0.180630 2018-03-04 01:54:45+01:00 Europe/Brussels
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Additions
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binaries: new script clust2mapper.pl (to reflect clusters in tree formatting)
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binaries: added option --keep-strain to fetch-tax.pl
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Changes
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IdMapper: improved handling of underscore-containing (valid) ids
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Taxonomy: get_taxonomy_from_seq_id now also accepts lineages (stringified or as ArrayRefs)
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Fixes
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Taxonomy: setup-taxdir.pl should be more robust to out-of-sync NCBI files
0.180230 2018-01-23 23:44:19+01:00 Europe/Brussels
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Additions
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Ali: added option to allow more control on FASTA file format
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Ali::Stash: improved documentation
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Ali::Temporary: added option to control the lifespan of FASTA file
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Changes
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GeneticCode::Factory: hard-coded NCBI gc.prt file for robustness
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Fixes
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IdList: fixed regression bug preventing FortyTwo to work
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Taxonomy: improved robustness of setup-taxdir.pl-related methods
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Taxonomy: better described dependencies for more robust deployment
0.180190 2018-01-19 10:00:47+01:00 Europe/Brussels
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Changes
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Ali: improved consistency of guessing default value (always on)
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Seq: ungapped seqs ending in '*' are now trimmed and considered non-aligned
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Fixes
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Ali::Temporary: fixed regression bug preventing IdList application
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GeneticCode::Factory: tests should now pass on more platforms
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PostPred::Composition: tests should now pass on more platforms
0.180140 2018-01-14 22:36:55+01:00 Europe/Brussels
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Additions
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Ali::Temporary: new args attribute (to fine-tune FASTA file creation)
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Ali::Temporary: improved documentation
0.173620 2017-12-29 00:58:54+01:00 Europe/Brussels
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Additions
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Ali: new clone method
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Ali: improved documentation
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Changes
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Tree: shorten_ids/restore_ids now ignore missing ids in IdMapper
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Fixes
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Rates: tests should now pass on more platforms
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Taxonomy: GCA-based taxon ids now retain their true taxonomic rank
0.173500 2017-12-17 00:35:51+01:00 Europe/Brussels
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Additions
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binaries: new script split-matrix.pl (to extract genes from a supermatrix)
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Changes
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Taxonomy: LCA inference algorithm can now follow a majority-rule approach
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Fixes
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Taxonomy: tests are now disabled by default
0.173470 2017-12-13 09:14:04+01:00 Europe/Brussels
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first release