Search results for "distribution:BioPerl Bio::DB::Taxonomy::flatfile"
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::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::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
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
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