0.200510  2020-02-21 00:18:30+01:00 Europe/Brussels
    - Changes
      - Taxonomy: improved method eq_tax to optionally return both got and exp labels
    - Fixes
      - Taxonomy: fixed missing species ranks in GCA-based lineages
      - Taxonomy: fixed warnings due to merged/deleted nodes when using setup-taxdir.pl

0.191300  2019-05-10 08:44:29+02:00 Europe/Brussels
    - Additions
      - Ali: added method all_but_new_seqs
      - Seq: added method clear_new_tag (also in Ali as clear_new_tags)
    - Changes
      - Listable: improved regex to capture multiple chunks (as in abbr-id-fas.pl)
    - Fixes
      - ColorScheme: fixed loophole in dependency resolution for Graphics::ColorNames::WWW
      - Tree: temporarily disabled tests relying on phyml

0.190900  2019-03-31 22:19:09+02:00 Europe/Brussels
    - Changes
      - all: improved warning and error messages (now prefixed by [BMC])
      - Seq: ungapped seqs ending in '*' are now again considered as aligned (restored Seq-checking behavior to pre-v0.180190)
      
0.190690  2019-03-10 01:18:33+01:00 Europe/Brussels
    - Additions
      - Ali: added method all_new_seqs
    - Fixes
      - IdList: fixed private hash not being updated after adding new ids
      
0.190500  2019-02-19 15:41:48+01:00 Europe/Brussels
    - Additions
      - binaries: added --item-type 'strain' to fetch-tax.pl
    - Fixes
      - ColorScheme: fixed incompatibility with recent Graphics::ColorNames

0.182420  2018-08-30 15:45:19+02:00 Europe/Brussels
    - Additions
      - Ali: added class method instant_store
    - Fixes
      - binaries: fixed --legacy-nom bug in fetch-tax.pl

0.181310  2018-05-11 23:52:11+02:00 Europe/Brussels
    - Additions
      - GeneticCode::Factory: codes now accept ambiguous codons in translation
    - Changes
      - Taxonomy: splitting of lineages should be more robust

0.181180  2018-04-28 13:43:41+02:00 Europe/Brussels
    - Fixes
      - ColorScheme: fixed bug #125225 (rt.cpan.org): depends on module not on CPAN

0.181170  2018-04-27 14:19:02+02:00 Europe/Brussels
    - Additions
      - ColorScheme: improved delegation to internal classifier (and tests)
      - Trees: switch_branch_lengths_and_labels_for_entities method is now compatible with treeplot
      
0.181120  2018-04-23 00:34:53+02:00 Europe/Brussels
    - Additions
      - ColorScheme: revamped its internal classifier (which now requires Taxonomy)
      - ColorScheme: added handling of indexed colors (like those required by gnuplot)
      - Taxonomy: new Taxable role to provide a Taxonomy attribute to any class
      - Taxonomy: new alias methods fetch_lineage and compute_lca
    - Changes
      - binaries: removal of classify_ali.pl (now distributed with Bio::MUST::Tools::Mcl)
      - ColorScheme: moved under Taxonomy namespace
      - Taxonomy: again refined handling of taxonomically ambiguous NCBI names

0.181000  2018-04-11 00:27:02+02:00 Europe/Brussels
    - Additions
      - Taxonomy: new eq_tax method
    - Changes
      - Taxonomy: much improved handling of taxonomically ambiguous NCBI names
    - Fixes
      - Taxonomy: (hopefully) at last fixed setup-taxdir.pl warnings

0.180630  2018-03-04 01:54:45+01:00 Europe/Brussels
    - Additions
      - binaries: new script clust2mapper.pl (to reflect clusters in tree formatting)
      - binaries: added option --keep-strain to fetch-tax.pl
    - Changes
      - IdMapper: improved handling of underscore-containing (valid) ids
      - Taxonomy: get_taxonomy_from_seq_id now also accepts lineages (stringified or as ArrayRefs)
    - Fixes
      - 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
    - Additions
      - Ali: added option to allow more control on FASTA file format
      - Ali::Stash: improved documentation
      - Ali::Temporary: added option to control the lifespan of FASTA file
    - Changes
      - GeneticCode::Factory: hard-coded NCBI gc.prt file for robustness
    - Fixes
      - IdList: fixed regression bug preventing FortyTwo to work
      - Taxonomy: improved robustness of setup-taxdir.pl-related methods
      - Taxonomy: better described dependencies for more robust deployment

0.180190  2018-01-19 10:00:47+01:00 Europe/Brussels
    - Changes
      - Ali: improved consistency of guessing default value (always on)
      - Seq: ungapped seqs ending in '*' are now trimmed and considered non-aligned
    - Fixes
      - Ali::Temporary: fixed regression bug preventing IdList application
      - GeneticCode::Factory: tests should now pass on more platforms
      - PostPred::Composition: tests should now pass on more platforms

0.180140  2018-01-14 22:36:55+01:00 Europe/Brussels
    - Additions
      - Ali::Temporary: new args attribute (to fine-tune FASTA file creation)
      - Ali::Temporary: improved documentation

0.173620  2017-12-29 00:58:54+01:00 Europe/Brussels
    - Additions
      - Ali: new clone method
      - Ali: improved documentation
    - Changes
      - Tree: shorten_ids/restore_ids now ignore missing ids in IdMapper
    - Fixes
      - Rates: tests should now pass on more platforms
      - Taxonomy: GCA-based taxon ids now retain their true taxonomic rank

0.173500  2017-12-17 00:35:51+01:00 Europe/Brussels
    - Additions
      - binaries: new script split-matrix.pl (to extract genes from a supermatrix)
    - Changes
      - Taxonomy: LCA inference algorithm can now follow a majority-rule approach
    - Fixes
      - Taxonomy: tests are now disabled by default

0.173470  2017-12-13 09:14:04+01:00 Europe/Brussels
    - first release