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Description: Eric's personal Biopython branch
Homepage: http://biopython.org/wiki/User:EricTalevich
Clone URL: git://github.com/etal/biopython.git 
Tree: consistent function naming -- leaf nodes are "terminals"
etal (author)
Mon Oct 12 12:02:18 -0700 2009
commit  ac2facc6c70b521a9655d996bfd741ef45f6945a
tree    4caceaad223bb177780fe211203ffb423856a63d
parent  e144e44559d2dd48e8371c225ec5c2408c87032a
biopython / Bio
name age
history
message
..
directory Affy/ Sat Apr 25 11:06:53 -0700 2009 Simplifying this parser and making it more Biop... [mdehoon]
directory Align/ Loading commit data...
directory AlignAce/ Fri Aug 21 02:12:16 -0700 2009 Info on migrating from Bio.AlignAce and Bio.MEM... [bartek]
directory AlignIO/
directory Alphabet/ Sun Dec 07 09:22:48 -0800 2008 Docstrings [peterjc]
directory Application/ Tue Aug 11 09:07:56 -0700 2009 Declare Bio.Application.generic_run and Applica... [peterjc]
directory Blast/
directory CAPS/ Thu Feb 17 23:08:57 -0800 2005 *** empty log message *** [idoerg]
directory Clustalw/ Mon Aug 24 03:31:53 -0700 2009 Explicitly say that Bio.Clustalw is now obsolet... [peterjc]
directory Cluster/ Thu Sep 10 20:58:00 -0700 2009 C Clustering Library version 1.47. Updating the... [mdehoon]
directory Compass/ Wed Nov 26 20:28:50 -0800 2008 Removing deprecated string functions. See bug #... [mdehoon]
directory Crystal/ Thu Nov 27 05:18:38 -0800 2008 Removing unused imports; see bug #2683. [mdehoon]
directory Data/ Mon Jul 27 08:06:07 -0700 2009 Set iteration order is Python implementation de... [peterjc]
file DocSQL.py Thu Oct 23 08:59:30 -0700 2008 Updating raise exception style (see PEP8) for f... [peterjc]
file EZRetrieve.py Thu Sep 10 03:25:16 -0700 2009 Deprecating Bio.EZRetrieve, Bio.NetCatch, Bio.F... [peterjc]
directory Emboss/
directory Encodings/ Thu May 13 09:58:34 -0700 2004 Removal of __all__ tags from files. These are p... [chapmanb]
directory Entrez/
directory Enzyme/ Tue Mar 24 22:13:10 -0700 2009 Declaring Bio.Enzyme obsolete in favor of Bio.E... [mdehoon]
directory ExPASy/ Tue Mar 24 18:56:35 -0700 2009 Updating Bio/ExPASy/Enzyme.py to handle the lat... [mdehoon]
directory FSSP/ Thu Nov 27 03:08:17 -0800 2008 Removal of deprecated string functions; see bug... [mdehoon]
directory Fasta/ Wed Aug 05 03:26:03 -0700 2009 Deprecating Bio.Fasta module (see mailing list) [peterjc]
file File.py Thu Sep 10 03:25:16 -0700 2009 Deprecating Bio.EZRetrieve, Bio.NetCatch, Bio.F... [peterjc]
file FilteredReader.py Thu Sep 10 03:25:16 -0700 2009 Deprecating Bio.EZRetrieve, Bio.NetCatch, Bio.F... [peterjc]
directory GA/ Sat Sep 06 13:03:10 -0700 2008 Docstring changes to improve the epydoc API pages. [peterjc]
directory GFF/ Tue Jun 23 07:05:26 -0700 2009 Use Seq object translate method instead of depr... [peterjc]
directory GenBank/ Mon Jul 20 13:12:07 -0700 2009 Cope with missing date in GenBank LOCUS lines (... [peterjc]
directory Geo/ Fri Jun 27 19:53:18 -0700 2008 Removing deprecated stuff for release 1.46. [mdehoon]
directory Graphics/ Wed May 20 08:28:47 -0700 2009 Trivial correction to docstring [peterjc]
