Module Hierarchy

• Bio: Collection of modules for dealing with biological data in Python.
  • Bio.Affy: Deal with Affymetrix related data such as cel files.
    • Bio.Affy.CelFile: Reading information from Affymetrix CEL files version 3 and 4.
  • Bio.Align: Code for dealing with sequence alignments.
    • Bio.Align.AlignInfo: Extract information from alignment objects.
    • Bio.Align.Applications: Alignment command line tool wrappers.
      • Bio.Align.Applications._ClustalOmega: Command line wrapper for the multiple alignment program Clustal Omega.
      • Bio.Align.Applications._Clustalw: Command line wrapper for the multiple alignment program Clustal W.
      • Bio.Align.Applications._Dialign: Command line wrapper for the multiple alignment program DIALIGN2-2.
      • Bio.Align.Applications._MSAProbs: Command line wrapper for the multiple sequence alignment program MSAProbs.
      • Bio.Align.Applications._Mafft: Command line wrapper for the multiple alignment programme MAFFT.
      • Bio.Align.Applications._Muscle: Command line wrapper for the multiple alignment program MUSCLE.
      • Bio.Align.Applications._Prank: Command line wrapper for the multiple alignment program PRANK.
      • Bio.Align.Applications._Probcons: Command line wrapper for the multiple alignment program PROBCONS.
      • Bio.Align.Applications._TCoffee: Command line wrapper for the multiple alignment program TCOFFEE.
    • Bio.Align._aligners: C extension module implementing pairwise alignment algorithms
    • Bio.Align.substitution_matrices: Substitution matrices.
  • Bio.AlignIO: Multiple sequence alignment input/output as alignment objects.
    • Bio.AlignIO.ClustalIO: Bio.AlignIO support for "clustal" output from CLUSTAL W and other tools.
    • Bio.AlignIO.EmbossIO: Bio.AlignIO support for "emboss" alignment output from EMBOSS tools.
    • Bio.AlignIO.FastaIO: Bio.AlignIO support for "fasta-m10" output from Bill Pearson's FASTA tools.
    • Bio.AlignIO.Interfaces: AlignIO support module (not for general use).
    • Bio.AlignIO.MafIO: Bio.AlignIO support for the "maf" multiple alignment format.
    • Bio.AlignIO.MauveIO: Bio.AlignIO support for "xmfa" output from Mauve/ProgressiveMauve.
    • Bio.AlignIO.MsfIO: Bio.AlignIO support for GCG MSF format.
    • Bio.AlignIO.NexusIO: Bio.AlignIO support for the "nexus" file format.
    • Bio.AlignIO.PhylipIO: AlignIO support for "phylip" format from Joe Felsenstein's PHYLIP tools.
    • Bio.AlignIO.StockholmIO: Bio.AlignIO support for "stockholm" format (used in the PFAM database).
  • Bio.Alphabet: Alphabets used in Seq objects etc to declare sequence type and letters (OBSOLETE).
    • Bio.Alphabet.IUPAC: Standard nucleotide and protein alphabets defined by IUPAC.
    • Bio.Alphabet.Reduced: Reduced alphabets which lump together several amino-acids into one letter.
  • Bio.Application: General mechanisms to access applications in Biopython.
  • Bio.Blast: Code for dealing with BLAST programs and output.
    • Bio.Blast.Applications: Definitions for interacting with BLAST related applications.
    • Bio.Blast.NCBIWWW: Code to invoke the NCBI BLAST server over the internet.
    • Bio.Blast.NCBIXML: Code to work with the BLAST XML output.
    • Bio.Blast.ParseBlastTable: A parser for the NCBI blastpgp version 2.2.5 output format.
    • Bio.Blast.Record: Record classes to hold BLAST output.
  • Bio.CAPS: Cleaved amplified polymorphic sequence (CAPS) markers.
  • Bio.Cluster: Cluster Analysis.
    • Bio.Cluster._cluster: C Clustering Library
  • Bio.Compass: Code to deal with COMPASS output, a program for profile/profile comparison.
  • Bio.Crystal: Represent the NDB Atlas structure (a minimal subset of PDB format) (OBSOLETE).
  • Bio.Data: Collections of various bits of useful biological data.
    • Bio.Data.CodonTable: Codon tables based on those from the NCBI.
    • Bio.Data.IUPACData: Information about the IUPAC alphabets.
    • Bio.Data.SCOPData: Additional protein alphabets used in the SCOP database and PDB files.
