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PyPI · #1947 most downloaded on PyPI
Freely available tools for computational molecular biology.
Last release 1 months ago
06 Aug 2026
Ships fairly regularly
a new release about every 6 months
Nearly every release is documented
notes for 55 of 55 stable releases
Nothing withdrawn
no release was ever pulled
17 years old
65 releases · first in 2009
Martel added back into the released package
Martel added back into the released package
new AlignACE module by Bartek Wilczynski
Andreas Kuntzagk fix for GenBank Iterator on empty files
added Andrew Dalke's EUtils library
added Andrew Dalke's EUtils library
added Michiel de Hoon's gene expression analysis package
updates to setup code, now smarter about dependencies
updates to test suite, now smarter about code that is imported
Michael Hoffman's fixes to DocSQL
syntax fixes in triemodule.c to compile on SGI, Python 2.1 compatible
updates in NCBIStandalone, short query error
Sebastian Bassi submitted code to calculate LCC complexity
Greg Kettler's NCBIStandalone fix for long query lengths
slew of miscellaneous fixes from George Paci
miscellaneous cleanups and updates from Andreas Kuntzagk
Peter Bienstman's fixes to Genbank code -- now parses whole database
Kayte Lindner's LocusLink package
miscellaneous speedups and code cleanup in ParserSupport by Brad Chapman
miscellaneous BLAST fixes and updates
Iddo added new code to parse BLAST table output format
Karl Diedrich's patch to read T_Coffee files
Larry Heisler's fix for primer3 output
Bio.Medline now uses proper iterator objects
copen now handles SIGTERM correctly
small bugfixes and updates in Thomas Hamelryck's PDB package
bugfixes and updates to SeqIO.FASTA reader
updates to Registry system, conforms to 2003 hackathon OBDA spec
Yu Huang patch to support tblastn in wublast expression
One column per quarter.
removed deprecated Sequence.py package
Python requirement bumped up to 2.2
hierarchy reorg, many things moved upwards into Bio namespace
pairwise2 replaces fastpairwise and pairwise
removed deprecated Sequence.py package
minor bug fix in File.SGMLStripper
added Scripts/debug/debug_blast_parser.py to diagnose blast parsing errors
IPI supported by SwissProt/SProt.py parser
large speedup for kmeans
new registry framework for generic access to databases and parsers
small bug fix in stringfns.split
scripts that access NCBI moved over to new EUtils system
new crc module
biblio.py supports the EBI Bibliographic database
new CDD parser
new Ndb parser
new ECell parser
new Geo parser
access to GFF databases
new KDTree data structure
new LocusLink parser
new MarkovModel algorithm
new Saf parser
miscellaneous sequence handling functions in sequtils
new SVDSuperimpose algorithm
minor bug fix in NCBIStandalone.blastall
minor bug fix in NCBIStandalone.blastall
optimization in dynamic programming code
new modules for logistic regression and maximum entropy
minor bug fix in ParserSupport
minor bug fixes in SCOP package
minor updates in the kMeans cluster selection code
minor bug fixes in SubsMat code
support for XML-formatted MEDLINE files
added MultiProc.run to simplify splitting code across processors
listfns.items now supports lists with unhashable items
new data type for pathways
new support for intelligenetics format
new support for metatool format
new support for NBRF format
new support for generalized launching of applications
new support for genetic algorithms
minor bug fixes in GenBank parsing
new support for Primer in the Emboss package
new support for chromosome graphics
new support for HMMs
new support for NeuralNetwork
slew of Martel fixes (see Martel docs)
added sequtils module for computations on sequences
added package to support KEGG
added sequtils module for computations on sequences
added pairwise sequence alignment algorithm
major bug fixes in UndoHandle
format updates in PubMed
Tk interface to kMeans clustering
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