.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.NeuralNetwork.Gene.Signature.SignatureFinder-class.html">Bio.NeuralNetwork.Gene.Signature.SignatureFinder</a></strong>:
<em class="summary">Find Signatures in a group of sequence records.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.PopGen.SimCoal.Cache.SimCoalCache-class.html">Bio.PopGen.SimCoal.Cache.SimCoalCache</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.PopGen.SimCoal.Controller.SimCoalController-class.html">Bio.PopGen.SimCoal.Controller.SimCoalController</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.NeuralNetwork.Gene.Schema.SimpleFinisher-class.html">Bio.NeuralNetwork.Gene.Schema.SimpleFinisher</a></strong>:
<em class="summary">Determine when we are done evolving motifs.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.GA.Mutation.Simple.SinglePositionMutation-class.html">Bio.GA.Mutation.Simple.SinglePositionMutation</a></strong>:
<em class="summary">Perform a conversion mutation, but only at a single point in the
genome.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.sourcegen.SourceFile-class.html">Bio.EUtils.sourcegen.SourceFile</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.sourcegen.SourceGen-class.html">Bio.EUtils.sourcegen.SourceGen</a></strong>:
<em class="summary">SourceGen(outfile, [bangline]) An instance of this SourceGen class
is a factory for generating python source code, by writing to a
file object.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.PopGen.FDist.Async.SplitFDist-class.html">Bio.PopGen.FDist.Async.SplitFDist</a></strong>:
<em class="summary">Splits a FDist run.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.config._stanzaformat.Stanza-class.html">Bio.config._stanzaformat.Stanza</a></strong>:
<em class="summary">Contains information about one stanza in a file.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.config._stanzaformat.StanzaFormat-class.html">Bio.config._stanzaformat.StanzaFormat</a></strong>:
<em class="summary">Contains information from a stanza-formatted file.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Std.StdTerm-class.html">Bio.Std.StdTerm</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.GA.Evolver.SteadyStateEvolver-class.html">Bio.GA.Evolver.SteadyStateEvolver</a></strong>:
<em class="summary">Evolve a population in place.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Nexus.Nexus.StepMatrix-class.html">Bio.Nexus.Nexus.StepMatrix</a></strong>:
<em class="summary">Calculate a stepmatrix for weighted parsimony.</em>
</li>
<li> <strong class="uidlink"><a href="Martel.test.support.Storage-class.html">Martel.test.support.Storage</a></strong>
</li>
<li> <strong class="uidlink"><a href="Martel.Iterator.StoreEvents-class.html">Martel.Iterator.StoreEvents</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.PDB.StructureAlignment%27.StructureAlignment-class.html">Bio.PDB.StructureAlignment'.StructureAlignment</a></strong>:
<em class="summary">This class aligns two structures based on a FASTA alignment of
their sequences.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.PDB.StructureBuilder.StructureBuilder-class.html">Bio.PDB.StructureBuilder.StructureBuilder</a></strong>:
<em class="summary">Deals with contructing the Structure object.</em>
</li>
<li> <strong class="uidlink"><a href="Martel.msre_parse.SubPattern-class.html">Martel.msre_parse.SubPattern</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.Datatypes.Summary-class.html">Bio.EUtils.Datatypes.Summary</a></strong>:
<em class="summary">Store information from calling eSummary</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Align.AlignInfo.SummaryInfo-class.html">Bio.Align.AlignInfo.SummaryInfo</a></strong>:
<em class="summary">Calculate summary info about the alignment.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.PDB.Superimposer%27.Superimposer-class.html">Bio.PDB.Superimposer'.Superimposer</a></strong>:
<em class="summary">Rotate/translate one set of atoms on top of another, thereby
minimizing the RMSD.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.GenBank.LocationParser.Symbol-class.html">Bio.GenBank.LocationParser.Symbol</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.Pathway.System-class.html">Bio.Pathway.System</a></strong>:
<em class="summary">Abstraction for a collection of reactions.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Search.TableInfo-class.html">Bio.Search.TableInfo</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.config.DBRegistry.TextLikeMixin-class.html">Bio.config.DBRegistry.TextLikeMixin</a></strong>:
<em class="summary">Mixin class with useful functionality for retrival of text files.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.config.DBRegistry.CGIDB-class.html">Bio.config.DBRegistry.CGIDB</a></strong>:
<em class="summary">This class implements DBObject for accessing CGI databases.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.config.DBRegistry.EUtilsDB-class.html">Bio.config.DBRegistry.EUtilsDB</a></strong>:
<em class="summary">Implement DBObject for accessing EUtils databases at NCBI.</em>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.ThinClient.ThinClient-class.html">Bio.EUtils.ThinClient.ThinClient</a></strong>:
<em class="summary">Client-side interface to the EUtils services</em>
</li>
<li> <strong class="uidlink"><a href="Bio.GenBank.LocationParser.Token-class.html">Bio.GenBank.LocationParser.Token</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.Decode.Token-class.html">Bio.Decode.Token</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.Decode.ValueToken-class.html">Bio.Decode.ValueToken</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.Decode.Float-class.html">Bio.Decode.Float</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.Decode.FunctionName-class.html">Bio.Decode.FunctionName</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.Decode.Integer-class.html">Bio.Decode.Integer</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.Decode.String-class.html">Bio.Decode.String</a></strong>
</li>
</ul>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.LocusLink.web_parse.Token-class.html">Bio.LocusLink.web_parse.Token</a></strong>
</li>
<li> <strong class="uidlink"><a href="Martel.msre_parse.Tokenizer-class.html">Martel.msre_parse.Tokenizer</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.NeuralNetwork.Training.TrainingExample-class.html">Bio.NeuralNetwork.Training.TrainingExample</a></strong>:
