fastDMAml
Overview
fastDNAml is a program derived from Joseph Felsenstein's version 3.3
DNAML program (part of his PHYLIP package). Like DNAML, it implements
the maximum likelihood method for DNA sequences but attempts to do it
faster and using less memory so that larger trees and/or more bootstrap
replicates become tractable.
Setup
To use fastDNAml it is necessary to set your fastDNAml environment by
running a special command sequence once per login session. You may
optionally place these commands in your .cshrc (C Shell users) or
.profile (Bourne Shell users) to avoid having to manually run these
commands on login.
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For csh and tcsh:
source /usr/local/setup/fastDNAml.setup.csh
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For sh and bash:
. /usr/local/setup/fastDNAml.setup.sh
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Usage
fastDNAml is invoked with the command fastDNAml. It expects to get its
input from STDIN (standard input) and writes its output to STDOUT (standard
output).
Examples
The following is an example PBS script to run a fastDNAml job on LION-XE for
a maximum of 2 hours. The input file is called input.phy and the output is
set to go to a file called fastDNAml.out. The input file is in the directory
/home/foo/fastDNAml.
#PBS -l nodes=1:ppn=1
#PBS -l walltime=2:00:00
#PBS -j oe
#PBS -q lionxe-serial
# setup the fastDNAml environment
. /usr/local/setup/fastDNAml.setup.sh
# change the current working directory to the directory where
# the input file can be found
cd /home/foo/fastDNAml
# run the fastDNAml command
fastDNAml < input.phy > fastDNAml.out
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Further information on PBS scripts and submitting jobs on the LION-XE cluster
can be found in the User Guides section of the HPC website.
Documentation
Documentation for fastDNAml can be found on LION-XE in the directory
/usr/global/fastDNAml/docs.
Please send questions or suggestions about this web page to beatnic@aset.psu.edu
ASET | ITS | Penn State
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