0.250380 2025-02-07 22:32:00+01:00 Europe/Brussels
- Additions
- binaries: new script resample-ali.pl (for bootstrap and jackknife)
- SeqMask::Weights: new class to implement bootstrap and jackknife masks
- Fixes
- binaries: improved robustness of change-ids-ali.pl towards mixed ids
- binaries: fixed replicate numbering in jack-ali-dir.pl
0.250200 2025-01-20 17:13:21+01:00 Europe/Brussels
- Additions
- SeqId and SeqId::Filter: refactored and expanded filters based on SeqId components
- binaries: added new strategies (tag, genus, species) for automated rooting to format-tree.pl
- Fixes
- Tree: fixed bug preventing to root a tree without bootstrap support
0.243430 2024-12-08 23:10:32+01:00 Europe/Brussels
- Additions
- binaries: new script tseq2ali.pl (for TinySeq files)
- binaries: idealize.pl and ali2phylip.pl are now codon-compatible
- Ali: new method load_tinyseq to import NCBI TinySeq XML files
- Seq: now silently converts '!' (used as a frameshift symbol) to 'x'
- SeqMask: new method codon_mask to allow all masks to preserve codons
- Changes
- Taxonomy: now silently handles GCF numbers as GCA numbers to spare space
- Fixes
- Ali::Stash: fixed missing method filename
- Taxonomy: restored support for GTDB setup (following remote changes)
0.242020 2024-07-20 12:23:52+02:00 Europe/Rome
- Additions
- Filterable: new role to generalize filtering of SeqId objects beyond taxonomy
- Listable: added method desc_seq_len_list
- SeqId: added method instance for memoized object construction (to speed up Splits analysis)
- SeqId::Filter: new class to implement method SeqId::family_filter
- Tree: added method get_node_that_maximizes (e.g., to look for long branch lengths)
- Tree: added method newick_str as a robust wrapper around Bio::Phylo to_newick method
- Tree: finally added full-working method root_tree!
- Tree::Splits: new class to handle splits and preserve node metadata after rooting
- binaries: added automated rooting on taxon or family to format-tree.pl
- Changes
- Listable: refactored complete_seq_list method to optionally report seq lengths
- Listable: refactored (and renamed) long_leaf_list method (to long_branch_list)
- SeqId: now automatically (and silently) removes quotes around ids (especially in trees)
- Taxonomy: reduced redundancy of Note messages about merged taxa
- Fixes
- IdList: fixed SeqId-related bug preventing seqs to be batch-extracted in some cases
- binaries: improved robustness of classify-ali.pl and inst-abbr-ids.pl
0.240390 2024-02-08 21:59:31+01:00 Europe/Brussels
- Additions
- Ali: temp_fasta can now be passed an existing IdMapper
- Listable: std_mapper can now accept an offset for numbering seqs
- SeqId: added warning for unparsable ids due to trailing spaces
- Changes
- Listable: changed interface of std_mapper
- Fixes
- binaries: improved robustness of import-itol.pl
0.212670 2021-09-24 16:25:23+02:00 Europe/Brussels
- Changes
- Ali: refactored store_phylip method for speed (visible in ali2phylip.pl)
- Seq: rolled back changes to gapify method (to preserve generality)
0.212650 2021-09-22 22:37:09+02:00 Europe/Brussels
- Changes
- Seq: refactored gapify method for speed (visible in ali2phylip.pl)
0.212530 2021-09-10 23:55:21+02:00 Europe/Brussels
- Changes
- binaries: moved 'inst' executables to 'bin' dir (for default install)
- Fixes
- binaries: improved command-line robustness towards enum-like option values
0.211470 2021-05-27 22:53:20+02:00 Europe/Brussels
- Additions
- binaries: split-rates-ali.pl can now analyse pairs of profiles
- SeqMask::Pmsf: new class to support IQ-TREE sitefreq files
- Taxonomy: added support for GTDB Taxonomy
- Changes
- binaries: prune-tree.pl now preserves bootstrap values