directory HMM/ Thu Nov 27 17:33:41 -0800 2008 Removal of deprecated string functions; see bug... [mdehoon]
file HotRand.py Fri Nov 28 21:01:05 -0800 2008 See bug #2685; simplify the hex_convert functio... [mdehoon]
file Index.py Thu Nov 27 17:51:58 -0800 2008 Removal of deprecated string functions; see bug... [mdehoon]
directory InterPro/ Thu Oct 30 11:32:20 -0700 2008 Using key in dict instead of dict.has_key(key) ... [peterjc]
directory KDTree/ Mon Nov 17 04:04:48 -0800 2008 Distinguish between memory errors and not findi... [mdehoon]
directory KEGG/ Tue Feb 03 10:10:22 -0800 2009 Fix for extra colons in references, e.g. in ftp... [peterjc]
file LogisticRegression.py Fri May 08 14:20:19 -0700 2009 Removing simple Python 2.3 specific code (e.g. ... [peterjc]
directory MEME/ Fri Aug 21 02:12:16 -0700 2009 Info on migrating from Bio.AlignAce and Bio.MEM... [bartek]
file MarkovModel.py Sat Nov 01 00:49:54 -0700 2008 Moving the import statement. [mdehoon]
file MaxEntropy.py Fri May 08 14:20:19 -0700 2009 Removing simple Python 2.3 specific code (e.g. ... [peterjc]
directory Medline/ Wed Sep 09 21:16:06 -0700 2009 Removing deprecated functions from Bio.Medline [mdehoon]
directory Motif/ Fri Aug 28 06:54:46 -0700 2009 Sort dictionary keys for consistent results on ... [peterjc]
directory NMR/ Thu Nov 27 20:16:58 -0800 2008 Removal of deprecated string functions; see bug... [mdehoon]
file NaiveBayes.py Fri May 08 14:20:19 -0700 2009 Removing simple Python 2.3 specific code (e.g. ... [peterjc]
directory Ndb/ Fri Nov 28 22:01:53 -0800 2008 Removal of deprecated string functions; see bug... [mdehoon]
file NetCatch.py Thu Sep 10 03:25:16 -0700 2009 Deprecating Bio.EZRetrieve, Bio.NetCatch, Bio.F... [peterjc]
directory NeuralNetwork/ Thu Nov 27 19:02:07 -0800 2008 Removal of deprecated string functions; see bug... [mdehoon]
directory Nexus/ Mon Jul 27 05:25:22 -0700 2009 Fix for bug 2788; allow internal node labels on... [chapmanb]
directory PDB/ Thu Aug 06 07:15:38 -0700 2009 This should work with any alignment, not just o... [peterjc]
file ParserSupport.py Thu Oct 23 08:58:10 -0700 2008 Updating raise exception style (see PEP8) for f... [peterjc]
directory Parsers/ Thu Nov 27 20:22:31 -0800 2008 Removal of deprecated string functions; see bug... [mdehoon]
directory Pathway/ Thu Oct 30 12:02:39 -0700 2008 Using key in dict instead of dict.has_key(key) ... [peterjc]
directory PopGen/
file PropertyManager.py Thu Oct 23 09:05:07 -0700 2008 Updating raise exception style (see PEP8) for f... [peterjc]
directory Prosite/ Wed Aug 19 19:34:31 -0700 2009 Make deprecations permanent. [mdehoon]
file PubMed.py Fri Dec 05 03:24:55 -0800 2008 Provide a little more information for moving fr... [peterjc]
directory Restriction/ Tue Jun 23 04:08:45 -0700 2009 Fix from Frédéric Sohm for Bug 2856 [peterjc]
directory SCOP/ Wed Aug 19 19:50:30 -0700 2009 Add a proper deprecation warning. [mdehoon]
directory SVDSuperimposer/ Sat Nov 01 00:31:25 -0700 2008 Some additional changes for the Numeric -> NumP... [mdehoon]
file Search.py Mon Oct 08 04:13:49 -0700 2007 Removes Bio.FormatIO and associated code in Bio... [peterjc]
file Seq.py
file SeqFeature.py
