====== PAML ======

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

===== Information =====

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

===== Usage =====

See which versions of paml are available:
<code>$ module avail paml</code>

Load paml
<code>$ module load paml/4.9a</code>

===== Installation ======

Notes from the sysadmin during installation:

<code>$ 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/
</code>