| 2013-09-02 |
Chris Fields | fix POD syntax
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commit | commitdiff | tree |
| 2013-09-02 |
Matt Oates | Added script to cut subsequences out of a set of sequence...
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commit | commitdiff | tree |
| 2013-09-02 |
Matt Oates | Added script for breaking sequence files into equal...
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commit | commitdiff | tree |
| 2013-09-02 |
antony03 | FastAlign.pl
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commit | commitdiff | tree |
| 2013-09-02 |
Brian Osborne | Fix warning, 'inclusion threshold'
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commit | commitdiff | tree |
| 2013-09-02 |
Florent Angly | Fixed some "undefined value" warnings when taxonomy...
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commit | commitdiff | tree |
| 2013-09-02 |
Jean-Frédéric Berthelot | Add unit test for SearchIO::Exonerate negative score...
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commit | commitdiff | tree |
| 2013-09-02 |
Jean-Frédéric Berthelot | Fix bug with score parsing in SearchIO::Exonerate
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commit | commitdiff | tree |
| 2013-09-02 |
Brian Osborne | Sorry about this, analyzing new output files is leading...
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commit | commitdiff | tree |
| 2013-09-02 |
Brian Osborne | Minor regex change
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commit | commitdiff | tree |
| 2013-09-02 |
Brian Osborne | Remove unused
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commit | commitdiff | tree |
| 2013-09-02 |
Brian Osborne | Corrected, all SearchIO tests pass
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commit | commitdiff | tree |
| 2013-09-02 |
Brian Osborne | Back this out, related tests are failing
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commit | commitdiff | tree |
| 2013-09-02 |
Brian Osborne | Add strand() so nhmmer can get strand data
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commit | commitdiff | tree |
| 2013-09-02 |
Brian Osborne | Add partial support for nhmmer (version 3.1)
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commit | commitdiff | tree |
| 2013-07-12 |
Lincoln Stein | add version number to LoadHelper
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commit | commitdiff | tree |
| 2013-07-12 |
Lincoln Stein | dramatically improve performance when loading multiple...
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commit | commitdiff | tree |
| 2013-07-12 |
Florent Angly | Fixed bug where not all nodes in lineage were merged...
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commit | commitdiff | tree |
| 2013-07-12 |
Florent Angly | More tests
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commit | commitdiff | tree |
| 2013-07-12 |
Florent Angly | Better distinguish ambiguous taxon names
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commit | commitdiff | tree |
| 2013-07-12 |
Florent Angly | Fixed issue where ambiguous taxa names got the same...
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commit | commitdiff | tree |
| 2013-07-12 |
Florent Angly | Fixed bug where taxon rank was missing
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commit | commitdiff | tree |
| 2013-07-12 |
Florent Angly | More Bio::DB::Taxonomy::list tests
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commit | commitdiff | tree |
| 2013-07-12 |
Florent Angly | Boolean return status for merge_lineage()
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commit | commitdiff | tree |
| 2013-07-12 |
Florent Angly | Fixed number of tests in t/ClusterIO/SequenceFamily.t
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commit | commitdiff | tree |
| 2013-07-12 |
Florent Angly | Fixed use of uninitialized value $reporttype
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commit | commitdiff | tree |
| 2013-07-12 |
Florent Angly | Fixed redefined variable
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commit | commitdiff | tree |
| 2013-07-12 |
Florent Angly | Small POD and and error message change
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commit | commitdiff | tree |
| 2013-07-12 |
Florent Angly | Adding arbitrary branch length in Bio::DB::Taxonomy...
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commit | commitdiff | tree |
| 2013-07-12 |
Florent Angly | Use a default format for as_string
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commit | commitdiff | tree |
| 2013-07-12 |
Florent Angly | Test uses species, not intermediary node
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commit | commitdiff | tree |
| 2013-07-12 |
Florent Angly | Avoid use of an undefined value as an ARRAY reference
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commit | commitdiff | tree |
| 2013-07-12 |
Florent Angly | Use list context instead of scalar context to include...
