-
Affy : Deal with Affymetrix related data such as cel files.
-
Ais : Immune system simulation based on ideas from Immunocomputing: a survey.
-
Align : Code for dealing with sequence alignments.
-
AlignInfo : Extract information from alignment objects.
-
FormatConvert : Utility for conversion between different formats for representing
alignments.
-
Generic : Contains classes to deal with generic sequence alignment stuff not
specific to a particular program or format.
-
AlignAce : Parser and code for dealing with the standalone version of AlignAce, a
motif search program.
-
AlignAceStandalone : This module provides code to work with the standalone version of
AlignACE, for motif search in DNA sequences.
-
Applications : Definitions for interacting with AlignAce.
-
CompareAceStandalone : This module provides code to work with the standalone version of
CompareAce, for motif comparison
-
Motif : Implementation of sequence motifs.
-
Parser : Classes for pparsing AlignAce and CompareACE files
-
Scanner : Consumers for AlignACE and CompareACE parsers.
-
Alphabet
-
Application : General mechanisms to access applications in biopython.
-
Blast : Code for dealing with BLAST programs and output.
-
Applications : Definitions for interacting with Blast related applications.
-
NCBIStandalone : This module provides code to work with the standalone version of
BLAST, either blastall or blastpgp, provided by the NCBI.
-
NCBIWWW : This module provides code to work with the WWW version of BLAST
provided by the NCBI.
-
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
-
ParseBlastTable
-
Record : Record classes to hold BLAST output.
-
builders
-
CAPS : This module deals with CAPS markers.
-
Compass : Code to deal with COMPASS output, a program for profile/profile
comparison.
-
config
-
DBRegistry : Implements Registry to access databases.
-
FormatRegistry : Implements a Registry to store Martel-type format expressions.
-
Registry : This module implements some base classes used in the Registry system
for Biopython.
-
SeqDBRegistry : This module handles seqdatabase.INI file.
-
crc
-
Crystal : Hetero, Crystal and Chain exist to represent the NDB Atlas
structure.
-
Data : Collections of various bits of useful biological data.
-
dbdefs
-
DBXRef
-
Decode
-
distance : This module provides code for various distance measures.
-
Emboss : Code to interact with the ever-so-useful EMBOSS programs.
-
Applications : Code to interact with and run various EMBOSS programs.
-
Primer : Code to interact with various Primer-related programs from EMBOSS.
-
primer3_format : Martel definitions for the output files produced by primer3.
-
primersearch_format : Martel format for primersearch output files,
-
Encodings : Properties for functionality such as transcription and
translation.
-
Enzyme : This module provides code to work with the enzyme.dat file from
Enzyme.
-
EUtils : EUtils is a client-side library for the Entrez databases at NCBI.
-
Config : Configuration information about NCBI's databases
-
Datatypes : various EUtils datatypes
-
DBIdsClient : Search and retrieve information given a set of database
identifiers.
-
dtd2py : Internal class to convert DTDs to python form.
-
DTDs
-
HistoryClient : Search and retreive information using the EUtils history.
-
Mixins : implements functionality shared between HistoryClient and
DBIdsClient
-
MultiDict : Dictionary-like objects which allow multiple keys
Python dictionaries map a key to a value.
-
parse
-
POM : This module implements the XML POM -- the Python Object Model for
XML.
-
ReseekFile : Wrap a file handle to allow seeks back to the beginning
Sometimes data coming from a socket or other input file handle isn't
what it was supposed to be.
-
setup
-
sourcegen : This module can be used to generate python source code.
-
ThinClient : Low-level interface to NCBI's EUtils for Entrez search and retrieval.
-
expressions
-
blast
-
blocks
-
embl
-
embl65 : Format from EMBL Nucleotide Sequence Database Release 65, December
2000
-
fasta
-
genbank : Martel based parser to read GenBank formatted files.
-
hmmpfam : Martel expression for the hmmpfam database search program in
hmmer.
-
transfac : A Martel format to parse the output from transfac.
-
EZRetrieve : This module contains code to access EZRetrieve.
-
File : Code for more fancy file handles.
-
FilteredReader : Code for more fancy file handles.
-
formatdefs
-
FormatIO
-
FSSP
-
GA
-
Crossover
-
General : General functionality for crossover that doesn't apply.
-
GeneralPoint : Generalized N-Point Crossover.
-
Point : Perform two-point crossovers between the genomes of two organisms.
-
TwoPoint : Perform two-point crossovers between the genomes of two organisms.
-
Uniform : Perform uniform crossovers between the genomes of two organisms.
-
Evolver : Evolution Strategies for a Population.
-
Mutation
-
General : General functionality for mutations.
-
Simple : Perform Simple mutations on an organism's genome.
-
Organism : Deal with an Organism in a Genetic Algorithm population.
-
Repair
-
Stabilizing : Methods for performing repairs that will Stabilize genomes.
-
Selection
-
Abstract : Base selection class from which all Selectors should derive.