0.210610 2021-03-02 23:22:29+01:00 Europe/Brussels
- Additions
- binaries: new script inst-split-seqs.pl
- Seq: added methods purity and wrapped_str
- SeqId: added method abbr_with_regex
- Changes
- binaries: refactored 'inst' executables (still no default install)
- Ali: cascaded additions and changes in Seq methods
- IdMapper: refactored regex_mapper to use abbr_with_regex
- Seq: changed some method names for API consistency (raw_seq, recode_seq, uc_seq)
- Tree: iTOL output now labels all internal nodes (instead of only collapsed nodes)
0.210380 2021-02-07 12:29:46+01:00 Europe/Brussels
- Additions
- binaries: new script tax-mask-ali.pl
- SeqMask::Rates: added support for IQ-TREE rate files
- Taxonomy::Classifier: added method tax_masks
- Types: reintroduced unused type coercions for IdList
- Changes
- Tree: modified store_itol_datasets to allow coloring leaf labels
- Fixes
- binaries: fixed incorrect outfile names for iTOL output in format-tree.pl
0.210230 2021-01-23 14:01:23+01:00 Europe/Brussels
- Additions
- binaries: new script export-itol.pl
- Changes
- binaries: renamed upload2itol.pl into import-itol.pl and added support for tree id output
- binaries: reinstated extract-ali.pl executable
- binaries: removed clust2mapper.pl executable
- distribution: removed dependency on Bio::FastParsers
- distribution: improved MANIFEST.SKIP
- Fixes
- SeqMask and Tree: tests should now pass on Solaris too (again)
0.210120 2021-01-12 16:53:42+01:00 Europe/Brussels
- Changes
- binaries: reinstated classify-ali.pl and jack-ali-dir.pl executables
- Fixes
- SeqId: expanded max tag length to 6 (lowercase) chars (e.g., nuppct#)
- SeqMask: tests should now pass on Solaris too
- Taxonomy::Criterion: fixed bug for positively avoided taxa (i.e., max_org_count: 0)
0.203490 2020-12-14 13:36:11+01:00 Europe/Brussels
- Additions
- binaries: added new collapsing modes to format-tree.pl
- Changes
- binaries: moved 'inst' executables to 'instant' dir (no default install)
- binaries: moved specialized and obsolete executables to 'private' dir (no default install)
- Constants: expanded suffix list for Ali files
- Taxonomy::ColorScheme and Tree: refactored iTOL coloring and collapsing for robustness
0.202310 2020-08-18 12:59:49+02:00 Europe/Brussels
- Fixes
- binaries: fixed spurious comment line bug in fetch-tax.pl output files
- Taxonomy and Tree: fixed underscore-like bug in iTOL coloring and collapsing
0.202070 2020-07-26 00:24:07+02:00 Europe/Rome
- Additions
- binaries: added support for iTOL coloring and collapsing to format-tree.pl
- binaries: new script upload2itol.pl
- binaries: new scripts inst-abbr-ids.pl, inst-qual-filter.pl and inst-tax-filter.pl
- Taxonomy::ColorScheme: added method store_itol_colors
- Tree: added method store_itol_collapse
- Fixes
- Taxonomy: fixed bug when trying to recover unknown lineages (visible in fetch-tax.pl)
- Taxonomy: updated NCBI Taxonomy ranks
0.201060 2020-04-15 12:27:22+02:00 Europe/Brussels
- Additions
- binaries: added two options (--column and --separator) and --item-type 'lineage' to fetch-tax.pl
- Ali: added method instant_count
- Taxonomy: added method get_taxid_from_taxonomy to parse NCBI (or SILVA) lineages
- Changes
- IdList: improved method load to use any column (from a flat table) as ids
- Taxonomy: revamped handling of ambiguous NCBI names (none is overlooked anymore)
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
- Taxonomy::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
- Taxonomy::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
- Taxonomy::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
- Taxonomy::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
- SeqMask::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