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commit | commitdiff | tree |
| 2013-07-12 |
Florent Angly | Fixed POD indentation
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commit | commitdiff | tree |
| 2013-07-12 |
Florent Angly | Tests for Bio::Taxonomy::get_tree
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commit | commitdiff | tree |
| 2013-07-12 |
Chris Fields | update tests for perl 5.18
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commit | commitdiff | tree |
| 2013-07-12 |
hyphaltip | make explicit
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commit | commitdiff | tree |
| 2013-07-12 |
Brian Osborne | Bug 3415
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commit | commitdiff | tree |
| 2013-07-12 |
Carnë Draug | maint: remove hard tabs and trailing whitespace
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commit | commitdiff | tree |
| 2013-07-12 |
Brian Osborne | Merge branch 'master' of github.com:bioperl/bioperl...
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commit | commitdiff | tree |
| 2013-07-12 |
Brian Osborne | Add dna_to_aa_aln method and tests
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commit | commitdiff | tree |
| 2013-07-12 |
Carnë Draug | Annotation: fix typo on test
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commit | commitdiff | tree |
| 2013-07-12 |
Carnë Draug | Bio::Cluster::SequenceFamily - bug fixes and performance
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commit | commitdiff | tree |
| 2013-07-12 |
Brian Osborne | Add support for version 4, all tests pass
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commit | commitdiff | tree |
| 2013-07-11 |
hyphaltip | missing request for marker name in the call
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commit | commitdiff | tree |
| 2013-07-11 |
Carnë Draug | recover GenericWebAgent from Bio-EUtilities
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commit | commitdiff | tree |
| 2013-07-11 |
Benjamin Vaisvil | Per: http://www.bioperl.org/wiki/Bioperl_Best_Practices and
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commit | commitdiff | tree |
| 2013-07-11 |
Benjamin Vaisvil | fix conflict
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commit | commitdiff | tree |
| 2013-07-11 |
Benjamin Vaisvil | typo, removed ->
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commit | commitdiff | tree |
| 2013-07-11 |
Brian Osborne | Bio::AlignIO::fasta was not always using />\s*(\S+...
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commit | commitdiff | tree |
| 2013-07-11 |
Francisco J. Ossandon | Fix for Bug #3251, plus fixed a couple of regular expression...
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commit | commitdiff | tree |
| 2013-07-11 |
Francisco J. Ossandon | Revert "Fixed no-hit blast bug and faulty regexs, added...
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commit | commitdiff | tree |
| 2013-07-11 |
unknown | Fixed no-hit blast bug and faulty regexs, added tests
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commit | commitdiff | tree |
| 2013-07-11 |
Carnë Draug | Bio::Perl - fix indentation (remove tabs, and weird...
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commit | commitdiff | tree |
| 2013-07-11 |
Paul Cantalupo | updating Changes file
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commit | commitdiff | tree |
| 2013-07-11 |
Paul Cantalupo | Merge branch 'topic/bug3302'
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commit | commitdiff | tree |
| 2013-07-11 |
Carnë Draug | Don't use a separate default scalar when there's a...
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commit | commitdiff | tree |
| 2013-07-11 |
Carnë Draug | follow perl recommendations:
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commit | commitdiff | tree |
| 2013-07-11 |
Carnë Draug | fix indentation (remove tabs, and weird 3 spaces indentation)
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commit | commitdiff | tree |
| 2013-07-11 |
Carnë Draug | follow perl recommendations:
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commit | commitdiff | tree |
| 2013-07-11 |
Carnë Draug | use until instead of while(1){last if...}
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commit | commitdiff | tree |
| 2013-07-11 |
Carnë Draug | fix indentation (remove tabs, 3 space and 2 space indentation)
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commit | commitdiff | tree |
| 2013-07-11 |
Paul Cantalupo | fixing bug 3421 and adding test (hmmer2 now correctly...
