Man page - bp_taxonomy2tree(1)
Packages contas this manual
- bp_process_sgd(1)
- bp_genbank2gff3(1)
- bp_make_mrna_protein(1)
- bp_search2alnblocks(1)
- bp_seqret(1)
- bp_fetch(1)
- bp_seqretsplit(1)
- bp_mrtrans(1)
- bp_index(1)
- bp_extract_feature_seq(1)
- bp_seqcut(1)
- bp_nexus2nh(1)
- bp_aacomp(1)
- bp_gccalc(1)
- bp_unflatten_seq(1)
- bp_local_taxonomydb_query(1)
- bp_dbsplit(1)
- bp_process_gadfly(1)
- bp_oligo_count(1)
- bp_nrdb(1)
- bp_seqpart(1)
- bp_tree2pag(1)
- bp_taxonomy2tree(1)
- bp_filter_search(1)
- bp_bioflat_index(1)
- bp_taxid4species(1)
- bp_split_seq(1)
- bp_find-blast-matches(1)
- bp_mask_by_search(1)
- bp_mutate(1)
- bp_seqconvert(1)
- bp_search2gff(1)
- bp_fastam9_to_table(1)
- bp_seq_length(1)
- bp_biogetseq(1)
- bp_translate_seq(1)
- bp_search2table(1)
- bp_sreformat(1)
- bp_revtrans-motif(1)
- bp_search2tribe(1)
apt-get install bioperl
Manual
| BP_TAXONOMY2TREE(1p) | User Contributed Perl Documentation | BP_TAXONOMY2TREE(1p) |
NAME
bp_taxonomy2tree - Building a taxonomic tree based on the full lineages of a set of species names
DESCRIPTION
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_taxonomy2tree.pl -s Orangutan -s Gorilla -s Chimpanzee -s "Homo Sapiens"
Can also provide -d to specify the directory to store index files in, -o to specify the location of your NCBI nodes file, and -a for the NCBI names file. Or the option -e to use the web-based Entrez taxonomy database if you do not have the NCBI flatfiles installed.
This script requires that the bioperl-run pkg be also installed.
Providing the nodes.dmp and names.dmp files from the NCBI Taxonomy dump (see Bio::DB::Taxonomy::flatfile for more info) is only necessary on the first time running. This will create the local indexes and may take quite a long time. However once created, these indexes will allow fast access for species to taxon id OR taxon id to species name lookups.
AUTHOR - Gabriel Valiente, reimplemented by Sendu Bala
Email valiente@lsi.upc.edu Email bix@sendu.me.uk
| 2021-08-15 | perl v5.32.1 |