1BP_TAXONOMY2TREE(1) User Contributed Perl Documentation BP_TAXONOMY2TREE(1)
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6 taxonomy2tree - Building a taxonomic tree based on the full lineages of
7 a set of species names
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10 taxonomy2tree.PLS: -s Orangutan -s Gorilla -s Chimpanzee -s Human
11 taxonomy2tree.PLS: -s Orangutan -s Gorilla -s Chimpanzee -s "Homo
12 Sapiens"
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14 Can also provide -d to specific the directory to store index files in,
15 -o to specific the location of your nodes file, and -a for the names
16 file. Or the option -e to use the web-based entrez taxonomy database
17 if you don't have the flatfiles installed.
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19 This script requires that the bioperl-run pkg be also installed.
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21 Providing the nodes.dmp and names.dmp files from the NCBI Taxonomy dump
22 (see Bio::DB::Taxonomy::flatfile for more info) is only necessary on
23 the first time running. This will create the local indexes and may
24 take quite a long time. However once created, these indexes will allow
25 fast access for species to taxon id OR taxon id to species name
26 lookups.
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29 Email valiente@lsi.upc.edu Email bix@sendu.me.uk
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33perl v5.12.0 2010-04-29 BP_TAXONOMY2TREE(1)