view release on metacpan or  search on metacpan

lib/Bio/Tools/Run/Alignment/MSAProbs.pm  view on Meta::CPAN

# You may distribute this module under the same terms as perl itself
#
# POD documentation - main docs before the code

=head1 NAME

Bio::Tools::Run::Alignment::MSAProbs - Object for the calculation of a
multiple sequence alignment (MSA) from a set of unaligned sequences using 
the MSAProbs program

=head1 SYNOPSIS

  # Build a msaprobs alignment factory
  $factory = Bio::Tools::Run::Alignment::MSAProbs->new(@params);

  # Pass the factory a list of sequences to be aligned.
  $inputfilename = 't/cysprot.fa';
  # $aln is a SimpleAlign object.
  $aln = $factory->align($inputfilename);

  # or where @seq_array is an array of Bio::Seq objects
  $seq_array_ref = \@seq_array;
  $aln = $factory->align($seq_array_ref);

  #There are various additional options and input formats available.
  #See the DESCRIPTION section that follows for additional details.

=head1 DESCRIPTION

MSAProbs is Liu, Schmidt, and Maskell's (2010) alignment program using HMM 
and partition function posterior probabilities.  For more a more in-depth 
description see the original publication:

    Liu, Y., Schmidt, B., and Maskell, D. L. (2010) MSAProbs: multiple
    sequence alignment based on pair hidden Markov models and partition 
    function posterior probabilities. I<Bioinformatics> 26(16): 1958-1964
    doi:10.1093/bioinformatics/btq338
    
                                -OR-

    http://bioinformatics.oxfordjournals.org/content/26/16/1958.abstract

You can download the source code from
http://sourceforge.net/projects/msaprobs/

It is recommended you use at least version 0.9; behaviour with earlier 
versions is questionable.

=head2 Helping the module find your executable 

You will need to help MSAProbs to find the 'msaprobs' executable. This can 
be done in (at least) three ways:

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

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

=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://bugzilla.open-bio.org/

=head1 AUTHOR - Jessen Bredeson

Email jessenbredeson@berkeley.edu

=head1 CONTRIBUTIONS

This MSAProbs module was adapted from the Bio::Tools::Run::Alignment::Muscle 
module, written by Jason Stajich and almost all of the credit should be given
to him.

Email jason-at-bioperl-dot-org

=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::Alignment::MSAProbs;

use vars qw($AUTOLOAD @ISA $PROGRAMNAME $PROGRAM %DEFAULTS %MSAPROBS_PARAMS 
            %MSAPROBS_SWITCHES %OK_FIELD
            );
use strict;