  • Bio.Emboss: Code to interact with the ever-so-useful EMBOSS programs.
    • Bio.Emboss.Applications: Code to interact with and run various EMBOSS programs.
    • Bio.Emboss.Primer3: Code to parse output from the EMBOSS eprimer3 program.
    • Bio.Emboss.PrimerSearch: Code to interact with the primersearch program from EMBOSS.
  • Bio.Entrez: Provides code to access NCBI over the WWW.
    • Bio.Entrez.Parser: Parser for XML results returned by NCBI's Entrez Utilities.
  • Bio.ExPASy: Code to access resources at ExPASy over the WWW.
    • Bio.ExPASy.Enzyme: Parse the enzyme.dat file from Enzyme at ExPASy.
    • Bio.ExPASy.Prodoc: Code to work with the prosite.doc file from Prosite.
    • Bio.ExPASy.Prosite: Parser for the prosite dat file from Prosite at ExPASy.
    • Bio.ExPASy.ScanProsite: Code for calling and parsing ScanProsite from ExPASy.
    • Bio.ExPASy.cellosaurus: Parser for the cellosaurus.txt file from ExPASy.
  • Bio.FSSP: Parser for FSSP files, used in a database of protein fold classifications.
    • Bio.FSSP.FSSPTools: Several routines used to extract information from FSSP sections.
    • Bio.FSSP.fssp_rec: A superclass for reading [f]ixed-column type [f]lat-[f]ile records.
  • Bio.File: Code for more fancy file handles.
  • Bio.GenBank: Code to work with GenBank formatted files.
    • Bio.GenBank.Record: Hold GenBank data in a straightforward format.
    • Bio.GenBank.Scanner: Internal code for parsing GenBank and EMBL files (PRIVATE).
    • Bio.GenBank.utils: Useful utilities for helping in parsing GenBank files.
  • Bio.Geo: Parser for files from NCBI's Gene Expression Omnibus (GEO).
    • Bio.Geo.Record: Hold GEO data in a straightforward format.
  • Bio.Graphics: Bio.Graphics offers several graphical outputs, all using ReportLab.
    • Bio.Graphics.BasicChromosome: Draw representations of organism chromosomes with added information.
    • Bio.Graphics.ColorSpiral: Generate RGB colours suitable for distinguishing categorical data.
    • Bio.Graphics.Comparative: Plots to compare information between different sources.
    • Bio.Graphics.DisplayRepresentation: Represent information for graphical display.
    • Bio.Graphics.Distribution: Display information distributed across a Chromosome-like object.
    • Bio.Graphics.GenomeDiagram: GenomeDiagram module integrated into Biopython.
      • Bio.Graphics.GenomeDiagram._AbstractDrawer: AbstractDrawer module (considered to be a private module, the API may change!).
      • Bio.Graphics.GenomeDiagram._CircularDrawer: CircularDrawer module for GenomeDiagram.
      • Bio.Graphics.GenomeDiagram._Colors: Colors module.
      • Bio.Graphics.GenomeDiagram._CrossLink: Genome Diagram Feature cross-link module.
      • Bio.Graphics.GenomeDiagram._Diagram: Provides a container for information concerning the tracks to be drawn in a diagram.
      • Bio.Graphics.GenomeDiagram._Feature: Feature module.
      • Bio.Graphics.GenomeDiagram._FeatureSet: FeatureSet module.
      • Bio.Graphics.GenomeDiagram._Graph: Graph module.
      • Bio.Graphics.GenomeDiagram._GraphSet: GraphSet module.
      • Bio.Graphics.GenomeDiagram._LinearDrawer: Linear Drawer module.
      • Bio.Graphics.GenomeDiagram._Track: Track module.
    • Bio.Graphics.KGML_vis: Classes and functions to visualise a KGML Pathway Map.
  • Bio.HMM: A selection of Hidden Markov Model code.
    • Bio.HMM.DynamicProgramming: Dynamic Programming algorithms for general usage.
    • Bio.HMM.MarkovModel: Deal with representations of Markov Models.
    • Bio.HMM.Trainer: Provide trainers which estimate parameters based on training sequences.
    • Bio.HMM.Utilities: Generic functions which are useful for working with HMMs.
  • Bio.Index: Index text files.
  • Bio.KDTree: KD tree data structure for searching N-dimensional vectors (DEPRECATED).
