Bio::Tools::Run::Alignment::Probalign(3pm)		User Contributed Perl Documentation		Bio::Tools::Run::Alignment::Probalign(3pm)

NAME

       Bio::Tools::Run::Alignment::Probalign - Object for the calculation of a multiple sequence alignment from a set of unaligned sequences or
       alignments using the Probalign program

SYNOPSIS

	 # Build a muscle alignment factory
	 $factory = Bio::Tools::Run::Alignment::Probalign->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.

	 $factory = Bio::Tools::Run::Alignment::Probalign->new();
	 $factory->outfile_name("$dir/$subdir/$outdir/outfile.afa");
	 $aln = $factory->align($seq_array_ref);

DESCRIPTION

       Probalign: multiple sequence alignment using partition function posterior probabilities.

       Probalign uses partition function posterior probability estimates to compute maximum expected accuracy multiple sequence alignments.  You
       can get it and see information about it at this URL http://www.cs.njit.edu/usman/probalign

   Helping the module find your executable
       You will need to enable Probalign to find the probalign program. This can be done in (at least) three ways:

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

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

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 -  Albert Vilella
       Email avilella-at-gmail-dot-com

APPENDIX

       The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

   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	:

   new
	Title	: new
	Usage	: my $probalign = Bio::Tools::Run::Alignment::Probalign->new();
	Function: Constructor
	Returns : Bio::Tools::Run::Alignment::Probalign
	Args	: -outfile_name => $outname

   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;
	       # @seq_array is array of Seq objs
	       $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 (eg 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
	Title	:  _run
	Usage	:  Internal function, not to be called directly
	Function:  makes actual system call to probalign program
	Example :
	Returns : nothing; probalign 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 probalign

   _setinput
	Title	:  _setinput
	Usage	:  Internal function, not to be called directly
	Function:  Create input file for probalign program
	Example :
	Returns : name of file containing probalign 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 probalign program
	Example :
	Returns : parameter string to be passed to probalign
		  during align or profile_align
	Args	: name of calling object

   aformat
	Title	: aformat
	Usage	: my $alignmentformat = $self->aformat();
	Function: Get/Set alignment format
	Returns : string
	Args	: string

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 = $probalign->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	: $probalign->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

perl v5.12.3							    2011-06-18				Bio::Tools::Run::Alignment::Probalign(3pm)