<em class="summary">Hold inputs and outputs of a training example.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.HMM.Trainer.TrainingSequence-class.html">Bio.HMM.Trainer.TrainingSequence</a></strong>:
<em class="summary">Hold a training sequence with emissions and optionally, a state
path.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Transcribe.Transcribe-class.html">Bio.Transcribe.Transcribe</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.Translate.Translator-class.html">Bio.Translate.Translator</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.GenBank.LocationParser.TwoBound-class.html">Bio.GenBank.LocationParser.TwoBound</a></strong>
</li>
<li> <strong class="uidlink">urllib.URLopener</strong>:
<em class="summary">Class to open URLs.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.File.UndoHandle-class.html">Bio.File.UndoHandle</a></strong>:
<em class="summary">A Python handle that adds functionality for saving lines.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.GA.Crossover.Uniform.UniformCrossover-class.html">Bio.GA.Crossover.Uniform.UniformCrossover</a></strong>:
<em class="summary">Perform single point crossover between genomes at some defined
rates.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.UniGene.UnigeneProtsimRecord-class.html">Bio.UniGene.UnigeneProtsimRecord</a></strong>:
<em class="summary">Store the information for one PROTSIM line from a Unigene file</em>
</li>
<li> <strong class="uidlink"><a href="Bio.UniGene.UnigeneRecord-class.html">Bio.UniGene.UnigeneRecord</a></strong>:
<em class="summary">Store a Unigene record</em>
</li>
<li> <strong class="uidlink"><a href="Bio.UniGene.UnigeneSTSRecord-class.html">Bio.UniGene.UnigeneSTSRecord</a></strong>:
<em class="summary">Store the information for one STS line from a Unigene file</em>
</li>
<li> <strong class="uidlink"><a href="Bio.UniGene.UnigeneSequenceRecord-class.html">Bio.UniGene.UnigeneSequenceRecord</a></strong>:
<em class="summary">Store the information for one SEQUENCE line from a Unigene file</em>
</li>
<li> <strong class="uidlink"><a href="Bio.DBXRef.UnknownDBName-class.html">Bio.DBXRef.UnknownDBName</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.NetCatch.Url-class.html">Bio.NetCatch.Url</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.LocusLink.web_parse.Url-class.html">Bio.LocusLink.web_parse.Url</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.parse.UsePOMParser-class.html">Bio.EUtils.parse.UsePOMParser</a></strong>
</li>
<li> <strong class="uidlink">UserDict.UserDict</strong>
</li>
<li> <strong class="uidlink"><a href="Bio.NeuralNetwork.StopTraining.ValidationIncreaseStop-class.html">Bio.NeuralNetwork.StopTraining.ValidationIncreaseStop</a></strong>:
<em class="summary">Class to stop training on a network when the validation error
increases.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.PDB.Vector%27.Vector-class.html">Bio.PDB.Vector'.Vector</a></strong>:
<em class="summary">3D vector</em>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.Datatypes.WithinNDays-class.html">Bio.EUtils.Datatypes.WithinNDays</a></strong>:
<em class="summary">Restrict a search to matches in the last N days</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Mindy.BaseDB.WriteDB-class.html">Bio.Mindy.BaseDB.WriteDB</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.Mindy.FlatDB.MemoryFlatDB-class.html">Bio.Mindy.FlatDB.MemoryFlatDB</a></strong>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.Writer.Writer-class.html">Bio.Writer.Writer</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.writers.SeqRecord.embl.WriteEmbl-class.html">Bio.writers.SeqRecord.embl.WriteEmbl</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.writers.SeqRecord.empty.WriteEmpty-class.html">Bio.writers.SeqRecord.empty.WriteEmpty</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.writers.SeqRecord.fasta.WriteFasta-class.html">Bio.writers.SeqRecord.fasta.WriteFasta</a></strong>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.POM.XMLAttribute-class.html">Bio.EUtils.POM.XMLAttribute</a></strong>
</li>
<li> <strong class="uidlink">xml.sax.xmlreader.XMLReader</strong>:
<em class="summary">Interface for reading an XML document using callbacks.</em>
<ul>
<li> <strong class="uidlink"><a href="Martel.Parser.HeaderFooterParser-class.html">Martel.Parser.HeaderFooterParser</a></strong>:
<em class="summary">Header followed by 0 or more records followed by a footer</em>
</li>
<li> <strong class="uidlink"><a href="Martel.Parser.Parser-class.html">Martel.Parser.Parser</a></strong>:
<em class="summary">Parse the input data all in memory</em>
</li>
<li> <strong class="uidlink"><a href="Martel.Parser.RecordParser-class.html">Martel.Parser.RecordParser</a></strong>:
<em class="summary">Parse the input data a record at a time</em>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.NMR.xpktools.XpkEntry-class.html">Bio.NMR.xpktools.XpkEntry</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.Application._AbstractParameter-class.html" onclick="show_private();">Bio.Application._AbstractParameter</a></strong>:
<em class="summary">A class to hold information about a parameter for a commandline.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.Application._Argument-class.html" onclick="show_private();">Bio.Application._Argument</a></strong>:
<em class="summary">Represent an argument on a commandline.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Application._Option-class.html" onclick="show_private();">Bio.Application._Option</a></strong>:
<em class="summary">Represent an option that can be set for a program.</em>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.Blast.NCBIStandalone._AlignmentConsumer-class.html" onclick="show_private();">Bio.Blast.NCBIStandalone._AlignmentConsumer</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.Blast.NCBIStandalone._BlastConsumer-class.html" onclick="show_private();">Bio.Blast.NCBIStandalone._BlastConsumer</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.Blast.NCBIStandalone._BlastErrorConsumer-class.html" onclick="show_private();">Bio.Blast.NCBIStandalone._BlastErrorConsumer</a></strong>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.Blast.NCBIStandalone._PSIBlastConsumer-class.html" onclick="show_private();">Bio.Blast.NCBIStandalone._PSIBlastConsumer</a></strong>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.MultiDict._BaseMultiDict-class.html" onclick="show_private();">Bio.EUtils.MultiDict._BaseMultiDict</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.EUtils.MultiDict.OrderedMultiDict-class.html">Bio.EUtils.MultiDict.OrderedMultiDict</a></strong>:
