- Bio.Affy: Deal with Affymetrix related data such as cel files.
- Bio.Ais: Immune system simulation based on ideas from Immunocomputing: a survey.
- Bio.Align: Code for dealing with sequence alignments.
- Bio.Align.AlignInfo: Extract information from alignment objects.
- Bio.Align.FormatConvert: Utility for conversion between different formats for representing
alignments.
- Bio.Align.Generic: Contains classes to deal with generic sequence alignment stuff not
specific to a particular program or format.
- Bio.AlignAce: Parser and code for dealing with the standalone version of
AlignAce, a motif search program.
- Bio.AlignIO: Alignment input/output designed to look similar to Bio.SeqIO.
- Bio.Alphabet
- 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.NCBIStandalone: This module provides code to work with the standalone version of
BLAST, either blastall or blastpgp, provided by the NCBI.
- Bio.Blast.NCBIWWW: This module provides code to work with the WWW version of BLAST
provided by the NCBI.
- Bio.Blast.NCBIXML: This module provides code to work with the BLAST XML output
following the DTD available on the NCBI FTP
ftp://ftp.ncbi.nlm.nih.gov/blast/documents/xml/NCBI_BlastOutput.dtd
- Bio.Blast.ParseBlastTable
- Bio.Blast.Record: Record classes to hold BLAST output.
- Bio.CAPS: This module deals with CAPS markers.
- Bio.CDD: Deal with Conserved Domain Database (CDD) entries from NCBI.
- Bio.Clustalw: A set of classes to interact with the multiple alignment command
line program clustalw.
- Bio.Cluster
- Bio.Compass: Code to deal with COMPASS output, a program for profile/profile
comparison.
- Bio.Crystal: Hetero, Crystal and Chain exist to represent the NDB Atlas
structure.
- Bio.DBXRef
- Bio.Data: Collections of various bits of useful biological data.
- Bio.Decode
- Bio.DocSQL
- Bio.ECell
- Bio.EUtils: EUtils is a client-side library for the Entrez databases at NCBI.
- Bio.EZRetrieve: This module contains code to access EZRetrieve.
- Bio.Emboss: Code to interact with the ever-so-useful EMBOSS programs.
- Bio.Encodings: Properties for functionality such as transcription and translation.
- Bio.Entrez: Provides code to access NCBI over the WWW.
- Bio.Enzyme: This module provides code to work with the enzyme.dat file from
Enzyme.
- Bio.ExPASy: This module provides code to access resources at ExPASy over the
WWW.
- Bio.FSSP
- Bio.Fasta: Utilities for working with FASTA-formatted sequences.
- Bio.File: Code for more fancy file handles.
- Bio.FilteredReader: Code for more fancy file handles.
- Bio.GA
- Bio.GFF: Access to General Feature Format databases created with Bio::DB:GFF
- Bio.GenBank: Code to work with GenBank formatted files.
- Bio.Geo: Parser for files from NCBI's Gene Expression Omnibus (GEO).
- Bio.Gobase: This module provides code to work with files from Gobase.
- Bio.Graphics
- Bio.HMM
- Bio.HotRand: handles true random numbers supplied from the the web server of
fourmilab.
- Bio.Index: Index.py
- Bio.IntelliGenetics: Parser for the MASE/Intelligenetics alignment file format.
- Bio.InterPro: This module provides code to work with html files from InterPro,
and code to access resources at InterPro over the WWW.
- Bio.KDTree: The KD tree data structure can be used for all kinds of searches
that involve N-dimensional vectors.
- Bio.KEGG: This module provides code to work with data from the KEGG database.
- Bio.KEGG.Compound: This module provides code to work with the KEGG Ligand/Compound
database.
- Bio.KEGG.Enzyme: This module provides code to work with the KEGG Enzyme database.
- Bio.KEGG.Map: This module provides code to import KEGG Pathway maps for use with
the Biopython Pathway module.
- Bio.LocusLink
- Bio.LogisticRegression: This module provides code for doing logistic regressions.
- Bio.MEME: Parser for dealing with text output from the MEME motif search
program
- Bio.MarkovModel: This is an implementation of a state-emitting MarkovModel.
- Bio.MaxEntropy: Maximum Entropy code.
- Bio.Medline: This module provides code to work with Medline.
- Bio.MetaTool: Parser for output from MetaTool, a program which defines metabolic
routes within networks.
- Bio.Mindy
- Bio.NBRF: Parser for the NBRF/PIR file format.
- Bio.NMR: Code for working with NMR data
- Bio.NaiveBayes: This provides code for a general Naive Bayes learner.
- Bio.Ndb: This module provides code to work with html files from NDB.
- Bio.NetCatch: NetCatch enables the user to scan a list of labelled urls and
select a subset to read into a file.
