PAML-Teaching: Difference between revisions
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=== Description === | === Description === | ||
"PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood." | "PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood." | ||
A summary of the types of analyses performed by different programs: | |||
'''baseml''': ML analysis of nucleotide sequences | |||
'''basemlg''': ML analysis of nucleotide sequences under the model of gamma rates among sites. | |||
'''codonml''' (codeml with seqtype = 1): ML analysis of protein-coding DNA sequences | |||
'''aaml''' (codeml with seqtype = 2): ML analysis of amino acid sequences under a number of amino acid substitution models | |||
'''pamp''': Parsimony-based analyses for a given tree topology | |||
'''mcmctree''': Bayesian estimation of phylogenies using DNA sequence data | |||
'''evolver''': This program used to be named listtree | |||
'''yn00:''' estimating synonymous and nonsynonymous substitution rates in pairwise comparison of protein-coding DNA sequences. | |||
Please refer to [http://abacus.gene.ucl.ac.uk/software/paml.html#introduction PAML] for more details. | |||
=== Running Program === | === Running Program === | ||
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<pre class="gcommand"> | <pre class="gcommand"> | ||
ml PAML/4.9h-foss-2016b | ml PAML/4.9h-foss-2016b | ||
cd /usr/local/apps/eb/PAML/4.9h-foss-2016b/bin | |||
/usr/local/apps/eb/PAML/4.9h-foss-2016b/bin | ls | ||
baseml basemlg chi2 codeml evolver pamp yn00 | |||
</pre> | </pre> | ||
Revision as of 14:32, 10 August 2018
Category
Bioinformatics
Program On
Teaching
Version
4.9h
Author / Distributor
Description
"PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood."
A summary of the types of analyses performed by different programs:
baseml: ML analysis of nucleotide sequences
basemlg: ML analysis of nucleotide sequences under the model of gamma rates among sites.
codonml (codeml with seqtype = 1): ML analysis of protein-coding DNA sequences
aaml (codeml with seqtype = 2): ML analysis of amino acid sequences under a number of amino acid substitution models
pamp: Parsimony-based analyses for a given tree topology
mcmctree: Bayesian estimation of phylogenies using DNA sequence data
evolver: This program used to be named listtree
yn00: estimating synonymous and nonsynonymous substitution rates in pairwise comparison of protein-coding DNA sequences.
Please refer to PAML for more details.
Running Program
The last version of this application is at /usr/local/apps/eb/PAML/4.9h-foss-2016b
To use this version, please load the module with
ml PAML/4.9h-foss-2016b
Here is an example of a shell script, sub.sh, to run on the batch queue:
#!/bin/bash
#SBATCH --job-name=j_PAML
#SBATCH --partition=batch
#SBATCH --mail-type=ALL
#SBATCH --mail-user=username@uga.edu
#SBATCH --ntasks=1
#SBATCH --mem=10gb
#SBATCH --time=08:00:00
#SBATCH --output=PAML.%j.out
#SBATCH --error=PAML.%j.err
cd $SLURM_SUBMIT_DIR
ml PAML/4.9h-foss-2016b
which baseml [options]
In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.
Please refer to Running_Jobs_on_the_teaching_cluster, Run X window Jobs and Run interactive Jobs for more details of running jobs at Teaching cluster.
Here is an example of job submission command:
sbatch ./sub.sh
Documentation
ml PAML/4.9h-foss-2016b cd /usr/local/apps/eb/PAML/4.9h-foss-2016b/bin ls baseml basemlg chi2 codeml evolver pamp yn00
Installation
Source code is obtained from PAML
System
64-bit Linux