PAML

PAML(Phylogenetic Analysis by Maximum Likelihood) is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood.

• Version: 4.9a
• Added: November, 2012
• Updated: May, 2016
• Link: http://abacus.gene.ucl.ac.uk/software/paml.html

See which versions of paml are available:

$ module avail paml

Load paml

$ module load paml/4.9a

Notes from the sysadmin during installation:

$ cd /tmp
$ scl enable devtoolset-2 bash
$ wget http://abacus.gene.ucl.ac.uk/software/paml4.9a.tgz
$ tar -xvf paml4.9a.tgz
$ cd paml4.9a
$ rm -f bin/*.exe
$ cd src
$ make
$ cp baseml basemlg chi2 codeml evolver infinitesites mcmctree pamp yn00 ../bin/
$ cd ../
$ sudo mkdir /export/apps/paml/4.9a/
$ sudo cp -r . /export/apps/paml/4.9a/