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#
# BioPerl module for Bio::Tools::Run::Simprot
#
# Please direct questions and support issues to <bioperl-l@bioperl.org> 
#
# Cared for by Albert Vilella <avilella-at-gmail-dot-com>
#
# Copyright Albert Vilella
#
# You may distribute this module under the same terms as perl itself

# POD documentation - main docs before the code

=head1 NAME

Bio::Tools::Run::Simprot - Wrapper around the Simprot program. Wrapper for the calculation of a multiple sequence alignment from a phylogenetic tree

=head1 SYNOPSIS

  use Bio::Tools::Run::Simprot;
  use Bio::TreeIO;

  my $treeio = Bio::TreeIO->new(
      -format => 'nh', -file => 't/data/tree.nh');

  my $tree = $treeio->next_tree;

  my $simprot = Bio::Tools::Run::Simprot->new();
  $simprot->tree($tree);
  my ($rc,$aln,$seq) = $simprot->run();

=head1 DESCRIPTION

This is a wrapper around the Simprot program by Andy Pang, Andrew D
Smith, Paulo AS Nuin and Elisabeth RM Tillier.

Simprot allows for several models of amino acid substitution (PAM, JTT
and PMB), allows for gamma distributed sites rates according to Yang's
model, and implements a parameterised Qian and Goldstein distribution
model for insertion and deletion.

See http://www.uhnres.utoronto.ca/labs/tillier/software.htm for more
information.


=head2 Helping the module find your executable 

You will need to enable SIMPROTDIR to find the simprot program. This can be
done in (at least) three ways:

  1. Make sure the simprot executable is in your path (i.e. 
     'which simprot' returns a valid program
  2. define an environmental variable SIMPROTDIR which points to a 
     directory containing the 'simprot' app:
   In bash 
	export SIMPROTDIR=/home/progs/simprot   or
   In csh/tcsh
        setenv SIMPROTDIR /home/progs/simprot

  3. include a definition of an environmental variable SIMPROTDIR 
      in every script that will
     BEGIN {$ENV{SIMPROTDIR} = '/home/progs/simprot'; }
     use Bio::Tools::Run::Simprot;

=head1 FEEDBACK

=head2 Mailing Lists

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists.  Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

=head2 Support 

Please direct usage questions or support issues to the mailing list:

I<bioperl-l@bioperl.org>

rather than to the module maintainer directly. Many experienced and 
reponsive experts will be able look at the problem and quickly 
address it. Please include a thorough description of the problem 
with code and data examples if at all possible.

=head2 Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution.  Bug reports can be submitted via the web:

 http://redmine.open-bio.org/projects/bioperl/

=head1 AUTHOR -  Albert Vilella

Email avilella-at-gmail-dot-com

=head1 APPENDIX

The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _

=cut

package Bio::Tools::Run::Simprot;

use vars qw(@ISA %VALIDVALUES $PROGRAMNAME $PROGRAM);

use strict;
use Bio::SimpleAlign;
use Bio::AlignIO;
use Bio::SeqIO;
use Bio::TreeIO;
use Bio::Root::Root;
use Bio::Root::IO;
use Bio::Tools::Run::WrapperBase;
@ISA = qw(Bio::Root::Root Bio::Tools::Run::WrapperBase);