<em class="summary">Store key/value mappings.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.MultiDict.UnorderedMultiDict-class.html">Bio.EUtils.MultiDict.UnorderedMultiDict</a></strong>:
<em class="summary">Store key/value mappings.</em>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.Compass._Consumer-class.html" onclick="show_private();">Bio.Compass._Consumer</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.POM._ContentModelGenerator-class.html">Bio.EUtils.POM._ContentModelGenerator</a></strong>:
<em class="summary">_ContentModelGenerator(rawmodel) The DTD parser generated and final
content model are so different that a different content model
generator is used for this object.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Blast.NCBIStandalone._DatabaseReportConsumer-class.html" onclick="show_private();">Bio.Blast.NCBIStandalone._DatabaseReportConsumer</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.Blast.NCBIStandalone._BlastConsumer-class.html" onclick="show_private();">Bio.Blast.NCBIStandalone._BlastConsumer</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.Blast.NCBIStandalone._BlastErrorConsumer-class.html" onclick="show_private();">Bio.Blast.NCBIStandalone._BlastErrorConsumer</a></strong>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.Blast.NCBIStandalone._PSIBlastConsumer-class.html" onclick="show_private();">Bio.Blast.NCBIStandalone._PSIBlastConsumer</a></strong>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.Blast.NCBIStandalone._DescriptionConsumer-class.html" onclick="show_private();">Bio.Blast.NCBIStandalone._DescriptionConsumer</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.Blast.NCBIStandalone._BlastConsumer-class.html" onclick="show_private();">Bio.Blast.NCBIStandalone._BlastConsumer</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.Blast.NCBIStandalone._BlastErrorConsumer-class.html" onclick="show_private();">Bio.Blast.NCBIStandalone._BlastErrorConsumer</a></strong>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.Blast.NCBIStandalone._PSIBlastConsumer-class.html" onclick="show_private();">Bio.Blast.NCBIStandalone._PSIBlastConsumer</a></strong>
</li>
</ul>
</li>
<li> <strong class="uidlink">reportlab.graphics.shapes._DrawTimeResizeable</strong>:
<em class="summary">Addin class to provide the horribleness of _drawTimeResize</em>
<ul>
<li> <strong class="uidlink">reportlab.graphics.shapes.UserNode</strong>:
<em class="summary">A simple template for creating a new node.</em>
<ul>
<li> <strong class="uidlink">reportlab.graphics.widgetbase.Widget</strong>:
<em class="summary">Base for all user-defined widgets.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.Graphics.BasicChromosome._ChromosomeComponent-class.html" onclick="show_private();">Bio.Graphics.BasicChromosome._ChromosomeComponent</a></strong>:
<em class="summary">Base class specifying the interface for a component of the system.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.Graphics.BasicChromosome.Chromosome-class.html">Bio.Graphics.BasicChromosome.Chromosome</a></strong>:
<em class="summary">Class for drawing a chromosome of an organism.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Graphics.BasicChromosome.ChromosomeSegment-class.html">Bio.Graphics.BasicChromosome.ChromosomeSegment</a></strong>:
<em class="summary">Draw a segment of a chromosome.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.Graphics.BasicChromosome.TelomereSegment-class.html">Bio.Graphics.BasicChromosome.TelomereSegment</a></strong>:
<em class="summary">A segment that is located at the end of a linear chromosome.</em>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.Graphics.BasicChromosome.Organism-class.html">Bio.Graphics.BasicChromosome.Organism</a></strong>:
<em class="summary">Top level class for drawing chromosomes.</em>
</li>
</ul>
</li>
</ul>
</li>
</ul>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.Blast.NCBIStandalone._HSPConsumer-class.html" onclick="show_private();">Bio.Blast.NCBIStandalone._HSPConsumer</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.Blast.NCBIStandalone._BlastConsumer-class.html" onclick="show_private();">Bio.Blast.NCBIStandalone._BlastConsumer</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.Blast.NCBIStandalone._BlastErrorConsumer-class.html" onclick="show_private();">Bio.Blast.NCBIStandalone._BlastErrorConsumer</a></strong>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.Blast.NCBIStandalone._PSIBlastConsumer-class.html" onclick="show_private();">Bio.Blast.NCBIStandalone._PSIBlastConsumer</a></strong>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.Blast.NCBIStandalone._HeaderConsumer-class.html" onclick="show_private();">Bio.Blast.NCBIStandalone._HeaderConsumer</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.Blast.NCBIStandalone._BlastConsumer-class.html" onclick="show_private();">Bio.Blast.NCBIStandalone._BlastConsumer</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.Blast.NCBIStandalone._BlastErrorConsumer-class.html" onclick="show_private();">Bio.Blast.NCBIStandalone._BlastErrorConsumer</a></strong>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.Blast.NCBIStandalone._PSIBlastConsumer-class.html" onclick="show_private();">Bio.Blast.NCBIStandalone._PSIBlastConsumer</a></strong>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Martel.LAX._IsIn-class.html" onclick="show_private();">Martel.LAX._IsIn</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.MEME.Parser._MASTConsumer-class.html" onclick="show_private();">Bio.MEME.Parser._MASTConsumer</a></strong>:
<em class="summary">Consumer that can receive events from _MASTScanner.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.MEME.Parser._MASTScanner-class.html" onclick="show_private();">Bio.MEME.Parser._MASTScanner</a></strong>:
<em class="summary">Scanner for MAST text output.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.MEME.Parser._MEMEConsumer-class.html" onclick="show_private();">Bio.MEME.Parser._MEMEConsumer</a></strong>:
<em class="summary">Consumer that can receive events from MEME Scanner.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.MEME.Parser._MEMEScanner-class.html" onclick="show_private();">Bio.MEME.Parser._MEMEScanner</a></strong>:
<em class="summary">Scanner for MEME output.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.PDB.Polypeptide._PPBuilder-class.html" onclick="show_private();">Bio.PDB.Polypeptide._PPBuilder</a></strong>:
