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Denis BAURAIN > Bio-MUST-Core-0.181310


This Release Bio-MUST-Core-0.181310  [Download] [Browse 11 May 2018
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License The Perl 5 License (Artistic 1 & GPL 1)
Special Files


Bio::MUST::Core Core classes and utilities for Bio::MUST     0.181310
Bio::MUST::Core::Ali Multiple sequence alignment     0.181310
Bio::MUST::Core::Ali::Stash Thin wrapper for an indexed Ali read from disk     0.181310
Bio::MUST::Core::Ali::Temporary Thin wrapper for a temporary mapped Ali written on disk     0.181310
Bio::MUST::Core::Constants Distribution-wide constants for Bio::MUST::Core     0.181310
Bio::MUST::Core::GeneticCode Genetic code for conceptual translation     0.181310
Bio::MUST::Core::GeneticCode::Factory Genetic code factory based on NCBI gc.prt file     0.181310
Bio::MUST::Core::IdList Id list for selecting specific sequences     0.181310
Bio::MUST::Core::IdMapper Id mapper for translating sequence ids     0.181310
Bio::MUST::Core::PostPred Posterior predictive tests for sequences     0.181310
Bio::MUST::Core::PostPred::Composition Posterior predictive test for compositional bias     0.181310
Bio::MUST::Core::Roles::Aliable Aliable Moose role (pure interface) for Ali-like objects     0.181310
Bio::MUST::Core::Roles::Commentable Commentable Moose role for storable objects     0.181310
Bio::MUST::Core::Roles::Listable Listable Moose role for objects with implied id lists     0.181310
Bio::MUST::Core::Roles::Taxable Taxable Moose role for objects that query a taxonomy     0.181310
Bio::MUST::Core::Seq Nucleotide or protein sequence     0.181310
Bio::MUST::Core::SeqId Modern and legacy MUST-compliant sequence id     0.181310
Bio::MUST::Core::SeqMask Sequence mask for selecting specific sites     0.181310
Bio::MUST::Core::SeqMask::Freqs Arbitrary frequencies for sequence sites     0.181310
Bio::MUST::Core::SeqMask::Profiles Evolutionary profiles for sequence sites     0.181310
Bio::MUST::Core::SeqMask::Rates Evolutionary rates for sequence sites     0.181310
Bio::MUST::Core::Taxonomy NCBI Taxonomy one-stop shop     0.181310
Bio::MUST::Core::Taxonomy::Category Helper class for multiple-criterion classifier based on taxonomy     0.181310
Bio::MUST::Core::Taxonomy::Classifier Helper class for multiple-criterion classifier based on taxonomy     0.181310
Bio::MUST::Core::Taxonomy::ColorScheme Helper class providing color scheme for taxonomic annotations     0.181310
Bio::MUST::Core::Taxonomy::Criterion Helper class for multiple-criterion classifier based on taxonomy     0.181310
Bio::MUST::Core::Taxonomy::Filter Helper class for filtering seqs according to taxonomy     0.181310
Bio::MUST::Core::Taxonomy::Labeler Helper class for simple labeler based on taxonomy     0.181310
Bio::MUST::Core::Taxonomy::MooseNCBI Wrapper class for serializing Bio::LITE::Taxonomy::NCBI object     0.181310
Bio::MUST::Core::Tree Thin wrapper around Bio::Phylo trees     0.181310
Bio::MUST::Core::Tree::Forest Collection of (bootstrap) trees     0.181310
Bio::MUST::Core::Types Distribution-wide Moose types for Bio::MUST::Core     0.181310
Bio::MUST::Core::Utils Utility functions for enabling multiple file processing     0.181310

Documentation 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 Build id mapper from UCLUST/CD-HIT clusters for tree formatting  
codegen/templates/ 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