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Denis BAURAIN > Bio-MUST-Core-0.181000


This Release Bio-MUST-Core-0.181000  [Download] [Browse 10 Apr 2018
Latest Release Bio-MUST-Core-0.181120  [Download] [Browse 22 Apr 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     0.181000
Bio::MUST::Core::Ali Multiple sequence alignment     0.181000
Bio::MUST::Core::Ali::Stash Thin wrapper for an indexed Ali read from disk     0.181000
Bio::MUST::Core::Ali::Temporary Thin wrapper for a temporary mapped Ali written on disk     0.181000
Bio::MUST::Core::ColorScheme Color scheme for taxonomic annotations     0.181000
Bio::MUST::Core::Constants Distribution-wide constants for Bio::MUST::Core     0.181000
Bio::MUST::Core::GeneticCode Genetic code for conceptual translation     0.181000
Bio::MUST::Core::GeneticCode::Factory Genetic code factory based on NCBI gc.prt file     0.181000
Bio::MUST::Core::IdList Id list for selecting specific sequences     0.181000
Bio::MUST::Core::IdMapper Id mapper for translating sequence ids     0.181000
Bio::MUST::Core::PostPred Posterior predictive tests for sequences     0.181000
Bio::MUST::Core::PostPred::Composition Posterior predictive test for compositional bias     0.181000
Bio::MUST::Core::Roles::Aliable Aliable Moose role (pure interface) for Ali-like objects     0.181000
Bio::MUST::Core::Roles::Commentable Commentable Moose role for storable objects     0.181000
Bio::MUST::Core::Roles::Listable Listable Moose role for objects with implied id lists     0.181000
Bio::MUST::Core::Seq Nucleotide or protein sequence     0.181000
Bio::MUST::Core::SeqId Modern and legacy MUST-compliant sequence id     0.181000
Bio::MUST::Core::SeqMask Sequence mask for selecting specific sites     0.181000
Bio::MUST::Core::SeqMask::Freqs Arbitrary frequencies for sequence sites     0.181000
Bio::MUST::Core::SeqMask::Profiles Evolutionary profiles for sequence sites     0.181000
Bio::MUST::Core::SeqMask::Rates Evolutionary rates for sequence sites     0.181000
Bio::MUST::Core::Taxonomy NCBI Taxonomy one-stop shop     0.181000
Bio::MUST::Core::Taxonomy::Category Helper class for multiple-criterion classifier based on taxonomy     0.181000
Bio::MUST::Core::Taxonomy::Classifier Helper class for multiple-criterion classifier based on taxonomy     0.181000
Bio::MUST::Core::Taxonomy::Criterion Helper class for multiple-criterion classifier based on taxonomy     0.181000
Bio::MUST::Core::Taxonomy::Filter Helper class for filtering seqs according to taxonomy     0.181000
Bio::MUST::Core::Taxonomy::MooseNCBI Wrapper class for serializing Bio::LITE::Taxonomy::NCBI object     0.181000
Bio::MUST::Core::Tree Thin wrapper around Bio::Phylo trees     0.181000
Bio::MUST::Core::Tree::Forest Collection of (bootstrap) trees     0.181000
Bio::MUST::Core::Types Distribution-wide Moose types for Bio::MUST::Core     0.181000
Bio::MUST::Core::Utils Utility functions for enabling multiple file processing     0.181000

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 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