<em class="summary">Base class to extract polypeptides.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.PDB.Polypeptide.CaPPBuilder-class.html">Bio.PDB.Polypeptide.CaPPBuilder</a></strong>:
<em class="summary">Use CA--CA distance to find polypeptides.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.PDB.Polypeptide.PPBuilder-class.html">Bio.PDB.Polypeptide.PPBuilder</a></strong>:
<em class="summary">Use C--N distance to find polypeptides.</em>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.Blast.NCBIStandalone._ParametersConsumer-class.html" onclick="show_private();">Bio.Blast.NCBIStandalone._ParametersConsumer</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.Blast.NCBIStandalone._BlastConsumer-class.html" onclick="show_private();">Bio.Blast.NCBIStandalone._BlastConsumer</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.Blast.NCBIStandalone._BlastErrorConsumer-class.html" onclick="show_private();">Bio.Blast.NCBIStandalone._BlastErrorConsumer</a></strong>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.Blast.NCBIStandalone._PSIBlastConsumer-class.html" onclick="show_private();">Bio.Blast.NCBIStandalone._PSIBlastConsumer</a></strong>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.Emboss.Primer._Primer3Scanner-class.html" onclick="show_private();">Bio.Emboss.Primer._Primer3Scanner</a></strong>:
<em class="summary">Scan output from the primer3 program.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Emboss.Primer._PrimerSearchScanner-class.html" onclick="show_private();">Bio.Emboss.Primer._PrimerSearchScanner</a></strong>:
<em class="summary">Scan output from the primersearch program.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.NBRF._RecordConsumer-class.html" onclick="show_private();">Bio.NBRF._RecordConsumer</a></strong>:
<em class="summary">Create an NBRF Record object from scanner generated information.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.MetaTool._RecordConsumer-class.html">Bio.MetaTool._RecordConsumer</a></strong>:
<em class="summary">Create a MetaTool Record object from scanner generated information.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.IntelliGenetics._RecordConsumer-class.html" onclick="show_private();">Bio.IntelliGenetics._RecordConsumer</a></strong>:
<em class="summary">Create an IntelliGenetics Record object from scanner generated
information.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.ECell._RecordConsumer-class.html" onclick="show_private();">Bio.ECell._RecordConsumer</a></strong>:
<em class="summary">Create an ECell Record object from scanner generated information.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Compass._Scanner-class.html" onclick="show_private();">Bio.Compass._Scanner</a></strong>:
<em class="summary">Reads compass output and generate events</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Sequencing.Ace._Scanner-class.html" onclick="show_private();">Bio.Sequencing.Ace._Scanner</a></strong>:
<em class="summary">Scans an ACE-formatted file.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.NBRF._Scanner-class.html" onclick="show_private();">Bio.NBRF._Scanner</a></strong>:
<em class="summary">Start up Martel to do the scanning of the file.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Sequencing.Phd._Scanner-class.html" onclick="show_private();">Bio.Sequencing.Phd._Scanner</a></strong>:
<em class="summary">Scans a PHD-formatted file.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.ECell._Scanner-class.html" onclick="show_private();">Bio.ECell._Scanner</a></strong>:
<em class="summary">Start up Martel to do the scanning of the file.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.CDD._Scanner-class.html" onclick="show_private();">Bio.CDD._Scanner</a></strong>:
<em class="summary">Start up Martel to do the scanning of the file.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.MetaTool._Scanner-class.html">Bio.MetaTool._Scanner</a></strong>:
<em class="summary">Start up Martel to do the scanning of the file.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.UniGene._Scanner-class.html" onclick="show_private();">Bio.UniGene._Scanner</a></strong>:
<em class="summary">Scans a Unigene Flat File Format file</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Blast.NCBIStandalone._Scanner-class.html" onclick="show_private();">Bio.Blast.NCBIStandalone._Scanner</a></strong>:
<em class="summary">Scan BLAST output from blastall or blastpgp.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Prosite._Scanner-class.html" onclick="show_private();">Bio.Prosite._Scanner</a></strong>:
<em class="summary">Scans Prosite-formatted data.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Prosite.Prodoc._Scanner-class.html" onclick="show_private();">Bio.Prosite.Prodoc._Scanner</a></strong>:
<em class="summary">Scans Prodoc-formatted data.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.PopGen.GenePop._Scanner-class.html" onclick="show_private();">Bio.PopGen.GenePop._Scanner</a></strong>:
<em class="summary">Scans a GenePop record.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.SwissProt.KeyWList._Scanner-class.html" onclick="show_private();">Bio.SwissProt.KeyWList._Scanner</a></strong>:
<em class="summary">Scan the keywlist.txt file included with the SwissProt
distribution.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Medline._Scanner-class.html" onclick="show_private();">Bio.Medline._Scanner</a></strong>:
<em class="summary">Scans a Medline record.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Gobase._Scanner-class.html" onclick="show_private();">Bio.Gobase._Scanner</a></strong>:
<em class="summary">Scans a gobase file.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Saf._Scanner-class.html" onclick="show_private();">Bio.Saf._Scanner</a></strong>:
<em class="summary">Start up Martel to do the scanning of the file.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Rebase._Scanner-class.html" onclick="show_private();">Bio.Rebase._Scanner</a></strong>:
<em class="summary">Scans a rebase file.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.LocusLink._Scanner-class.html" onclick="show_private();">Bio.LocusLink._Scanner</a></strong>:
<em class="summary">Start up Martel to do the scanning of the file.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.SwissProt.SProt._Scanner-class.html" onclick="show_private();">Bio.SwissProt.SProt._Scanner</a></strong>:
<em class="summary">Scans SwissProt-formatted data.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.IntelliGenetics._Scanner-class.html" onclick="show_private();">Bio.IntelliGenetics._Scanner</a></strong>:
<em class="summary">Start up Martel to do the scanning of the file.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.PopGen.FDist._Scanner-class.html">Bio.PopGen.FDist._Scanner</a></strong>:
<em class="summary">Scans a FDist record.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Enzyme._Scanner-class.html" onclick="show_private();">Bio.Enzyme._Scanner</a></strong>:
<em class="summary">Scans Enzyme data.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Blast.NCBIWWW._Scanner-class.html" onclick="show_private();">Bio.Blast.NCBIWWW._Scanner</a></strong>:
<em class="summary">Scan BLAST output from NCBI's web server at:
http://www.ncbi.nlm.nih.gov/BLAST/</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Search._SeqLength-class.html" onclick="show_private();">Bio.Search._SeqLength</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.Search.HSP-class.html">Bio.Search.HSP</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.Search.HSPSeq-class.html">Bio.Search.HSPSeq</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.Search.HomologySeq-class.html">Bio.Search.HomologySeq</a></strong>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Martel.Generate._call_call-class.html" onclick="show_private();">Martel.Generate._call_call</a></strong>
</li>
<li> <strong class="uidlink"><a href="Martel.Generate._call_calltag-class.html" onclick="show_private();">Martel.Generate._call_calltag</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.KDTree.CKDTree._object-class.html" onclick="show_private();">Bio.KDTree.CKDTree._object</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.Sequencing.Ace.af-class.html">Bio.Sequencing.Ace.af</a></strong>:
<em class="summary">AF lines, define the location of the read within the contig.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.pairwise2.affine_penalty-class.html">Bio.pairwise2.affine_penalty</a></strong>:
<em class="summary">affine_penalty(open, extend[, penalize_extend_when_opening]) ->
gap_fn</em>
</li>
<li> <strong class="uidlink"><a href="Bio.FSSP.fssp_rec.align-class.html">Bio.FSSP.fssp_rec.align</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.Sequencing.Ace.bs-class.html">Bio.Sequencing.Ace.bs</a></strong>:
<em class="summary">"BS (base segment), which read was chosen as the consensus at
each position.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Sequencing.Ace.ct-class.html">Bio.Sequencing.Ace.ct</a></strong>:
<em class="summary">CT (consensus tags).</em>
</li>
<li> <strong class="uidlink"><a href="Bio.pairwise2.dictionary_match-class.html">Bio.pairwise2.dictionary_match</a></strong>:
<em class="summary">dictionary_match(score_dict[, symmetric]) -> match_fn</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Sequencing.Ace.ds-class.html">Bio.Sequencing.Ace.ds</a></strong>:
<em class="summary">DS lines, include file name of a read's chromatogram file.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.FSSP.fssp_rec.fff_rec-class.html">Bio.FSSP.fssp_rec.fff_rec</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.pairwise2.identity_match-class.html">Bio.pairwise2.identity_match</a></strong>:
<em class="summary">identity_match([match][, mismatch]) -> match_fn</em>
</li>
<li> <strong class="uidlink"><a href="Bio.kNN.kNN-class.html">Bio.kNN.kNN</a></strong>:
<em class="summary">Holds information necessary to do nearest neighbors classification.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.config._support.make_cached_expression-class.html">Bio.config._support.make_cached_expression</a></strong>:
<em class="summary">make_cached_expression(expression) -> cached expression object</em>
</li>
<li> <strong class="uidlink"><a href="Bio.config._support.make_rate_limited_function-class.html">Bio.config._support.make_rate_limited_function</a></strong>:
<em class="summary">make_rate_limited_function(function, delay) -> callable object</em>
</li>
<li> <strong class="uidlink">object</strong>:
<em class="summary">The most base type</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.GFF.GenericTools.ArgsParser-class.html">Bio.GFF.GenericTools.ArgsParser</a></strong>:
<em class="summary"> </em>
</li>
<li> <strong class="uidlink">exceptions.BaseException</strong>:
<em class="summary">Common base class for all exceptions</em>
<ul>
<li> <strong class="uidlink">exceptions.Exception</strong>:
<em class="summary">Common base class for all non-exit exceptions.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.Wise.psw.AlignmentColumnFullException-class.html">Bio.Wise.psw.AlignmentColumnFullException</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.CAPS.AlignmentHasDifferentLengthsError-class.html">Bio.CAPS.AlignmentHasDifferentLengthsError</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.SubsMat.BadMatrix-class.html">Bio.SubsMat.BadMatrix</a></strong>:
<em class="summary">Exception raised when verifying a matrix</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Nexus.Nodes.ChainException-class.html">Bio.Nexus.Nodes.ChainException</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.Datatypes.EUtilsError-class.html">Bio.EUtils.Datatypes.EUtilsError</a></strong>:
<em class="summary">Base class for all EUtils-specific errors</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.EUtils.Datatypes.EUtilsSearchError-class.html">Bio.EUtils.Datatypes.EUtilsSearchError</a></strong>:
<em class="summary">Used when the ESearch XML says there is an ERROR</em>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.Crystal.Error-class.html">Bio.Crystal.Error</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.Crystal.CrystalError-class.html">Bio.Crystal.CrystalError</a></strong>:
<em class="summary">message - description of error</em>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.ECell.Error-class.html">Bio.ECell.Error</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.ECell.ECellError-class.html">Bio.ECell.ECellError</a></strong>:
<em class="summary">message - description of error</em>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.GenBank.LocationParserError-class.html">Bio.GenBank.LocationParserError</a></strong>:
<em class="summary">Could not Properly parse out a location from a GenBank file.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Blast.NCBIStandalone.LowQualityBlastError-class.html">Bio.Blast.NCBIStandalone.LowQualityBlastError</a></strong>:
<em class="summary">Error caused by running a low quality sequence through BLAST.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.MissingExternalDependencyError-class.html">Bio.MissingExternalDependencyError</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.Nexus.Nexus.NexusError-class.html">Bio.Nexus.Nexus.NexusError</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.Nexus.Nodes.NodeException-class.html">Bio.Nexus.Nodes.NodeException</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.GenBank.ParserFailureError-class.html">Bio.GenBank.ParserFailureError</a></strong>:
<em class="summary">Failure caused by some kind of problem in the parser.</em>
</li>
<li> <strong class="uidlink">xml.sax._exceptions.SAXException</strong>:
<em class="summary">Encapsulate an XML error or warning.</em>
<ul>
<li> <strong class="uidlink"><a href="Martel.Parser.ParserException-class.html">Martel.Parser.ParserException</a></strong>:
<em class="summary">used when a parse cannot be done</em>
<ul>
<li> <strong class="uidlink"><a href="Martel.Parser.ParserPositionException-class.html">Martel.Parser.ParserPositionException</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Martel.Parser.ParserIncompleteException-class.html">Martel.Parser.ParserIncompleteException</a></strong>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Martel.Parser.ParserRecordException-class.html">Martel.Parser.ParserRecordException</a></strong>:
<em class="summary">used by the RecordParser when it can't read a record</em>
</li>
</ul>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.Blast.NCBIStandalone.ShortQueryBlastError-class.html">Bio.Blast.NCBIStandalone.ShortQueryBlastError</a></strong>:
<em class="summary">Error caused by running a short query sequence through BLAST.</em>
</li>
<li> <strong class="uidlink">exceptions.StandardError</strong>:
<em class="summary">Base class for all standard Python exceptions that do not represent
interpreter exiting.</em>
<ul>
<li> <strong class="uidlink">exceptions.EnvironmentError</strong>:
<em class="summary">Base class for I/O related errors.</em>
<ul>
<li> <strong class="uidlink">exceptions.IOError</strong>:
<em class="summary">I/O operation failed.</em>
</li>
</ul>
</li>
<li> <strong class="uidlink">exceptions.TypeError</strong>:
<em class="summary">Inappropriate argument type.</em>
<ul>
<li> <strong class="uidlink"><a href="Martel.RecordReader.ReaderError-class.html">Martel.RecordReader.ReaderError</a></strong>
</li>
</ul>
</li>
<li> <strong class="uidlink">exceptions.ValueError</strong>:
<em class="summary">Inappropriate argument value (of correct type).</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.Restriction._Update.Update.FtpNameError-class.html">Bio.Restriction._Update.Update.FtpNameError</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.Restriction._Update.Update.FtpPasswordError-class.html">Bio.Restriction._Update.Update.FtpPasswordError</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.Restriction._Update.RestrictionCompiler.OverhangError-class.html">Bio.Restriction._Update.RestrictionCompiler.OverhangError</a></strong>:
<em class="summary">Exception for dealing with overhang.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.POM.ValidationError-class.html">Bio.EUtils.POM.ValidationError</a></strong>:
<em class="summary">ValidationError This exception is raised when an attempt is made to
construct an XML POM tree that would be invalid.</em>
</li>
</ul>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.Data.CodonTable.TranslationError-class.html">Bio.Data.CodonTable.TranslationError</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.Nexus.Trees.TreeError-class.html">Bio.Nexus.Trees.TreeError</a></strong>
</li>
<li> <strong class="uidlink"><a href="Martel.msre_constants.error-class.html">Martel.msre_constants.error</a></strong>
</li>
</ul>
</li>
</ul>
</li>
<li> <strong class="uidlink">sets.BaseSet</strong>:
<em class="summary">Common base class for mutable and immutable sets.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.Datatypes.CheckLinkSet-class.html">Bio.EUtils.Datatypes.CheckLinkSet</a></strong>:
<em class="summary">Results from 'ncheck' and 'lcheck' searches</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Wise.psw.ColumnUnit-class.html">Bio.Wise.psw.ColumnUnit</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DBIdsClient.DBIdsLookup-class.html">Bio.EUtils.DBIdsClient.DBIdsLookup</a></strong>:
<em class="summary">Look up information about a DBIds</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.EUtils.DBIdsClient.BaseDBIdsRecordSet-class.html">Bio.EUtils.DBIdsClient.BaseDBIdsRecordSet</a></strong>:
<em class="summary">Base class for dealing with a set of records, reference by
identifier</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.EUtils.DBIdsClient.PublicationDBIdsRecordSet-class.html">Bio.EUtils.DBIdsClient.PublicationDBIdsRecordSet</a></strong>:
<em class="summary">a set of publication records, referenced by database identifier</em>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DBIdsClient.SequenceDBIdsRecordSet-class.html">Bio.EUtils.DBIdsClient.SequenceDBIdsRecordSet</a></strong>:
<em class="summary">a set of sequence records, referenced by database identifier</em>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DBIdsClient.DBIdsRecord-class.html">Bio.EUtils.DBIdsClient.DBIdsRecord</a></strong>:
<em class="summary">A single record on the server</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.EUtils.DBIdsClient.PublicationDBIdsRecord-class.html">Bio.EUtils.DBIdsClient.PublicationDBIdsRecord</a></strong>:
<em class="summary">a single publication record, referenced by database identifier</em>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.DBIdsClient.SequenceDBIdsRecord-class.html">Bio.EUtils.DBIdsClient.SequenceDBIdsRecord</a></strong>:
<em class="summary">a single sequence record, referenced by database identifier</em>
</li>
</ul>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder-class.html">Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.GFF.Feature-class.html">Bio.GFF.Feature</a></strong>:
<em class="summary">strand may be: +/0 = Watson -/1 = Crick</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Restriction.Restriction.FormattedSeq-class.html">Bio.Restriction.Restriction.FormattedSeq</a></strong>:
<em class="summary">FormattedSeq(seq, [linear=True])-> new FormattedSeq.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.HistoryClient.HistoryLookup-class.html">Bio.EUtils.HistoryClient.HistoryLookup</a></strong>:
<em class="summary">Look up information about a search in history</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.EUtils.HistoryClient.BaseHistoryRecordSet-class.html">Bio.EUtils.HistoryClient.BaseHistoryRecordSet</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.EUtils.HistoryClient.PublicationHistoryRecordSet-class.html">Bio.EUtils.HistoryClient.PublicationHistoryRecordSet</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.HistoryClient.SequenceHistoryRecordSet-class.html">Bio.EUtils.HistoryClient.SequenceHistoryRecordSet</a></strong>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.HistoryClient.HistoryRecord-class.html">Bio.EUtils.HistoryClient.HistoryRecord</a></strong>:
<em class="summary">Get information about a single record in a history</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.EUtils.HistoryClient.PublicationHistoryRecord-class.html">Bio.EUtils.HistoryClient.PublicationHistoryRecord</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.HistoryClient.SequenceHistoryRecord-class.html">Bio.EUtils.HistoryClient.SequenceHistoryRecord</a></strong>
</li>
</ul>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.DocSQL.IterationCursor-class.html">Bio.DocSQL.IterationCursor</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.Datatypes.LinkSetDb-class.html">Bio.EUtils.Datatypes.LinkSetDb</a></strong>:
<em class="summary">Used in eLink with cmd == neighbor</em>
</li>
<li> <strong class="uidlink"><a href="Bio.GFF.binning.Meta-class.html">Bio.GFF.binning.Meta</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.AlignAce.Motif.Motif-class.html">Bio.AlignAce.Motif.Motif</a></strong>:
<em class="summary">A class representing sequence motifs.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Nexus.Nexus.Nexus-class.html">Bio.Nexus.Nexus.Nexus</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.Restriction.PrintFormat.PrintFormat-class.html">Bio.Restriction.PrintFormat.PrintFormat</a></strong>:
<em class="summary">PrintFormat allow the printing of results of restriction analysis.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.DocSQL.Query-class.html">Bio.DocSQL.Query</a></strong>:
<em class="summary">SHOW TABLES</em>
</li>
<li> <strong class="uidlink"><a href="Bio.GFF.Segment-class.html">Bio.GFF.Segment</a></strong>:
<em class="summary">this will only work for the simplest of easy.Location objects</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Wise.dnal.Statistics-class.html">Bio.Wise.dnal.Statistics</a></strong>:
<em class="summary">Calculate statistics from an ALB report</em>
</li>
<li> <strong class="uidlink"><a href="Bio.GFF.GenericTools.Surrogate-class.html">Bio.GFF.GenericTools.Surrogate</a></strong>:
<em class="summary">the data is stored in _data</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Restriction._Update.RestrictionCompiler.TypeCompiler-class.html">Bio.Restriction._Update.RestrictionCompiler.TypeCompiler</a></strong>:
<em class="summary">Build the different types possible for Restriction Enzymes</em>
</li>
<li> <strong class="uidlink">basestring</strong>:
<em class="summary">Type basestring cannot be instantiated; it is the base for str and
unicode.</em>
<ul>
<li> <strong class="uidlink">str</strong>:
<em class="summary">str(object) -> string</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.EUtils.POM.IndentedText-class.html">Bio.EUtils.POM.IndentedText</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.EUtils.POM.Comment-class.html">Bio.EUtils.POM.Comment</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.POM.Text-class.html">Bio.EUtils.POM.Text</a></strong>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.Entrez.Parser.StringElement-class.html">Bio.Entrez.Parser.StringElement</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.POM._AttributeType-class.html">Bio.EUtils.POM._AttributeType</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.EUtils.POM.CDATA-class.html">Bio.EUtils.POM.CDATA</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.POM.ENTITY-class.html">Bio.EUtils.POM.ENTITY</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.POM.ID-class.html">Bio.EUtils.POM.ID</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.POM.IDREF-class.html">Bio.EUtils.POM.IDREF</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.POM.NMTOKEN-class.html">Bio.EUtils.POM.NMTOKEN</a></strong>
</li>
</ul>
</li>
</ul>
</li>
<li> <strong class="uidlink">unicode</strong>:
<em class="summary">unicode(string [, encoding[, errors]]) -> object</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.Entrez.Parser.UnicodeElement-class.html">Bio.Entrez.Parser.UnicodeElement</a></strong>
</li>
</ul>
</li>
</ul>
</li>
<li> <strong class="uidlink">dict</strong>:
<em class="summary">dict() -> new empty dictionary.</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.GFF.GenericTools.AppendableListDictionary-class.html">Bio.GFF.GenericTools.AppendableListDictionary</a></strong>:
<em class="summary">a dictionary of lists</em>
</li>
<li> <strong class="uidlink"><a href="Bio.PropertyManager.CreateDict-class.html">Bio.PropertyManager.CreateDict</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.Config.DatabaseDict-class.html">Bio.EUtils.Config.DatabaseDict</a></strong>:
<em class="summary">map from name to DatabaseInfo for that database name</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Entrez.Parser.DictionaryElement-class.html">Bio.Entrez.Parser.DictionaryElement</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.FSSP.FSSPAlignDict-class.html">Bio.FSSP.FSSPAlignDict</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.FSSP.FSSPTools.FSSPMultAlign-class.html">Bio.FSSP.FSSPTools.FSSPMultAlign</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.FSSP.FSSPSumDict-class.html">Bio.FSSP.FSSPSumDict</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.GFF.easy.FeatureDict-class.html">Bio.GFF.easy.FeatureDict</a></strong>:
<em class="summary">JH: accessing feature.qualifiers as a list is stupid.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.SCOP.FileIndex.FileIndex-class.html">Bio.SCOP.FileIndex.FileIndex</a></strong>:
<em class="summary">An in memory index that allows rapid random access into a file.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.SubsMat.FreqTable.FreqTable-class.html">Bio.SubsMat.FreqTable.FreqTable</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.SCOP.Cla.Index-class.html">Bio.SCOP.Cla.Index</a></strong>:
<em class="summary">A CLA file indexed by SCOP identifiers, allowing rapid random
