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