{"shas":[["6732d5b838ade764083f28cb31ef0bfdec12e7cb","a1dd320e7af18bab343813d9e27c88d8cf2d1bd8@gmail.com","PAML: fixed bug in print_options() when NSsites is None.","jakobcreutzfeldt"],["dfba303ff50927cca4184a7df647cafcb5d26711","a1dd320e7af18bab343813d9e27c88d8cf2d1bd8@gmail.com","PAML: shortened some codeml results keys","jakobcreutzfeldt"],["fc0be75d1231e219bdf38ef55513011a4179e054","a1dd320e7af18bab343813d9e27c88d8cf2d1bd8@gmail.com","PAML: fixed some yn00 results keys for consistency","jakobcreutzfeldt"],["60f28efdfe19fdcb2bb3ca4dc2ca6a222be97394","c01a39a76d96e917f87dcda7aac0ff07d778d5c1@googlemail.com","Fix float('-inf') on Python 2.5 or older under Windows (see PEP 754)","peterjc"],["a204425e5922348271726fdb4ae81f55bc63607a","a1dd320e7af18bab343813d9e27c88d8cf2d1bd8@gmail.com","Merge branch 'master' into paml-branch","Brandon Invergo"],["c6df02b8764d439df306725babf3b95a9432bc5b","2713355827c21e9da6b8e25fdbb80553768dad61@fhcrc.org","Trim trailing space\n\nRemove all trailing whitespace from PhylipIO and related files.","Connor McCoy"],["f4d200134029008f1bbc501ad898478423c902cf","2713355827c21e9da6b8e25fdbb80553768dad61@fhcrc.org","Implement ExtendedPhylip\n\n* Tweak PhylipIterator to be compatible with extended format\n* Set up PhylipWriter to take truncate argument\n* Implement ExtendedPhylipIterator, ExtendedPhylipWriter - mostly thin\n  layers on the standard Phylip IO classes.","Connor McCoy"],["4d5e57aa197bc4a566c5c64163b88a16c35838d5","2713355827c21e9da6b8e25fdbb80553768dad61@fhcrc.org","Update tests for extended phylip format\n\n* Update expected output for test_AlignIO, test_SeqIO\n* Apply most of the same exceptions affecting the phylip format to\n  extended phylip\n* Add a sample extended phylip format-file (primates.phyx, from the\n  Bodega Phylogenetics Wiki:\n  http://bodegaphylo.wikispot.org/RAxML_Tutorial)","Connor McCoy"],["2f972d42c43dc52045c0548d443ec643ce1d611a","2713355827c21e9da6b8e25fdbb80553768dad61@fhcrc.org","Refactor; rename to Extended -> Relaxed\n\n* Rename ExtendedPhylip to RelaxedPhylip\n* Add PhylipIterator._split_id, overridden for RelaxedPhylipIterator\n* Change mapping to RelaxedPhylip{Writer,Iterator} in AlignIO to\n  'phylip-relaxed'","Connor McCoy"],["52cfe599b2049c6b9b5a1ef40ec5d88dd04b4ad2","2713355827c21e9da6b8e25fdbb80553768dad61@fhcrc.org","Rename truncate parameter to id_width\n\nSince RelaxedPhylip doesn't truncate, this seems like a better label.","Connor McCoy"],["2fcda1fd9e9d091e939408293f351faeb207f5a0","2713355827c21e9da6b8e25fdbb80553768dad61@fhcrc.org","Update tests to match renamed classes","Connor McCoy"],["cf4d29e79027165ce31590b946106e7a16597cc2","c01a39a76d96e917f87dcda7aac0ff07d778d5c1@googlemail.com","Mention Connor's work on phylip-relaxed in NEWS","peterjc"],["eebf86f863f1d5bfc9a09ab53abf101a4cc8dc79","031b2c874c73f0894e2716cfcd696f81e80aaf20@gmail.com","test_Phylo: fixed a platform-specific error in testing float formatting","Eric Talevich"],["375fdb70bf0e28f9cbb50bb78fd20480d0ccc5ba","031b2c874c73f0894e2716cfcd696f81e80aaf20@gmail.com","Phylo/NewickIO: renamed & deprecated a few keyword arguments\n\nParser.parse:\n    values_are_support  =>  values_are_confidence\n\nWriter.write:\n    support_as_branchlengths  =>  confidence_as_branch_length\n    max_support  =>  max_confidence\n    branchlengths_only  =>  branch_length_only","Eric Talevich"],["5eaf6cb773a4ff1df1287556b39a65d30dabb43c","a1dd320e7af18bab343813d9e27c88d8cf2d1bd8@gmail.com","PAML: accounted for rare occurrence of numbers running into each other in codeml results files","jakobcreutzfeldt"],["0963fcc974b3924bc4c1053066f7023dbcd3baf2","a1dd320e7af18bab343813d9e27c88d8cf2d1bd8@gmail.com","Merge branch 'paml-branch' of https://github.com/brandoninvergo/biopython into paml-branch","jakobcreutzfeldt"],["47df415ab667326b90a52632e085fec2a28e4e54","29c47cac31e9e186ed59ffc1ed60aa4cb23634cc@50mail.com","Merge remote-tracking branch 'brandoninvergo/paml-branch'","chapmanb"],["a67473e7f710f58e84f0d6336da57935f607275f","29c47cac31e9e186ed59ffc1ed60aa4cb23634cc@50mail.com","Details on Brandon's PAML contribution","chapmanb"],["cd0dcf70bd6e61496b1b48902957d7f758c20e05","c01a39a76d96e917f87dcda7aac0ff07d778d5c1@googlemail.com","Short term hack to get PhyloXML to work on Python 2.4","peterjc"],["9531507124a398a2221d5cc197cfb9da0964b5a3","c01a39a76d96e917f87dcda7aac0ff07d778d5c1@googlemail.com","Must install new PAML module","peterjc"]],"ref":"refs/heads/master","size":37,"head":"00f2efd2facff06f8ca579168a463913679fb519","push_id":34872749}