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PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. It must be correctly installed before run Molevol::Complex. Concretely, an environment variable called "PAMLDIR" must be set with the value ...

This software can be downloaded for free from the author website:

http://abacus.gene.ucl.ac.uk/software/paml.html

Once PAML is installed, this environment variable can be set as follow:

$ export PAMLDIR='/path/to/paml4x/bin/' # for Bourne, bash, and related shells
$ setenv PAMLDIR='/path/to/paml4x/bin/' # for csh and related shells

2. DSSP - Dictionary of protein secondary structure

The DSSP program was designed by Wolfgang Kabsch and Chris Sander to standardize secondary structure assignment. It is used by this module to analyze the accesible surface of each residue.

Binaires can be donwloaded from the authors website:

http://swift.cmbi.ru.nl/gv/dssp/

The module calls this program as dssp by default, but this value can be modified in each run.