directory SeqIO/
file SeqRecord.py Fri Aug 21 06:24:21 -0700 2009 Adding __contains__ to SeqRecord (as a proxy fo... [peterjc]
directory SeqUtils/ Thu Jun 18 07:52:11 -0700 2009 Moved Bio.Translate import within the deprecate... [peterjc]
directory Sequencing/
directory Statistics/ Sun Nov 16 19:49:06 -0800 2008 See bug #2657; making this code faster. [mdehoon]
directory SubsMat/ Thu Sep 03 02:35:02 -0700 2009 The BadMatrix exception is not used anywhere; r... [mdehoon]
directory SwissProt/ Wed Aug 19 19:40:22 -0700 2009 Making older deprecations permanent. [mdehoon]
file Transcribe.py Thu Jun 18 03:09:17 -0700 2009 Deprecating Bio.Translate and Bio.Transcribe wh... [peterjc]
file Translate.py Thu Jun 18 03:09:17 -0700 2009 Deprecating Bio.Translate and Bio.Transcribe wh... [peterjc]
directory Tree/
directory TreeIO/
directory UniGene/ Fri Apr 24 05:03:45 -0700 2009 Updating the UniGene parser to be consistent wi... [mdehoon]
directory WWW/ Wed Aug 19 19:50:30 -0700 2009 Add a proper deprecation warning. [mdehoon]
directory Wise/ Wed Oct 22 14:40:19 -0700 2008 Updating raise exception style (see PEP8) [peterjc]
file __init__.py Wed Sep 23 02:51:32 -0700 2009 Bumping version numbers now that 1.52 is out [peterjc]
file cMarkovModelmodule.c Sun Sep 09 23:46:19 -0700 2007 Minimal change to avoid compiler warnings. [mdehoon]
file clistfnsmodule.c Sat Aug 10 20:05:50 -0700 2002 moving miscellaneous functions out of Tools int... [jchang]
file cmathfnsmodule.c Sat Aug 10 20:05:50 -0700 2002 moving miscellaneous functions out of Tools int... [jchang]
file cpairwise2module.c Sat Oct 08 05:04:33 -0700 2005 major optimization to cpairwise2module when get... [jchang]
file cstringfnsmodule.c Sat Aug 10 20:05:50 -0700 2002 moving miscellaneous functions out of Tools int... [jchang]
file csupport.c Tue Nov 26 17:38:13 -0800 2002 cMarkovModelmodule now uses code from csupport [jchang]
file csupport.h Sat Aug 10 20:05:50 -0700 2002 moving miscellaneous functions out of Tools int... [jchang]
file distance.py Thu Oct 23 09:05:07 -0700 2008 Updating raise exception style (see PEP8) for f... [peterjc]
file kNN.py Fri May 08 14:20:19 -0700 2009 Removing simple Python 2.3 specific code (e.g. ... [peterjc]
file listfns.py Wed Oct 29 10:30:32 -0700 2008 Declaring Bio.mathfns, Bio.stringfns, Bio.listf... [peterjc]
file mathfns.py Sat Nov 22 04:51:03 -0800 2008 Deprecating Bio.mathfns and Bio.stringfns [peterjc]
file pairwise2.py Fri Oct 31 08:53:44 -0700 2008 Using key in dict instead of dict.has_key(key) ... [peterjc]
file stringfns.py Tue Mar 24 23:23:05 -0700 2009 Removing code deprecated in Biopython release 1... [mdehoon]
file trie.c Sun Jul 16 11:57:27 -0700 2006 See Bug #1767. Avoid linking to msvcrt.dll in a... [mdehoon]
file trie.h Sun Jul 16 12:10:12 -0700 2006 Comply with ANSI standard. [mdehoon]
file triefind.py Sun Mar 21 08:56:54 -0800 2004 Small documentation changes across many Biopyth... [chapmanb]
file triemodule.c Tue Nov 18 17:39:21 -0800 2008 More changes for Python 2.5. See bug #2609. [mdehoon]
file utils.py Fri Nov 28 02:30:04 -0800 2008 Removal of deprecated string functions; see bug... [mdehoon]