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- License: perl_5
- Perl: v5.13.2
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Changes for version 0.173500 - 2017-12-17
- 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
Documentation
- ali2fasta.pl - Convert ALI files to FASTA files
- ali2phylip.pl - Convert ALI files to PHYLIP files
- app-len-ids-ali.pl - Appends seq lengths to ids in ALI files (as SCaFoS)
- change-ids-ali.pl - Change (abbreviate or restore) ids' org component in ALI files
- classify-ali.pl - Classify ALI files according to multiple (taxonomic) criteria
- fasta2ali.pl - Convert FASTA files to ALI files
- fetch-tax.pl - Fetch information from the NCBI Taxonomy database
- format-tree.pl - Format 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
- map-gis-ali.pl - Build a GI-to-taxid id mapper from GI numbers in ALI files
- mask-ali.pl - Mask an ALI file according to BLOCKS file(s)
- phylip2ali.pl - Convert PHYLIP files to ALI files
- ppred-comp-test.pl - Compute compositional test based on ppred data
- 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 - Restore 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-ppred-ali.pl - Split ALI files into subsets of sites based on ppred data
- 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
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 ungapped mapped Ali written on disk
- Bio::MUST::Core::ColorScheme - Color scheme for taxonomic annotations
- 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::Commentable - Commentable Moose role for storable objects
- Bio::MUST::Core::Roles::Listable - Listable Moose role for objects with implied id lists
- 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::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::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
