- Bio.Affy: Deal with Affymetrix related data such as cel files.
- Bio.Affy.CelFile: Classes for accessing the information in Affymetrix cel files.
- Bio.Align: Code for dealing with sequence alignments.
- Bio.AlignAce: Parser and code for dealing with the standalone version of
AlignAce, a motif search program (DEPRECATED).
- Bio.AlignIO: Multiple sequence alignment input/output as Alignment objects.
- Bio.Alphabet: Alphabets used in Seq objects etc to declare sequence type and
letters.
- 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, rpsblast 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: A parser for the NCBI blastpgp version 2.2.5 output format.
- Bio.Blast.Record: Record classes to hold BLAST output.
- Bio.CAPS: This module deals with CAPS markers.
- Bio.Clustalw: Code for calling ClustalW and parsing its output (OBSOLETE).
- Bio.Cluster
- Bio.Compass: Code to deal with COMPASS output, a program for profile/profile
comparison.
- Bio.Crystal: Module to represent the NDB Atlas structure (a minimal subset of
PDB format).
- Bio.Data: Collections of various bits of useful biological data.
- Bio.DocSQL: Bio.DocSQL: easy access to DB API databases.
- Bio.EZRetrieve: This module contains code to access EZRetrieve (DEPRECATED).
- 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: Module to work with enzyme.dat file (DEPRECATED).
- Bio.ExPASy: This module provides code to access resources at ExPASy over the
WWW.
- Bio.FSSP: Parser for FSSP files, used in a database of protein fold
classifications.
- Bio.Fasta: Utilities for working with FASTA-formatted sequences (DEPRECATED).
- Bio.File: Code for more fancy file handles.
- Bio.FilteredReader: Code for more fancy file handles (DEPRECATED).
- Bio.GA: A selection of genetic algorithm code.
- Bio.GFF: Access to General Feature Format databases created with BioPerl
(DEPRECATED).
- Bio.GenBank: Code to work with GenBank formatted files.
- Bio.Geo: Parser for files from NCBI's Gene Expression Omnibus (GEO).
- Bio.Graphics: Bio.Graphics offsers several graphical ouputs, all using ReportLab.
- Bio.HMM: A selection of Hidden Markov Model code.
- Bio.HotRand: handles true random numbers supplied from the the web server of
fourmilab.
- Bio.Index: Index.py
- 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.LogisticRegression: This module provides code for doing logistic regressions.
- Bio.MEME: Parser for dealing with text output from the MEME motif search
program (DEPRECATED).
- 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.Motif: Module containing different tools for sequence motif analysis.
- Bio.NMR: Code for working with NMR data
- Bio.NaiveBayes: This provides code for a general Naive Bayes learner.
- Bio.NetCatch: Code for dealing with lists of URLs (DEPRECATED).
- 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: Module for working with Prosite files from ExPASy (DEPRECATED).
- Bio.Restriction: Usage:
=====
- 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, which describe the SCOP hierarchy
in terms of SCOP unique identifiers (sunid).
- Bio.SCOP.Raf: ASTRAL RAF (Rapid Access Format) Sequence Maps.
- Bio.SCOP.Residues
- Bio.SCOP.Residues'
- Bio.SVDSuperimposer: SVDSuperimposer finds the best rotation and translation to put two
point sets on top of each other (minimizing the RMSD).
- Bio.Search
- Bio.Seq: Provides 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.SeqRecord: Represent a Sequence Record, a sequence with annotation.
- Bio.SeqUtils: Miscellaneous functions for dealing with sequences.
- Bio.Sequencing: Code to deal with various programs for sequencing and assembly.
- Bio.Statistics
- Bio.SubsMat: Substitution matrices, log odds matrices, and operations on them.
- Bio.SwissProt: This module provides code to work with the sprotXX.dat file from
SwissProt.
- Bio.SwissProt.KeyWList: This module provides code to work with the keywlist.txt file from
SwissProt.
- Bio.SwissProt.SProt: This module provides code to work with the sprotXX.dat file from
Utilities for working with FASTA-formatted sequences (DEPRECATED).
- Bio.Transcribe: Code to transcribe DNA into RNA or back (DEPRECATED).
- Bio.Translate: Code to translate DNA or RNA into proteins (DEPRECATED).
- Bio.UniGene: Parse Unigene flat file format files such as the Hs.data file.
- Bio.Wise
- Bio.kNN: This module provides code for doing k-nearest-neighbors classification.
- Bio.listfns: This provides useful general functions for working with lists
(DEPRECATED).
- Bio.mathfns: This provides useful general math tools (DEPRECATED).
- Bio.pairwise2: This package implements pairwise sequence alignment using a dynamic
programming algorithm.
- Bio.stringfns: This provides useful general functions for working with strings
(DEPRECATED).
- Bio.triefind: Given a trie, find all occurrences of a word in the trie in a
string.
- Bio.utils: Miscellaneous functions for dealing with sequences (obsolete?).
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