access into a file.</em>
</li>
<li> <strong class="uidlink"><a href="Martel.LAX.LAX-class.html">Martel.LAX.LAX</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Martel.LAX.LAXAttrs-class.html">Martel.LAX.LAXAttrs</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Martel.LAX.LAXPositions-class.html">Martel.LAX.LAXPositions</a></strong>
</li>
</ul>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.MetaTool.Record.Metabolite-class.html">Bio.MetaTool.Record.Metabolite</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.MetaTool.Record.MetaboliteRole-class.html">Bio.MetaTool.Record.MetaboliteRole</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.CDD.Record.Record-class.html">Bio.CDD.Record.Record</a></strong>:
<em class="summary">Hold CDD information in a format similar to the original record.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Ndb.Record-class.html">Bio.Ndb.Record</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.SwissProt.KeyWList.Record-class.html">Bio.SwissProt.KeyWList.Record</a></strong>:
<em class="summary">This record stores the information of one keyword or category in the
keywlist.txt as a Python dictionary.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.InterPro.Record-class.html">Bio.InterPro.Record</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.LocusLink.Record-class.html">Bio.LocusLink.Record</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.LocusLink.web_parse.Record-class.html">Bio.LocusLink.web_parse.Record</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.SCOP.Raf.SeqMapIndex-class.html">Bio.SCOP.Raf.SeqMapIndex</a></strong>:
<em class="summary">An RAF file index.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.SubsMat.SeqMat-class.html">Bio.SubsMat.SeqMat</a></strong>:
<em class="summary">A Generic sequence matrix class The key is a 2-tuple containing the
letter indices of the matrix.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Entrez.Parser.StructureElement-class.html">Bio.Entrez.Parser.StructureElement</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.GFF.GenericTools.VerboseDict-class.html">Bio.GFF.GenericTools.VerboseDict</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.Index._InMemoryIndex-class.html">Bio.Index._InMemoryIndex</a></strong>:
<em class="summary">This creates an in-memory index file.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Index._ShelveIndex-class.html" onclick="show_private();">Bio.Index._ShelveIndex</a></strong>:
<em class="summary">An index file wrapped around shelve.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.SCOP.FileIndex.defaultdict-class.html">Bio.SCOP.FileIndex.defaultdict</a></strong>
</li>
</ul>
</li>
<li> <strong class="uidlink">file</strong>:
<em class="summary">file(name[, mode[, buffering]]) -> file object</em>
</li>
<li> <strong class="uidlink">int</strong>:
<em class="summary">int(x[, base]) -> integer</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.Entrez.Parser.IntegerElement-class.html">Bio.Entrez.Parser.IntegerElement</a></strong>
</li>
</ul>
</li>
<li> <strong class="uidlink">list</strong>:
<em class="summary">list() -> new list list(sequence) -> new list initialized
from sequence's items</em>
<ul>
<li> <strong class="uidlink"><a href="Bio.Wise.psw.Alignment-class.html">Bio.Wise.psw.Alignment</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.Wise.psw.AlignmentColumn-class.html">Bio.Wise.psw.AlignmentColumn</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.POM.AttributeList-class.html">Bio.EUtils.POM.AttributeList</a></strong>
<ul>
<li> <strong class="uidlink"><a href="Bio.EUtils.POM.ENTITIES-class.html">Bio.EUtils.POM.ENTITIES</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.POM.IDREFS-class.html">Bio.EUtils.POM.IDREFS</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.POM.NMTOKENS-class.html">Bio.EUtils.POM.NMTOKENS</a></strong>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.EUtils.POM.Enumeration-class.html">Bio.EUtils.POM.Enumeration</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.GFF.FeatureAggregate-class.html">Bio.GFF.FeatureAggregate</a></strong>:
<em class="summary"> </em>
</li>
<li> <strong class="uidlink"><a href="Bio.Entrez.Parser.ListElement-class.html">Bio.Entrez.Parser.ListElement</a></strong>
</li>
<li> <strong class="uidlink"><a href="Bio.PDB.Polypeptide.Polypeptide-class.html">Bio.PDB.Polypeptide.Polypeptide</a></strong>:
<em class="summary">A polypeptide is simply a list of <a
href="Bio.PDB.Residue.Residue-class.html" class="link">Residue</a>
objects.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.GFF.GenericTools.VerboseList-class.html">Bio.GFF.GenericTools.VerboseList</a></strong>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Bio.Restriction._Update.RestrictionCompiler.newenzyme-class.html">Bio.Restriction._Update.RestrictionCompiler.newenzyme</a></strong>:
<em class="summary">construct the attributes of the enzyme corresponding to 'name'.</em>
</li>
<li> <strong class="uidlink">type</strong>:
<em class="summary">type(object) -> the object's type type(name, bases, dict) ->
a new type</em>
</li>
</ul>
</li>
<li> <strong class="uidlink"><a href="Martel.Generate.print_debug-class.html">Martel.Generate.print_debug</a></strong>:
<em class="summary">Print debug information</em>
</li>
<li> <strong class="uidlink"><a href="Martel.Generate.print_info-class.html">Martel.Generate.print_info</a></strong>:
<em class="summary">Print information after each expression match</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Sequencing.Ace.qa-class.html">Bio.Sequencing.Ace.qa</a></strong>:
<em class="summary">QA (read quality), including which part if any was used as the
consensus.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Sequencing.Ace.rd-class.html">Bio.Sequencing.Ace.rd</a></strong>:
<em class="summary">RD (reads), store a read with its name, sequence etc.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Sequencing.Ace.rt-class.html">Bio.Sequencing.Ace.rt</a></strong>:
<em class="summary">RT (transient read tags), generated by crossmatch and phrap.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Sequencing.Ace.wa-class.html">Bio.Sequencing.Ace.wa</a></strong>:
<em class="summary">WA (whole assembly tag), holds the assembly program name, version,
etc.</em>
</li>
<li> <strong class="uidlink"><a href="Bio.Sequencing.Ace.wr-class.html">Bio.Sequencing.Ace.wr</a></strong>:
<em class="summary">WR lines.</em>
</li>
</ul>
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