    • Bio.KDTree.KDTree
    • Bio.KDTree.KDTree': KD tree data structure for searching N-dimensional vectors.
    • Bio.KDTree._CKDTree
  • Bio.KEGG: Code to work with data from the KEGG database.
    • Bio.KEGG.Compound: Code to work with the KEGG Ligand/Compound database.
    • Bio.KEGG.Enzyme: Code to work with the KEGG Enzyme database.
    • Bio.KEGG.Gene: Code to work with the KEGG Gene database.
    • Bio.KEGG.KGML: Code to work with data from the KEGG database.
      • Bio.KEGG.KGML.KGML_parser: Classes and functions to parse a KGML pathway map.
      • Bio.KEGG.KGML.KGML_pathway: Classes to represent a KGML Pathway Map.
    • Bio.KEGG.Map: Load KEGG Pathway maps for use with the Biopython Pathway module.
    • Bio.KEGG.REST: Provides code to access the REST-style KEGG online API.
  • Bio.LogisticRegression: Code for doing logistic regressions.
  • Bio.MarkovModel: A state-emitting MarkovModel.
  • Bio.MaxEntropy: Maximum Entropy code.
  • Bio.Medline: Code to work with Medline from the NCBI.
  • Bio.NMR: Code for working with NMR data.
    • Bio.NMR.NOEtools: NOEtools: For predicting NOE coordinates from assignment data.
    • Bio.NMR.xpktools: Tools to manipulate data from nmrview .xpk peaklist files.
  • Bio.NaiveBayes: General Naive Bayes learner.
  • Bio.Nexus: The Bio.Nexus contains a NEXUS file parser and objects to model this data.
    • Bio.Nexus.Nexus: Nexus class. Parse the contents of a NEXUS file.
    • Bio.Nexus.Nodes: Linked list functionality for use in Bio.Nexus.
    • Bio.Nexus.StandardData: Objects to represent NEXUS standard data type matrix coding.
    • Bio.Nexus.Trees: Tree class to handle phylogenetic trees.
    • Bio.Nexus.cnexus
  • Bio.PDB: Classes that deal with macromolecular crystal structures.
    • Bio.PDB.AbstractPropertyMap: Class that maps (chain_id, residue_id) to a residue property.
    • Bio.PDB.Atom: Atom class, used in Structure objects.
    • Bio.PDB.Chain: Chain class, used in Structure objects.
    • Bio.PDB.DSSP
    • Bio.PDB.DSSP': Use the DSSP program to calculate secondary structure and accessibility.
    • Bio.PDB.Dice: Code for chopping up (dicing) a structure.
    • Bio.PDB.Entity: Base class for Residue, Chain, Model and Structure classes.
    • Bio.PDB.FragmentMapper
    • Bio.PDB.FragmentMapper': Classify protein backbone structure with Kolodny et al's fragment libraries.
    • Bio.PDB.HSExposure: Half-sphere exposure and coordination number calculation.
    • Bio.PDB.MMCIF2Dict: Turn an mmCIF file into a dictionary.
    • Bio.PDB.MMCIFParser
    • Bio.PDB.MMCIFParser': mmCIF parsers.
    • Bio.PDB.Model: Model class, used in Structure objects.
    • Bio.PDB.NACCESS: Interface for the program NACCESS.
    • Bio.PDB.NeighborSearch
    • Bio.PDB.NeighborSearch': Fast atom neighbor lookup using a KD tree (implemented in C).
    • Bio.PDB.PDBExceptions: Some Bio.PDB-specific exceptions.
    • Bio.PDB.PDBIO
    • Bio.PDB.PDBIO': Output of PDB files.
    • Bio.PDB.PDBList
    • Bio.PDB.PDBList': Access the PDB over the internet (e.g. to download structures).
    • Bio.PDB.PDBParser
    • Bio.PDB.PDBParser': Parser for PDB files.
    • Bio.PDB.PSEA: Wrappers for PSEA, a program for secondary structure assignment.
    • Bio.PDB.Polypeptide: Polypeptide-related classes (construction and representation).
    • Bio.PDB.QCPSuperimposer: Structural alignment using Quaternion Characteristic Polynomial (QCP).
      • Bio.PDB.QCPSuperimposer.qcprotmodule
    • Bio.PDB.Residue: Residue class, used by Structure objects.
    • Bio.PDB.ResidueDepth
    • Bio.PDB.ResidueDepth': Calculation of residue depth using command line tool MSMS.
