view release on metacpan or  search on metacpan

Changes  view on Meta::CPAN

0.252040  2025-07-23 23:59:32+02:00 Europe/Rome
    - Additions
      - Taxonomy::Criterion: added support for percentages
      - Taxonomy: added class method no_warnings (to silence most Taxonomy-related warnings)
    - Changes
      - Taxonomy: updated ranks (e.g., domain) to match recent versions of NCBI Taxonomy
      - Taxonomy: switched to https to download NCBI Taxonomy (setup-taxdir.pl)
      - Taxonomy: improved handling of GCF numbers as GCA numbers with GTDB

0.251810  2025-06-30 15:44:10+02:00 Europe/Brussels
    - Fixes
      - Taxonomy: updated URL for GTDB download (used in setup-taxdir.pl)

0.251140  2025-04-24 20:39:26+02:00 Europe/Brussels
    - Changes
      - SeqId: improved generation of MUST ids from NCBI names
    - Fixes
      - distribution: tried to fix failing cross-platform tests (cpantesters.org)

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