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  $seq_array_ref = \@seq_array;
  $aln = $factory->align($seq_array_ref);

  # Or one can pass the factory a pair of (sub)alignments
  #to be aligned against each other, e.g.:

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

  #To run probcons with training, try something like:

  #First round to generate train.params
  $factory = Bio::Tools::Run::Alignment::Probcons->new
      (
       'iterative-refinement'  => '1000',
       'consistency'   => '5',
       'pre-training' => '20',
       'emissions' => '',
       'verbose' => '',
       'train'   => "$dir/$subdir/$outdir/train.params",
      );
  $factory->outfile_name("$dir/$subdir/$outdir/train.params");

  #Second round to use train.params to get a high qual alignment

  $seq_array_ref = \@seq_array;
  $aln = $factory->align($seq_array_ref);
  $aln = '';
  $factory = '';

  $factory = Bio::Tools::Run::Alignment::Probcons->new
      (
       'iterative-refinement'  => '1000',
       'consistency'   => '5',
       'pre-training' => '20',
       'verbose' => '',
       'paramfile'   => "$dir/$subdir/$outdir/train.params",
      );
  $factory->outfile_name("$dir/$subdir/$outdir/outfile.afa");
  $aln = $factory->align($seq_array_ref);

=head1 DESCRIPTION

Probcons is a Probabilistic Consistency-based Multiple Alignment of
Amino Acid Sequences. You can get it and see information about it at this URL
http://probcons.stanford.edu/


=head2 Helping the module find your executable 

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

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

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

=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 -  Jason Stajich

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::Probcons;

use vars qw($AUTOLOAD @ISA $PROGRAMNAME $PROGRAM %DEFAULTS
            @PROBCONS_PARAMS @PROBCONS_SWITCHES @OTHER_SWITCHES 
            %OK_FIELD
            );
use strict;
use Bio::Seq;
use Bio::SeqIO;
use Bio::SimpleAlign;
use Bio::AlignIO;
use Bio::Root::Root;
use Bio::Root::IO;
use Bio::Factory::ApplicationFactoryI;