View on
MetaCPAN
search.cpan.org is shutting down
For details read Perl NOC. After June 25th this page will redirect to MetaCPAN.org
Denis BAURAIN > Bio-MUST-Core-0.181310

Bio-MUST-Core-0.181310

This Release Bio-MUST-Core-0.181310  [Download] [Browse 11 May 2018
Other Releases
Links Discussion Forum ] [ View/Report Bugs (0) ] [ Dependencies ] [ Other Tools ]
CPAN Testers PASS (384)   FAIL (1)   [ View Reports ] [ Perl/Platform Version Matrix ]
Rating      (0 Reviews) [ Rate this distribution ]
License The Perl 5 License (Artistic 1 & GPL 1)
Special Files
Changes
INSTALL
LICENSE
Makefile.PL
MANIFEST
META.yml
README

Modules

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

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  
clust2mapper.pl Build id mapper from UCLUST/CD-HIT clusters for tree formatting  
codegen/templates/Factory.tt  
codegen/templates/SeqId.tt  
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