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."
 
More details are at [http://abacus.gene.ucl.ac.uk/software/paml.html PAML]
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
which baseml
ls
/usr/local/apps/eb/PAML/4.9h-foss-2016b/bin/baseml
baseml basemlg  chi2  codeml  evolver  pamp  yn00


</pre>
</pre>

Revision as of 11:21, 15 August 2018

Category

Bioinformatics

Program On

Teaching

Version

4.9h

Author / Distributor

PAML

Description

"PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood." More details are at PAML

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 
which baseml 
/usr/local/apps/eb/PAML/4.9h-foss-2016b/bin/baseml

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Installation

Source code is obtained from PAML

System

64-bit Linux

Retrieved from "https://wiki.gacrc.uga.edu/index.php?title=PAML-Teaching&oldid=13531"