- Bio.NeuralNetwork
- Bio.Nexus: The Bio.Nexus contains a NEXUS file parser and objects to model
this data.
- 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
- Bio.PDB.Entity: Base class for Residue, Chain, Model and Structure classes.
- Bio.PDB.FragmentMapper
- Bio.PDB.FragmentMapper': Classify protein backbone structure according to Kolodny et al's
fragment libraries.
- Bio.PDB.HSExposure: Half sphere exposure and coordination number calculation.
- Bio.PDB.MMCIF2Dict
- Bio.PDB.MMCIFParser
- Bio.PDB.Model: Model class, used in Structure objects.
- Bio.PDB.NACCESS: Interface for the program NACCESS - http://wolf.bms.umist.ac.uk/naccess/
- Bio.PDB.NeighborSearch
- 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 (for example to download
structures).
- Bio.PDB.PDBParser
- Bio.PDB.PDBParser': Parser for PDB files.
- Bio.PDB.PSEA
- Bio.PDB.Polypeptide: Polypeptide related classes (construction and representation).
- Bio.PDB.Residue: Residue class, used by Structure objects.
- Bio.PDB.ResidueDepth
- Bio.PDB.ResidueDepth': Calculation of residue depth (using Michel Sanner's MSMS program for the
surface calculation).
- 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 the residues of two structures to each other based on a FASTA
alignment file.
- Bio.PDB.StructureBuilder: Consumer class that builds a Structure object.
- Bio.PDB.Superimposer
- Bio.PDB.Superimposer': Superimpose two structures.
- Bio.PDB.Vector
- Bio.PDB.Vector': Vector class, including rotation-related functions.
- Bio.PDB.mmCIF
- Bio.PDB.parse_pdb_header
- Bio.PDB.parse_pdb_header': Parse the header of a PDB file.
- Bio.ParserSupport: Code to support writing parsers.
- Bio.Parsers: Third party and other parsers useful internally to Biopython.
- Bio.Pathway: BioPython Pathway module.
- Bio.PopGen: PopGen: Population Genetics and Genomics library in Python
- Bio.PropertyManager
- Bio.Prosite: This module provides code to work with the prosite dat file from
Prosite.
- Bio.PubMed: This module provides code to work with PubMed from the NCBI.
- Bio.Rebase: This module provides code to work with files from Rebase.
- Bio.Restriction: Usage :
=====
- Bio.SCOP: SCOP: Structural Classification of Proteins.
- Bio.SGMLExtractor: Code for more fancy file handles.
- Bio.SVDSuperimposer: SVDSuperimposer finds the best rotation and translation to put two
point sets on top of each other (minimizing the RMSD).
- Bio.Saf: Parser for SAF (Simple Alignment Format).
- Bio.Search
- Bio.Seq
- Bio.SeqFeature: Represent a Sequence Feature holding info about a part of a sequence.
- Bio.SeqIO: Sequence input/output as SeqRecord objects.
- Bio.SeqRecord
- Bio.SeqUtils
- Bio.Sequencing: Code to deal with various programs for sequencing and assembly.
- Bio.Statistics
- Bio.Std
- Bio.StdHandler
- Bio.SubsMat: Substitution matrices, log odds matrices, and operations on them.
- Bio.SwissProt: Parsers for file formats from the SwissProt database.
- Bio.Transcribe
- Bio.Translate
- Bio.UniGene: Parse Unigene flat file format files such as the Hs.data file.
- Bio.WWW: Deal with various biological databases and services on the web.
- Bio.WWW.ExPASy: This module provides code to access resources at ExPASy over the
WWW.
- Bio.WWW.InterPro: This module is deprecated; its functions are now available from
Bio.InterPro.
- Bio.WWW.NCBI: Provides code to access NCBI over the WWW.
- Bio.WWW.SCOP: This module is deprecated; its functions are now available from
Bio.SCOP.
- Bio.Wise
- Bio.Writer
- Bio.biblio: This file implements a SOAP interface into the Bibliographic
database of the European Bioinformatics Institute.
- Bio.builders
- Bio.config
- Bio.dbdefs
- Bio.distance: This module provides code for various distance measures.
- Bio.expressions
- Bio.formatdefs
- Bio.kNN: This module provides code for doing k-nearest-neighbors classification.
- Bio.listfns: This provides useful general functions for working with lists.
- Bio.mathfns: This provides useful general math tools.
- Bio.pairwise2: This package implements pairwise sequence alignment using a dynamic
programming algorithm.
- Bio.stringfns: This provides useful general functions for working with strings.
- Bio.triefind: Given a trie, find all occurrences of a word in the trie in a
string.
- Bio.utils
- Bio.writers
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