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commit | commitdiff | tree |
| 2013-07-11 |
Florent Angly | More thoroughly documented options and defaults
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commit | commitdiff | tree |
| 2013-07-11 |
Florent Angly | Restoring intended behaviour... I think
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commit | commitdiff | tree |
| 2013-07-11 |
Florent Angly | Fixed failing DBD test
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commit | commitdiff | tree |
| 2013-02-20 |
Chris Fields | add test and TODO for Issue #3416
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commit | commitdiff | tree |
| 2013-02-20 |
Chris Fields | accession no longer valid, using updated one
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commit | commitdiff | tree |
| 2013-02-19 |
Chris Fields | squash another warning from Graph module oddities
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commit | commitdiff | tree |
| 2013-02-19 |
Chris Fields | fix problems with remote data changes
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commit | commitdiff | tree |
| 2013-02-19 |
Chris Fields | LOCUS IDs no longer work, bad for swissprot-like IDs...
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commit | commitdiff | tree |
| 2013-02-19 |
Chris Fields | fix ID example
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commit | commitdiff | tree |
| 2013-02-19 |
Chris Fields | MUSIGHBA1 no longer works as a primary ID, LOCUS apparently...
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commit | commitdiff | tree |
| 2013-02-19 |
Chris Fields | bulletproof test against remote data changes
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commit | commitdiff | tree |
| 2013-02-19 |
Chris Fields | squash warning
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commit | commitdiff | tree |
| 2013-02-19 |
Chris Fields | squash warning
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commit | commitdiff | tree |
| 2013-02-19 |
Chris Fields | HTML table parsing requires UTF8 decoding
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commit | commitdiff | tree |
| 2013-02-19 |
Chris Fields | Graph::Directed is giving warnings when using 'require...
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commit | commitdiff | tree |
| 2013-02-19 |
Chris Fields | squash warning
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commit | commitdiff | tree |
| 2013-02-19 |
Chris Fields | add v1 branch for CI
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commit | commitdiff | tree |
| 2013-02-06 |
Chris Fields | fix for bug #3410
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commit | commitdiff | tree |
| 2012-11-26 |
Chris Fields | allow additional nuc IUPAC when guessing, this was...
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commit | commitdiff | tree |
| 2012-11-04 |
Chris Fields | BLAST XML not allowing custom search handlers, fix...
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commit | commitdiff | tree |
| 2012-10-03 |
Chris Fields | fix deprecated usage warnings for perl 5.16
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commit | commitdiff | tree |
| 2012-10-03 |
Chris Fields | add Bio::ASN1::EntrezGene
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commit | commitdiff | tree |
| 2012-10-03 |
Chris Fields | comment out vestigial commit(), tests now pass
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commit | commitdiff | tree |
| 2012-10-02 |
Chris Fields | Should run check if SQLite or Pg drivers present
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commit | commitdiff | tree |
| 2012-10-02 |
Chris Fields | Only commit if AutoCommit is off
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commit | commitdiff | tree |
| 2012-10-02 |
Chris Fields | clean up last commit a little
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commit | commitdiff | tree |
| 2012-10-02 |
Chris Fields | returning undef to an array still creates an array...
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commit | commitdiff | tree |
| 2012-10-02 |
Chris Fields | mysql => Pg
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commit | commitdiff | tree |
| 2012-10-01 |
Chris Fields | um, when did IndexedBase come about? Fix to address...
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commit | commitdiff | tree |
| 2012-10-01 |
Chris Fields | fix text fail if HTML::TableExtract isn't present
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commit | commitdiff | tree |
| 2012-10-01 |
Chris Fields | squash a couple of warnings with more recent versions...
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commit | commitdiff | tree |
| 2012-08-25 |
Chris Fields | Revert "Fix for correctly parsing phylip format with...
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commit | commitdiff | tree |
| 2012-07-27 |
Chris Fields | test Bio::Phylo and Bio::ASN1::EntrezGene deps
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commit | commitdiff | tree |
| 2012-07-27 |
Chris Fields | add whitelist, switch to master (this disappeared somewhere...
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commit | commitdiff | tree |
| 2012-07-27 |
Chris Fields | test libxml dep
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commit | commitdiff | tree |
| 2012-07-27 |
Chris Fields | consolidate cpanm params
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commit | commitdiff | tree |
| 2012-07-26 |
Chris Fields | test GD again
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commit | commitdiff | tree |