    • Bio.PDB.Selection: Selection of atoms, residues, etc.
    • Bio.PDB.Structure: The structure class, representing a macromolecular structure.
    • Bio.PDB.StructureAlignment
    • Bio.PDB.StructureAlignment': Map residues of two structures to each other based on a FASTA alignment.
    • Bio.PDB.StructureBuilder: Consumer class that builds a Structure object.
    • Bio.PDB.Superimposer
    • Bio.PDB.Superimposer': Superimpose two structures.
    • Bio.PDB.kdtrees
    • Bio.PDB.mmcifio: Write an mmCIF file.
    • Bio.PDB.mmtf: Support for loading 3D structures stored in MMTF files.
      • Bio.PDB.mmtf.DefaultParser: Code handle loading mmtf-python into Biopython's structures.
      • Bio.PDB.mmtf.mmtfio: Write a MMTF file.
    • Bio.PDB.parse_pdb_header
    • Bio.PDB.parse_pdb_header': Parse header of PDB files into a python dictionary.
    • Bio.PDB.vectors: Vector class, including rotation-related functions.
  • Bio.Pathway: BioPython Pathway module.
    • Bio.Pathway.Rep: BioPython Pathway support module.
      • Bio.Pathway.Rep.Graph: get/set abstraction for graph representation.
      • Bio.Pathway.Rep.MultiGraph: get/set abstraction for multi-graph representation.
  • Bio.Phylo: Package for working with phylogenetic trees.
    • Bio.Phylo.Applications: Phylogenetics command line tool wrappers.
      • Bio.Phylo.Applications._Fasttree: Command-line wrapper for tree inference program Fasttree.
      • Bio.Phylo.Applications._Phyml: Command-line wrapper for the tree inference program PhyML.
      • Bio.Phylo.Applications._Raxml: Command-line wrapper for the tree inference program RAxML.
    • Bio.Phylo.BaseTree: Base classes for Bio.Phylo objects.
    • Bio.Phylo.CDAO: Classes corresponding to CDAO trees.
    • Bio.Phylo.CDAOIO: I/O function wrappers for the RDF/CDAO file format.
    • Bio.Phylo.Consensus: Classes and methods for finding consensus trees.
    • Bio.Phylo.NeXML: Classes corresponding to NeXML trees.
    • Bio.Phylo.NeXMLIO: I/O function wrappers for the NeXML file format.
    • Bio.Phylo.Newick: Classes corresponding to Newick trees, also used for Nexus trees.
    • Bio.Phylo.NewickIO: I/O function wrappers for the Newick file format.
    • Bio.Phylo.NexusIO: I/O function wrappers for Bio.Nexus trees.
    • Bio.Phylo.PAML: Support for PAML.
      • Bio.Phylo.PAML._paml: Base class for the support of PAML, Phylogenetic Analysis by Maximum Likelihood.
      • Bio.Phylo.PAML._parse_baseml: Methods for parsing baseml results files.
      • Bio.Phylo.PAML._parse_codeml: Methods for parsing codeml results files.
      • Bio.Phylo.PAML._parse_yn00: Methods for parsing yn00 results files.
      • Bio.Phylo.PAML.baseml: Classes for the support of baseml.
      • Bio.Phylo.PAML.chi2: Methods to calculate p-values from a Chi-squared cumulative distribution function.
      • Bio.Phylo.PAML.codeml: Classes for the support of CODEML.
      • Bio.Phylo.PAML.yn00: Classes for the support of yn00.
    • Bio.Phylo.PhyloXML: Classes corresponding to phyloXML elements.
    • Bio.Phylo.PhyloXMLIO: PhyloXML reader/parser, writer, and associated functions.
    • Bio.Phylo.TreeConstruction: Classes and methods for tree construction.
    • Bio.Phylo._cdao_owl: Classes to support Comparative Data Analysis Ontology (CDAO).
    • Bio.Phylo._io: I/O function wrappers for phylogenetic tree formats.
    • Bio.Phylo._utils: Utilities for handling, displaying and exporting Phylo trees.
  • Bio.PopGen: PopGen: Population Genetics and Genomics library in Python.
    • Bio.PopGen.GenePop: Code to work with GenePop.
      • Bio.PopGen.GenePop.Controller: Module to control GenePop.
      • Bio.PopGen.GenePop.EasyController: Control GenePop through an easier interface.
      • Bio.PopGen.GenePop.FileParser: Code to parse BIG GenePop files.
