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Bio-MUST-Core-0.210120
River stage one • 9 direct dependents • 9 total dependents
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Changes for version 0.210120 - 2021-01-12

  • 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)

Documentation

ali2fasta.pl
Convert ALI files to FASTA files
ali2phylip.pl
Convert (and filter) ALI files to PHYLIP files for tree building
app-len-ids-ali.pl
Appends seq lengths to ids in ALI files (as SCaFoS)
change-ids-ali.pl
Abbreviate or restore the org component of full seq ids in ALI files
classify-ali.pl
Classify ALI files based on taxonomic filters
clust2mapper.pl
Build id mapper from UCLUST/CD-HIT clusters for tree formatting
fasta2ali.pl
Convert FASTA files to ALI files
fetch-tax.pl
Fetch (and format) information from the NCBI Taxonomy database
format-tree.pl
Format (and annotate) trees for printing
idealize-ali.pl
Discard (nearly) gap-only sites from ALI files
jack-ali-dir.pl
Jackknife a directory of ALI files
list2mapper.pl
Build final id mapper from id list using the NCBI Taxonomy database
mask-ali.pl
Mask an ALI file according to BLOCKS file(s)
phylip2ali.pl
Convert PHYLIP files to ALI files
prune-ali.pl
Prune sequences from ALI files based on id lists
prune-tree.pl
Prune tips from TREE files based on id lists
rest-ids-ali.pl
Change (restore) full seq ids in ALI files
setup-taxdir.pl
Setup a local mirror of the NCBI Taxonomy database
split-matrix.pl
Extract individual gene ALIs from a SCaFoS supermatrix
split-rates-ali.pl
Split ALI files into subsets of sites based on evolutionary rates
stock2ali.pl
Convert STOCKHOLM files to ALI files
subs-forest.pl
Subsample forest (multiple trees) files (and restore ids)
tab2mapper.pl
Build an id mapper from a tabular file giving annotation strings
tax-filter-ali.pl
Apply a taxonomic filter to ALI files
tree2list.pl
Generate id lists from tree tips
tree2tpl.pl
Convert trees to TPL files
upload2itol.pl
Upload trees and associate metadata files to iTOL

Modules

Bio::MUST::Core
Core classes and utilities for Bio::MUST
Bio::MUST::Core::Ali
Multiple sequence alignment
Bio::MUST::Core::Ali::Stash
Thin wrapper for an indexed Ali read from disk
Bio::MUST::Core::Ali::Temporary
Thin wrapper for a temporary mapped Ali written on disk
Bio::MUST::Core::Constants
Distribution-wide constants for Bio::MUST::Core
Bio::MUST::Core::GeneticCode
Genetic code for conceptual translation
Bio::MUST::Core::GeneticCode::Factory
Genetic code factory based on NCBI gc.prt file
Bio::MUST::Core::IdList
Id list for selecting specific sequences
Bio::MUST::Core::IdMapper
Id mapper for translating sequence ids
Bio::MUST::Core::PostPred
Posterior predictive tests for sequences
Bio::MUST::Core::PostPred::Composition
Posterior predictive test for compositional bias
Bio::MUST::Core::Roles::Aliable
Aliable Moose role (pure interface) for Ali-like objects
Bio::MUST::Core::Roles::Commentable
Commentable Moose role for storable objects
Bio::MUST::Core::Roles::Listable
Listable Moose role for objects with implied id lists
Bio::MUST::Core::Roles::Taxable
Taxable Moose role for objects that query a taxonomy
Bio::MUST::Core::Seq
Nucleotide or protein sequence
Bio::MUST::Core::SeqId
Modern and legacy MUST-compliant sequence id
Bio::MUST::Core::SeqMask
Sequence mask for selecting specific sites
Bio::MUST::Core::SeqMask::Freqs
Arbitrary frequencies for sequence sites
Bio::MUST::Core::SeqMask::Profiles
Evolutionary profiles for sequence sites
Bio::MUST::Core::SeqMask::Rates
Evolutionary rates for sequence sites
Bio::MUST::Core::Taxonomy
NCBI Taxonomy one-stop shop
Bio::MUST::Core::Taxonomy::Category
Helper class for multiple-criterion classifier based on taxonomy
Bio::MUST::Core::Taxonomy::Classifier
Helper class for multiple-criterion classifier based on taxonomy
Bio::MUST::Core::Taxonomy::ColorScheme
Helper class providing color scheme for taxonomic annotations
Bio::MUST::Core::Taxonomy::Criterion
Helper class for multiple-criterion classifier based on taxonomy
Bio::MUST::Core::Taxonomy::Filter
Helper class for filtering seqs according to taxonomy
Bio::MUST::Core::Taxonomy::Labeler
Helper class for simple labeler based on taxonomy
Bio::MUST::Core::Taxonomy::MooseNCBI
Wrapper class for serializing Bio::LITE::Taxonomy::NCBI object
Bio::MUST::Core::Tree
Thin wrapper around Bio::Phylo trees
Bio::MUST::Core::Tree::Forest
Collection of (bootstrap) trees
Bio::MUST::Core::Types
Distribution-wide Moose types for Bio::MUST::Core
Bio::MUST::Core::Utils
Utility functions for enabling multiple file processing

Other files