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  # Make a PhastCons factory
  $factory = Bio::Tools::Run::Phylo::Phast::PhastCons->new();

  # Pass the factory an alignment and the corresponding species tree
  $align_filename = 't/data/apes.multi_fasta';
  $species_tree_filename = 't/data/apes.newick';
  @features = $factory->run($align_filename, $species_tree_filename);

  # or get a Bio::Align::AlignI (SimpleAlign) object from somewhere, and
  # generate the species tree automatically using a Bio::DB::Taxonomy database
  $tdb = Bio::DB::Taxonomy->new(-source => 'entrez');
  @features = $factory->run($aln_obj, $tdb);

  # @features is an array of Bio::SeqFeature::Annotated, one feature per
  # alignment sequence and prediction

=head1 DESCRIPTION

This is a wrapper for running the phastCons application by Adam Siepel. You
can get details here: http://compgen.bscb.cornell.edu/~acs/software.html 
phastCons is used for phylogenetic footprinting/ shadowing.

Currently the interface is extremely simplified, allowing only one
analysis method. The focus here is on ease of use, allowing phastCons
to estimate as many parameters as possible and having it output just
the 'most conserved' blocks it detects. You can, however, try
supplying normal phastCons arguments to new(), or calling arg-named
methods (excluding initial hyphens and converting others to
underscores, eg. $factory-E<gt>indels_only(1) to set the --indels-only
arg).

The particular analysis carried out here is to:

 1. Use phyloFit to generate a tree model for initialization of the nonconserved
    model from the supplied alignment (all data) and species tree
 2. Run phastCons in 'training' mode for parameter estimation using all the
    alignment data and the model from step 1
 3. Run phastCons with the trees from step 2 to discover the most conserved
    regions

See the 'HowTo' at http://compgen.bscb.cornell.edu/~acs/phastCons-HOWTO.html 
for details on how to improve results.

WARNING: the API is likely to change in the future to allow for alternative
analysis types.

You will need to enable this phastCons wrapper to find the phast programs (at
least phastCons and phyloFit).
This can be done in (at least) three ways:

 1. Make sure the phastCons and phyloFit executables are in your path.
 2. Define an environmental variable PHASTDIR which is a 
    directory which contains the phastCons and phyloFit applications:
    In bash:

    export PHASTDIR=/home/username/phast/bin

    In csh/tcsh:

    setenv PHASTDIR /home/username/phast/bin

 3. Include a definition of an environmental variable PHASTDIR in
    every script that will use this PhastCons wrapper module, e.g.:

    BEGIN { $ENV{PHASTDIR} = '/home/username/phast/bin' }
    use Bio::Tools::Run::Phylo::Phast::PhastCons;

=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
the Bioperl mailing list.  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
of the bugs and their resolution. Bug reports can be submitted via
the web:

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

=head1 AUTHOR - Sendu Bala

Email bix@sendu.me.uk

=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::Phylo::Phast::PhastCons;
use strict;

use Cwd;
use File::Basename;
use Clone qw(clone);
use Bio::AlignIO;
use Bio::Tools::Run::Phylo::Phast::PhyloFit;
use Bio::FeatureIO;
use Bio::Annotation::SimpleValue;

use base qw(Bio::Tools::Run::Phylo::PhyloBase);