view release on metacpan or  search on metacpan

lib/Bio/Tools/Run/Phylo/QuickTree.pm  view on Meta::CPAN

#
# BioPerl module for Bio::Tools::Run::Phylo::QuickTree
#
# Please direct questions and support issues to <bioperl-l@bioperl.org> 
#
# Cared for by Sendu Bala <bix@sendu.me.uk>
#
# Copyright Sendu Bala
#
# You may distribute this module under the same terms as perl itself

# POD documentation - main docs before the code

=head1 NAME

Bio::Tools::Run::Phylo::QuickTree - Wrapper for rapid reconstruction of
                                    phylogenies using QuickTree

=head1 SYNOPSIS

  use Bio::Tools::Run::Phylo::QuickTree;

  #  Make a QuickTree factory
  @params = ();
  $factory = Bio::Tools::Run::Phylo::QuickTree->new(@params);

  #  Pass the factory an alignment	
  $inputfilename = 't/data/cysprot.stockholm';
  $tree = $factory->run($inputfilename); # $tree is a Bio::Tree::Tree object.
  # or get a Bio::Align::AlignI (SimpleAlign) object from somewhere
  $tree = $factory->run($aln);

=head1 DESCRIPTION

This is a wrapper for running the QuickTree application by Kevin Howe. You
can download it here: http://www.sanger.ac.uk/Software/analysis/quicktree/

Currently only input with alignments and output of trees is supported. (Ie.
no support for distance matrix in/out.)

You will need to enable this QuickTree wrapper to find the quicktree program.
This can be done in (at least) three ways:

 1. Make sure the QuickTree executable is in your path.
 2. Define an environmental variable QUICKTREEDIR which is a 
    directory which contains the 'quicktree' application:
    In bash:

    export QUICKTREEDIR=/home/username/quicktree_1.1/bin

    In csh/tcsh:

    setenv QUICKTREEDIR /home/username/quicktree_1.1/bin

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

    BEGIN { $ENV{QUICKTREEDIR} = '/home/username/quicktree_1.1/bin' }
    use Bio::Tools::Run::Phylo::QuickTree;

=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::QuickTree;
use strict;

use Bio::AlignIO;
use Bio::TreeIO;

use base qw(Bio::Tools::Run::WrapperBase);

our $PROGRAM_NAME = 'quicktree';
our $PROGRAM_DIR = $ENV{'QUICKTREEDIR'};

=head2 program_name