Molevol-Complex

This module integrates a workflow aimed to address the evolvability of
the contact interfaces within a protein complex. Some structural and
evolutive analisys are performed by external software, which is needed
to be installed before install and/or run this module.

This README provides instructions on how to install the module.

REQUERIMENTS

1. PAML - Phylogenetic Analysis by Maximum Likelihood

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 of the PAML binaries directory.

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

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

Once PAML is intalled, 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.

3. Bioperl and Bioperl-run

The Bioperl and Bioperl-run packages are used to run the analysis. They
can be installed through public repositories sush as CPAN or Fink, or manually
after donwload from the community website:

http://www.bioperl.org/wiki/Getting_BioPerl


INSTALLATION

To install this module, run the following commands:

	perl Makefile.PL
	make
	make test
	make install

SUPPORT AND DOCUMENTATION

After installing, you can find documentation for this module with the
man command.

    man Molevol::Complex

You can also look for information at:

    Official Website
	http://mecom.hval.es


LICENSE AND COPYRIGHT

Copyright (C) 2013 Hector Valverde and Juan Carlos Aledo

This program is free software; you can redistribute it and/or modify it
under the terms of either: the GNU General Public License as published
by the Free Software Foundation; or the Artistic License.

See L<http://dev.perl.org/licenses/> for more information.