      • Bio.PopGen.GenePop.LargeFileParser: Large file parsing of Genepop files.
      • Bio.PopGen.GenePop.Utils: Utility functions to deal with GenePop files.
  • Bio.Restriction: Restriction Digest Enzymes.
    • Bio.Restriction.PrintFormat: Print the results of restriction enzyme analysis.
    • Bio.Restriction.Restriction: Restriction Enzyme classes.
    • Bio.Restriction.Restriction_Dictionary: Restriction Analysis Libraries.
  • Bio.SCOP: SCOP: Structural Classification of Proteins.
    • Bio.SCOP.Cla: Handle the SCOP CLAssification file, which describes SCOP domains.
    • Bio.SCOP.Des: Handle the SCOP DEScription file.
    • Bio.SCOP.Dom: Handle the SCOP DOMain file.
    • Bio.SCOP.Hie: Handle the SCOP HIErarchy files.
    • Bio.SCOP.Raf: ASTRAL RAF (Rapid Access Format) Sequence Maps.
    • Bio.SCOP.Residues: A collection of residues from a PDB structure.
  • Bio.SVDSuperimposer: Align on protein structure onto another using SVD alignment.
  • Bio.SearchIO: Biopython interface for sequence search program outputs.
    • Bio.SearchIO.BlastIO: Bio.SearchIO support for BLAST+ output formats.
      • Bio.SearchIO.BlastIO.blast_tab: Bio.SearchIO parser for BLAST+ tab output format, with or without comments.
      • Bio.SearchIO.BlastIO.blast_text: Bio.SearchIO parser for BLAST+ plain text output formats.
      • Bio.SearchIO.BlastIO.blast_xml: Bio.SearchIO parser for BLAST+ XML output formats.
    • Bio.SearchIO.BlatIO: Bio.SearchIO parser for BLAT output formats.
    • Bio.SearchIO.ExonerateIO: Bio.SearchIO support for Exonerate output formats.
      • Bio.SearchIO.ExonerateIO._base: Bio.SearchIO abstract base parser for Exonerate standard output format.
      • Bio.SearchIO.ExonerateIO.exonerate_cigar: Bio.SearchIO parser for Exonerate cigar output format.
      • Bio.SearchIO.ExonerateIO.exonerate_text: Bio.SearchIO parser for Exonerate plain text output format.
      • Bio.SearchIO.ExonerateIO.exonerate_vulgar: Bio.SearchIO parser for Exonerate vulgar output format.
    • Bio.SearchIO.FastaIO: Bio.SearchIO support for Bill Pearson's FASTA tools.
    • Bio.SearchIO.HHsuiteIO: Bio.SearchIO support for HHSUITE output formats.
      • Bio.SearchIO.HHsuiteIO.hhsuite2_text: Bio.SearchIO parser for HHSUITE version 2 and 3 plain text output format.
    • Bio.SearchIO.HmmerIO: Bio.SearchIO support for HMMER output formats.
      • Bio.SearchIO.HmmerIO._base: Bio.SearchIO base classes for HMMER-related code.
      • Bio.SearchIO.HmmerIO.hmmer2_text: Bio.SearchIO parser for HMMER 2 text output.
      • Bio.SearchIO.HmmerIO.hmmer3_domtab: Bio.SearchIO parser for HMMER domain table output format.
      • Bio.SearchIO.HmmerIO.hmmer3_tab: Bio.SearchIO parser for HMMER table output format.
      • Bio.SearchIO.HmmerIO.hmmer3_text: Bio.SearchIO parser for HMMER plain text output format.
    • Bio.SearchIO.InterproscanIO: Bio.SearchIO support for InterProScan output formats.
      • Bio.SearchIO.InterproscanIO.interproscan_xml: Bio.SearchIO parser for InterProScan XML output formats.
    • Bio.SearchIO._index: Custom indexing for Bio.SearchIO objects.
    • Bio.SearchIO._legacy: Legacy functionalities from other parts of Biopython used by SearchIO.
      • Bio.SearchIO._legacy.NCBIStandalone: Code for calling standalone BLAST and parsing plain text output (DEPRECATED).
      • Bio.SearchIO._legacy.ParserSupport: Code to support writing parsers (DEPRECATED).
    • Bio.SearchIO._model: Bio.SearchIO objects to model similarity search program outputs.
      • Bio.SearchIO._model._base: Abstract base classes for the SearchIO object model.
