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Denis BAURAIN > Bio-MUST-Core-0.173620


This Release Bio-MUST-Core-0.173620  [Download] [Browse 28 Dec 2017
Latest Release Bio-MUST-Core-0.180630  [Download] [Browse 03 Mar 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     0.173620
Bio::MUST::Core::Ali Multiple sequence alignment     0.173620
Bio::MUST::Core::Ali::Stash Thin wrapper for an indexed Ali read from disk     0.173620
Bio::MUST::Core::Ali::Temporary Thin wrapper for a temporary ungapped mapped Ali written on disk     0.173620
Bio::MUST::Core::ColorScheme Color scheme for taxonomic annotations     0.173620
Bio::MUST::Core::Constants Distribution-wide constants for Bio::MUST::Core     0.173620
Bio::MUST::Core::GeneticCode Genetic code for conceptual translation     0.173620
Bio::MUST::Core::GeneticCode::Factory Genetic code factory based on NCBI gc.prt file     0.173620
Bio::MUST::Core::IdList Id list for selecting specific sequences     0.173620
Bio::MUST::Core::IdMapper Id mapper for translating sequence ids     0.173620
Bio::MUST::Core::PostPred Posterior predictive tests for sequences     0.173620
Bio::MUST::Core::PostPred::Composition Posterior predictive test for compositional bias     0.173620
Bio::MUST::Core::Roles::Commentable Commentable Moose role for storable objects     0.173620
Bio::MUST::Core::Roles::Listable Listable Moose role for objects with implied id lists     0.173620
Bio::MUST::Core::Seq Nucleotide or protein sequence     0.173620
Bio::MUST::Core::SeqId Modern and legacy MUST-compliant sequence id     0.173620
Bio::MUST::Core::SeqMask Sequence mask for selecting specific sites     0.173620
Bio::MUST::Core::SeqMask::Freqs Arbitrary frequencies for sequence sites     0.173620
Bio::MUST::Core::SeqMask::Profiles Evolutionary profiles for sequence sites     0.173620
Bio::MUST::Core::SeqMask::Rates Evolutionary rates for sequence sites     0.173620
Bio::MUST::Core::Taxonomy NCBI Taxonomy one-stop shop     0.173620
Bio::MUST::Core::Taxonomy::Category Helper class for multiple-criterion classifier based on taxonomy     0.173620
Bio::MUST::Core::Taxonomy::Classifier Helper class for multiple-criterion classifier based on taxonomy     0.173620
Bio::MUST::Core::Taxonomy::Criterion Helper class for multiple-criterion classifier based on taxonomy     0.173620
Bio::MUST::Core::Taxonomy::Filter Helper class for filtering seqs according to taxonomy     0.173620
Bio::MUST::Core::Taxonomy::MooseNCBI Wrapper class for serializing Bio::LITE::Taxonomy::NCBI object     0.173620
Bio::MUST::Core::Tree Thin wrapper around Bio::Phylo trees     0.173620
Bio::MUST::Core::Tree::Forest Collection of (bootstrap) trees     0.173620
Bio::MUST::Core::Types Distribution-wide Moose types for Bio::MUST::Core     0.173620
Bio::MUST::Core::Utils Utility functions for enabling multiple file processing     0.173620

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 Classify ALI files according to multiple (taxonomic) criteria  
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