Provided by: libbio-perl-run-perl_1.7.3-9_all 
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
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.
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.
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;
FEEDBACK
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
Support
Please direct usage questions or support issues to the mailing list:
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.
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/
AUTHOR - Jason Stajich
Email jason-at-bioperl-dot-org
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are
usually preceded with a _
new
Title : new
Usage : my $muscle = Bio::Tools::Run::Alignment::Muscle->new();
Function: Constructor
Returns : Bio::Tools::Run::Alignment::Muscle
Args : -outfile_name => $outname
program_name
Title : program_name
Usage : $factory->program_name()
Function: holds the program name
Returns: string
Args : None
program_dir
Title : program_dir
Usage : $factory->program_dir(@params)
Function: returns the program directory, obtained from ENV variable.
Returns: string
Args :
error_string
Title : error_string
Usage : $obj->error_string($newval)
Function: Where the output from the last analysus run is stored.
Returns : value of error_string
Args : newvalue (optional)
version
Title : version
Usage : exit if $prog->version() < 1.8
Function: Determine the version number of the program
Example :
Returns : float or undef
Args : none
run
Title : run
Usage : my $output = $application->run(\@seqs);
Function: Generic run of an application
Returns : Bio::SimpleAlign object
Args : Arrayref of Bio::PrimarySeqI objects or
a filename to run on
align
Title : align
Usage : $inputfilename = 't/data/cysprot.fa';
$aln = $factory->align($inputfilename);
or
$seq_array_ref = \@seq_array;
$aln = $factory->align($seq_array_ref);
Function: Perform a multiple sequence alignment
Returns : Reference to a SimpleAlign object containing the
sequence alignment.
Args : Name of a file containing a set of unaligned fasta sequences
or else an array of references to Bio::Seq objects.
Throws an exception if argument is not either a string (e.g. a
filename) or a reference to an array of Bio::Seq objects. If
argument is string, throws exception if file corresponding to string
name can not be found. If argument is Bio::Seq array, throws
exception if less than two sequence objects are in array.
run_profile
Title : run_profile
Usage : $alnfilename = /t/data/cysprot.msa';
$seqsfilename = 't/data/cysprot.fa';
$aln = $factory->run_profile($alnfilename,$seqsfilename);
Function: Perform a profile alignment on a MSA to include more seqs
Returns : Reference to a SimpleAlign object containing the
sequence alignment.
Args : Name of a file containing the fasta MSA and name of a file
containing a set of unaligned fasta sequences
Comments: This only works for muscle version 3.52.
Some early versions of the 3.6 sources had a bug that
caused a segfault with -profile. The attached should fix
it, if not let Bob Edgar know.
aformat
Title : aformat
Usage : my $alignmentformat = $self->aformat();
Function: Get/Set alignment format
Returns : string
Args : string
_run
Title : _run
Usage : Internal function, not to be called directly
Function: makes actual system call to muscle program
Example :
Returns : nothing; muscle output is written to a
temporary file OR specified output file
Args : Name of a file containing a set of unaligned fasta sequences
and hash of parameters to be passed to muscle
_setinput
Title : _setinput
Usage : Internal function, not to be called directly
Function: Create input file for muscle program
Example :
Returns : name of file containing muscle data input AND
Args : Arrayref of Seqs or input file name
_setparams
Title : _setparams
Usage : Internal function, not to be called directly
Function: Create parameter inputs for muscle program
Example :
Returns : parameter string to be passed to muscle
during align or profile_align
Args : name of calling object
Bio::Tools::Run::BaseWrapper methods
no_param_checks
Title : no_param_checks
Usage : $obj->no_param_checks($newval)
Function: Boolean flag as to whether or not we should
trust the sanity checks for parameter values
Returns : value of no_param_checks
Args : newvalue (optional)
save_tempfiles
Title : save_tempfiles
Usage : $obj->save_tempfiles($newval)
Function:
Returns : value of save_tempfiles
Args : newvalue (optional)
outfile_name
Title : outfile_name
Usage : my $outfile = $muscle->outfile_name();
Function: Get/Set the name of the output file for this run
(if you wanted to do something special)
Returns : string
Args : [optional] string to set value to
tempdir
Title : tempdir
Usage : my $tmpdir = $self->tempdir();
Function: Retrieve a temporary directory name (which is created)
Returns : string which is the name of the temporary directory
Args : none
cleanup
Title : cleanup
Usage : $muscle->cleanup();
Function: Will cleanup the tempdir directory
Returns : none
Args : none
io
Title : io
Usage : $obj->io($newval)
Function: Gets a L<Bio::Root::IO> object
Returns : L<Bio::Root::IO>
Args : none