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
