Search results for "dist:BioPerl taxonomy"
Bio::DB::Taxonomy - Access to a taxonomy database
This is a front end module for access to a taxonomy database....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::DB::Taxonomy::list - An implementation of Bio::DB::Taxonomy that accepts lists of words to build a database
This is an implementation which uses supplied lists of words to create a database from which you can extract Bio::Taxon objects....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::DB::Taxonomy::silva - Use the Silva taxonomy
This is an implementation of Bio::DB::Taxonomy which stores and accesses the Silva taxonomy. Internally, Bio::DB::Taxonomy::silva keeps the taxonomy into memory by using Bio::DB::Taxonomy::list. As a consequence, note that the IDs assigned to the tax...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::DB::Taxonomy::flatfile - Use the NCBI taxonomy from local indexed flat files
This is an implementation of Bio::DB::Taxonomy which stores and accesses the NCBI taxonomy using flat files stored locally on disk and indexed using the DB_File module RECNO data structure for fast retrieval. The required database files, nodes.dmp an...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::DB::Taxonomy::greengenes - Use the Greengenes taxonomy
*This module is in beta. Its interface or its results may change in a future update.* Bio::DB::Taxonomy::greengenes is an implementation of Bio::DB::Taxonomy which stores and accesses the Greengenes taxonomy of Bacteria and Archaea. Internally, it ke...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
bp_taxonomy2tree - Building a taxonomic tree based on the full lineages of a set of species names
This scripts looks up the provided species names in the NCBI Taxonomy database, retrieves their full lineage and puts them in a Newick taxonomic tree displayed on screen. bp_taxonomy2tree.pl -s Orangutan -s Gorilla -s Chimpanzee -s Human bp_taxonomy2...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Taxon - A node in a represented taxonomy
This is the next generation (for Bioperl) of representing Taxonomy information. Previously all information was managed by a single object called Bio::Species. This new implementation allows representation of the intermediate nodes not just the specie...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Tools::CodonTable - Codon table object
Codon tables are also called translation tables or genetic codes since that is what they represent. A bit more complete picture of the full complexity of codon usage in various taxonomic groups is presented at the NCBI Genetic Codes Home page. CodonT...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
bp_local_taxonomydb_query - query a local TaxonomyDB for species or taxonid
This script provides an example implementation of access to a local Taxonomy database implemented with Berkeley DB (DB_File module is needed). Usage: bp_local_taxonomydb_query.PLS: [-v] --nodes nodes.dmp --names names.dmp "Genus1 species1" "Genus2 sp...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Tools::Run::Phylo::PhyloBase
For use by Bio::Tools::Run::Phylo modules as a base in place of Bio::Tools::Run::WrapperBase. This is based on WrapperBase but provides additional phylo-related private helper subs....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC