Changes for version 0.181000 - 2018-04-11

  • Additions
    • Taxonomy: new eq_tax method
  • Changes
    • Taxonomy: much improved handling of taxonomically ambiguous NCBI names
  • Fixes
    • Taxonomy: (hopefully) at last fixed warnings


Convert ALI files to FASTA files
Convert ALI files to PHYLIP files
Appends seq lengths to ids in ALI files (as SCaFoS)
Change (abbreviate or restore) ids' org component in ALI files
Classify ALI files according to multiple (taxonomic) criteria
Build id mapper from UCLUST/CD-HIT clusters for tree formatting
Convert FASTA files to ALI files
Fetch information from the NCBI Taxonomy database
Format trees for printing
Discard (nearly) gap-only sites from ALI files
Jackknife a directory of ALI files
Build final id mapper from id list using the NCBI Taxonomy database
Build a GI-to-taxid id mapper from GI numbers in ALI files
Mask an ALI file according to BLOCKS file(s)
Convert PHYLIP files to ALI files
Compute compositional test based on ppred data
Prune sequences from ALI files based on id lists
Prune tips from TREE files based on id lists
Restore ids in ALI files
Setup a local mirror of the NCBI Taxonomy database
Extract individual gene ALIs from a SCaFoS supermatrix
Split ALI files into subsets of sites based on ppred data
Split ALI files into subsets of sites based on evolutionary rates
Convert STOCKHOLM files to ALI files
Subsample forest (multiple trees) files (and restore ids)
Build an id mapper from a tabular file giving annotation strings.
Apply a taxonomic filter to ALI files
Generate id lists from tree tips
Convert trees to TPL files


Core classes and utilities for Bio::MUST
Multiple sequence alignment
Thin wrapper for an indexed Ali read from disk
Thin wrapper for a temporary mapped Ali written on disk
Color scheme for taxonomic annotations
Distribution-wide constants for Bio::MUST::Core
Genetic code for conceptual translation
Genetic code factory based on NCBI gc.prt file
Id list for selecting specific sequences
Id mapper for translating sequence ids
Posterior predictive tests for sequences
Posterior predictive test for compositional bias
Aliable Moose role (pure interface) for Ali-like objects
Commentable Moose role for storable objects
Listable Moose role for objects with implied id lists
Nucleotide or protein sequence
Modern and legacy MUST-compliant sequence id
Sequence mask for selecting specific sites
Arbitrary frequencies for sequence sites
Evolutionary profiles for sequence sites
Evolutionary rates for sequence sites
NCBI Taxonomy one-stop shop
Helper class for multiple-criterion classifier based on taxonomy
Helper class for multiple-criterion classifier based on taxonomy
Helper class for multiple-criterion classifier based on taxonomy
Helper class for filtering seqs according to taxonomy
Wrapper class for serializing Bio::LITE::Taxonomy::NCBI object
Thin wrapper around Bio::Phylo trees
Collection of (bootstrap) trees
Distribution-wide Moose types for Bio::MUST::Core
Utility functions for enabling multiple file processing