-
Diversity : Select individuals into a new population trying to maintain
diversity.
-
RouletteWheel : Implement Roulette Wheel selection on a population.
-
Tournament : Provide Tournament style selection.
-
Gobase : This module provides code to work with files from Gobase.
-
Graphics
-
BasicChromosome : Draw representations of organism chromosomes with added
information.
-
Comparative : Plots to compare information between different sources.
-
DisplayRepresentation : Represent information for graphical display.
-
Distribution : Display information distributed across a Chromosome-like object.
-
HMM
-
DynamicProgramming : Dynamic Programming algorithms for general usage.
-
MarkovModel : Deal with representations of Markov Models.
-
Trainer : Provide trainers which estimate parameters based on training
sequences.
-
Utilities : Generic functions which are useful for working with HMMs.
-
HotRand : handles true random numbers supplied from the the web server of
fourmilab.
-
Index : Index.py
-
InterPro : This module provides code to work with html files from InterPro.
-
KEGG : This module provides code to work with data from the KEGG
database.
-
kNN : This module provides code for doing k-nearest-neighbors classification.
-
lcc
-
listfns : This provides useful general functions for working with lists.
-
LogisticRegression : This module provides code for doing logistic regressions.
-
MarkovModel : This is an implementation of a state-emitting MarkovModel.
-
MarkupEditor : Simplify adding markup to a piece of text.
-
mathfns : This provides useful general math tools.
-
MaxEntropy : Maximum Entropy code.
-
Medline : This module provides code to work with Medline.
-
MEME : Parser for dealing with text output from the MEME motif search
program
-
Mindy
-
MultiProc : Code to schedule and run multiple processes.
-
copen : This implements a set of classes that wraps a file object interface
around code that executes in another process.
-
Scheduler : Simple scheduling of threads to be run.
-
Task : Task.py
-
NaiveBayes : This provides code for a general Naive Bayes learner.
-
Ndb : This module provides code to work with html files from NDB.
-
NetCatch : NetCatch enables the user to scan a list of labelled urls and select a
subset to read into a file.
-
NeuralNetwork
-
BackPropagation
-
Layer : Model a single layer in a nueral network.
-
Network : Represent Neural Networks.
-
Gene
-
Motif : Find and deal with motifs in biological sequence data.
-
Pattern : Generic functionality useful for all gene representations.
-
Schema : Deal with Motifs or Signatures allowing ambiguity in the
sequences.
-
Signature : Find and deal with signatures in biological sequence data.
-
StopTraining : Classes to help deal with stopping training a neural network.
-
Training : Provide classes for dealing with Training Neural Networks.
-
Nexus
-
NMR : Code for working with NMR data
-
pairwise2 : This package implements pairwise sequence alignment using a dynamic
programming algorithm.
-
Parsers : Third party and other parsers useful internally to Biopython.
-
ParserSupport : Code to support writing parsers.
-
Pathway : BioPython Pathway module.
-
Rep : BioPython Pathway support module.
-
PropertyManager
-
Prosite : This module provides code to work with the prosite dat file from
Prosite.
-
Pattern
-
Prodoc : This module provides code to work with the prosite.doc file from
Prosite.
-
PubMed : This module provides code to work with PubMed from the NCBI.
-
Rebase : This module provides code to work with files from Rebase.
-
Search
-
Seq
-
SeqFeature : Represent a Sequence Feature holding info about a part of a sequence.
-
SeqIO : Sequence input/output designed to look similar to the bioperl
design.
-
SeqRecord
-
Sequencing : Code to deal with various programs for sequencing and assembly.
-
Ace : Parser for (new) ACE files output by PHRAP.
-
Phd : Parser for PHD files output by PHRED and used by PHRAP and CONSED.
-
SGMLExtractor : Code for more fancy file handles.
-
Statistics
-
lowess : This module implements the Lowess function for nonparametric
regression.
-
Std
-
StdHandler
-
stringfns : This provides useful general functions for working with strings.
-
SubsMat : Substitution matrices, log odds matrices, and operations on them.
-
SVDSuperimposer : SVDSuperimposer finds the best rotation and translation to put two
point sets on top of each other (minimizing the RMSD).
-
SwissProt : Parsers for file formats from the SwissProt database.
-
KeyWList : This module provides code to work with the keywlist.txt file from
SwissProt.
-
SProt : This module provides code to work with the sprotXX.dat file from
SwissProt.
-
Transcribe
-
Translate
-
triefind : Given a trie, find all occurrences of a word in the trie in a
string.
-
UniGene
-
utils
-
Wise
-
Writer
-
writers
-
WWW : Deal with various biological databases and services on the web.
-
ExPASy : This module provides code to access resources at ExPASy over the
WWW.
-
InterPro : This module provides code to access resources at InterPro over the
WWW.
-
NCBI : Provides code to access NCBI over the WWW.
-
SCOP : Provides code to access SCOP over the WWW.
|