      • Bio.SearchIO._model.hit: Bio.SearchIO object to model a single database hit.
      • Bio.SearchIO._model.hsp: Bio.SearchIO objects to model high scoring regions between query and hit.
      • Bio.SearchIO._model.query: Bio.SearchIO object to model search results from a single query.
    • Bio.SearchIO._utils: Common SearchIO utility functions.
  • Bio.Seq: Provide objects to represent biological sequences with alphabets.
  • Bio.SeqFeature: Represent a Sequence Feature holding info about a part of a sequence.
  • Bio.SeqIO: Sequence input/output as SeqRecord objects.
    • Bio.SeqIO.AbiIO: Bio.SeqIO parser for the ABI format.
    • Bio.SeqIO.AceIO: Bio.SeqIO support for the "ace" file format.
    • Bio.SeqIO.FastaIO: Bio.SeqIO support for the "fasta" (aka FastA or Pearson) file format.
    • Bio.SeqIO.GckIO: Bio.SeqIO support for the "gck" file format.
    • Bio.SeqIO.IgIO: Bio.SeqIO support for the "ig" (IntelliGenetics or MASE) file format.
    • Bio.SeqIO.InsdcIO: Bio.SeqIO support for the "genbank" and "embl" file formats.
    • Bio.SeqIO.Interfaces: Bio.SeqIO support module (not for general use).
    • Bio.SeqIO.NibIO: Bio.SeqIO support for the UCSC nib file format.
    • Bio.SeqIO.PdbIO: Bio.SeqIO support for accessing sequences in PDB and mmCIF files.
    • Bio.SeqIO.PhdIO: Bio.SeqIO support for the "phd" file format.
    • Bio.SeqIO.PirIO: Bio.SeqIO support for the "pir" (aka PIR or NBRF) file format.
    • Bio.SeqIO.QualityIO: Bio.SeqIO support for the FASTQ and QUAL file formats.
    • Bio.SeqIO.SeqXmlIO: Bio.SeqIO support for the "seqxml" file format, SeqXML.
    • Bio.SeqIO.SffIO: Bio.SeqIO support for the binary Standard Flowgram Format (SFF) file format.
    • Bio.SeqIO.SnapGeneIO: Bio.SeqIO support for the SnapGene file format.
    • Bio.SeqIO.SwissIO: Bio.SeqIO support for the "swiss" (aka SwissProt/UniProt) file format.
    • Bio.SeqIO.TabIO: Bio.SeqIO support for the "tab" (simple tab separated) file format.
    • Bio.SeqIO.UniprotIO: Bio.SeqIO support for the "uniprot-xml" file format.
    • Bio.SeqIO.XdnaIO: Bio.SeqIO support for the "xdna" file format.
    • Bio.SeqIO._convert: Optimised sequence conversion code (PRIVATE).
    • Bio.SeqIO._index: Dictionary like indexing of sequence files (PRIVATE).
  • Bio.SeqRecord: Represent a Sequence Record, a sequence with annotation.
  • Bio.SeqUtils: Miscellaneous functions for dealing with sequences.
    • Bio.SeqUtils.CheckSum: Functions to calculate assorted sequence checksums.
    • Bio.SeqUtils.CodonUsage: Methods for codon usage calculations.
    • Bio.SeqUtils.CodonUsageIndices: Codon adaption indxes, including Sharp and Li (1987) E. coli index.
    • Bio.SeqUtils.IsoelectricPoint: Calculate isoelectric points of polypeptides using methods of Bjellqvist.
    • Bio.SeqUtils.MeltingTemp: Calculate the melting temperature of nucleotide sequences.
    • Bio.SeqUtils.ProtParam: Simple protein analysis.
    • Bio.SeqUtils.ProtParamData: Indices to be used with ProtParam.
    • Bio.SeqUtils.lcc: Local Composition Complexity.
  • Bio.Sequencing: Code to deal with various programs for sequencing and assembly.
    • Bio.Sequencing.Ace: Parser for ACE files output by PHRAP.
    • Bio.Sequencing.Applications: Main entry point for sequencing related command line application wrappers.
      • Bio.Sequencing.Applications._Novoalign: Command line wrapper for the short read aligner Novoalign by Novocraft.
      • Bio.Sequencing.Applications._bwa: Command line wrapper for bwa.
      • Bio.Sequencing.Applications._samtools: Command line wrapper for samtools.
