Difference between revisions of "Pancrustacean MegaTree"
From Ucsbgalaxy
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# 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". | # 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 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 accessions pulled at that time are in the file AccList.tx . There are 365 accessions in that list. |
# 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: | # 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 > mtGenomes.gb | ./getGB.pl AccList.tx > mtGenomes.gb | ||
Revision as of 22:51, 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 . There are 365 accessions in that list.
- 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 > mtGenomes.gb
this pulls accessions in AccList.tx from GenBank and writes the data into the file called mtGenomes.gb
