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#
# BioPerl module for Bio::Tools::Run::Alignment::Muscle
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Copyright Jason Stajich <jason-at-bioperl-dot-org>
#
# 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::Muscle - Object for the calculation of an
iterative multiple sequence alignment from a set of unaligned
sequences or alignments using the MUSCLE program

=head1 SYNOPSIS

  # Build a muscle alignment factory
  $factory = Bio::Tools::Run::Alignment::Muscle->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);

  # 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.

=head1 DESCRIPTION

Muscle is Robert Edgar's progressive alignment program.  You can get
it and see information about it at this URL
http://www.drive5.com/muscle

It is recommended you use at least version 3.6. Behaviour with earlier versions
is questionable.

=head2 Helping the module find your executable

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

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

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

=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::Muscle;

use strict;
use Bio::Seq;
use Bio::SeqIO;
use Bio::SimpleAlign;
use Bio::AlignIO;
use Bio::Root::IO;

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

our %DEFAULTS = ( 'AFORMAT' => 'fasta' );
our @MUSCLE_PARAMS = qw(in out tree1 log loga scorefile gapopen seqtype
  maxmb maxhours maxiters kband in1 in2 usetree usetree_nowarn