    • Bio.Sequencing.Phd: Parser for PHD files output by PHRED and used by PHRAP and CONSED.
  • Bio.Statistics: Basic statistics module.
    • Bio.Statistics.lowess: Implements the Lowess function for nonparametric regression.
  • Bio.SubsMat: Substitution matrices, log odds matrices, and operations on them.
    • Bio.SubsMat.FreqTable: A class to handle frequency tables or letter count files.
    • Bio.SubsMat.MatrixInfo: Substitution matrices for use in alignments, etc.
  • Bio.SwissProt: Code to work with the sprotXX.dat file from SwissProt.
    • Bio.SwissProt.KeyWList: Code to parse the keywlist.txt file from SwissProt/UniProt.
  • Bio.TogoWS: Provides code to access the TogoWS integrated websevices of DBCLS, Japan.
  • Bio.UniGene: Parse Unigene flat file format files such as the Hs.data file.
  • Bio.UniProt: Code for dealing with assorted UniProt file formats.
    • Bio.UniProt.GOA: Parsers for the GAF, GPA and GPI formats from UniProt-GOA.
  • Bio.Wise: Run and process output from the Wise2 package tools.
    • Bio.Wise.dnal: Run and process output from the Wise2 package tool dnal.
    • Bio.Wise.psw: Run and process output from the Wise2 package tool psw.
  • Bio._py3k: Python 3 compatibility tools (PRIVATE).
  • Bio._utils: Common utility functions for various Bio submodules.
  • Bio.bgzf: Read and write BGZF compressed files (the GZIP variant used in BAM).
  • Bio.codonalign: Code for dealing with Codon Alignments.
    • Bio.codonalign.chisq: Python implementation of chisqprob, to avoid SciPy dependency.
    • Bio.codonalign.codonalignment: Code for dealing with Codon Alignment.
    • Bio.codonalign.codonalphabet: Code for Codon Alphabet.
    • Bio.codonalign.codonseq: Code for dealing with coding sequence.
  • Bio.cpairwise2: Optimized C routines that complement pairwise2.py. These are called from within pairwise2.py.
  • Bio.kNN: Code for doing k-nearest-neighbors classification.
  • Bio.motifs: Tools for sequence motif analysis.
    • Bio.motifs._pwm: Fast calculations involving position-weight matrices
    • Bio.motifs.alignace: Parsing AlignACE output files.
    • Bio.motifs.applications: Motif command line tool wrappers.
      • Bio.motifs.applications._xxmotif: Command line wrapper for the motif finding program XXmotif.
    • Bio.motifs.clusterbuster: Parse Cluster Buster position frequency matrix files.
    • Bio.motifs.jaspar: JASPAR2014 module.
      • Bio.motifs.jaspar.db: Provides read access to a JASPAR5 formatted database.
    • Bio.motifs.mast: Module for the support of Motif Alignment and Search Tool (MAST).
    • Bio.motifs.matrix: Support for various forms of sequence motif matrices.
    • Bio.motifs.meme: Module for the support of MEME motif format.
    • Bio.motifs.minimal: Module for the support of MEME minimal motif format.
    • Bio.motifs.pfm: Parse various position frequency matrix format files.
    • Bio.motifs.thresholds: Approximate calculation of appropriate thresholds for motif finding.
    • Bio.motifs.transfac: Parsing TRANSFAC files.
    • Bio.motifs.xms: Parse XMS motif files.
  • Bio.pairwise2: Pairwise sequence alignment using a dynamic programming algorithm.
  • Bio.phenotype: phenotype data input/output.
    • Bio.phenotype.phen_micro: Classes to work with Phenotype Microarray data.
    • Bio.phenotype.pm_fitting: Growth curves fitting and parameters extraction for phenotype data.
  • Bio.trie: This module implements a trie data structure. This allows an O(M) lookup of a string in a dictionary, where M is the length of the string. It also supports approximate matches.
  • Bio.triefind: Given a trie, find all occurrences of a word in the trie in a string.
• BioSQL: Storing and retrieve biological sequences in a BioSQL relational database.
  • BioSQL.BioSeq: Implementations of Biopython-like Seq objects on top of BioSQL.
  • BioSQL.BioSeqDatabase: Connect with a BioSQL database and load Biopython like objects from it.
  • BioSQL.DBUtils: Helper code for Biopython's BioSQL code (for internal use).
  • BioSQL.Loader: Load biopython objects into a BioSQL database for persistent storage.