Difference between revisions of "Pancrustacean MegaTree"
From Ucsbgalaxy
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==Data Sets== | ==Data Sets== | ||
===Mitochondrial Genomes=== | ===Mitochondrial Genomes=== | ||
| − | # Accession numbers are available on the NCBI website, by searching with the taxon ID for Pancrustacea, which is 197562 [[http://www.ncbi.nlm.nih.gov/genomes/OrganelleResource.cgi?taxid=197562]]. As of July 1, 2012, there were 373 accessions available. Note that some of these are sub-species. | + | # Accession numbers are available on the NCBI website, by searching with the taxon ID for Pancrustacea, which is 197562 [[http://www.ncbi.nlm.nih.gov/genomes/OrganelleResource.cgi?taxid=197562]]. As of July 1, 2012, there were 373 accessions available. Note that some of these are sub-species. The list of accessions can be downloaded at the right near the top, clicking on "Download". |
| − | # | + | # The accessions downloaded in May along with scripts to directly pull and parse the data, written by THO, sit on macroevolution in the following directory: /labdata/nfs/lab/scripts/ATOLmt/ |
| + | # The accessions pulled at that time are in the file AccList.tx | ||
| + | # The next step is to use BioPerl to download all the GenBank files directly from GenBank. This is done using the script getGB.pl. The actual command is | ||
| + | ./getGB.pl AccList.tx | ||
| + | # | ||
=Results= | =Results= | ||
=Discussion= | =Discussion= | ||
Revision as of 22:36, 2 July 2012
Introduction
Methods
Data Sets
Mitochondrial Genomes
- Accession numbers are available on the NCBI website, by searching with the taxon ID for Pancrustacea, which is 197562 [[1]]. As of July 1, 2012, there were 373 accessions available. Note that some of these are sub-species. The list of accessions can be downloaded at the right near the top, clicking on "Download".
- The accessions downloaded in May along with scripts to directly pull and parse the data, written by THO, sit on macroevolution in the following directory: /labdata/nfs/lab/scripts/ATOLmt/
- The accessions pulled at that time are in the file AccList.tx
- The next step is to use BioPerl to download all the GenBank files directly from GenBank. This is done using the script getGB.pl. The actual command is
./getGB.pl AccList.tx
