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Bio::Tools::Run::SimprUser)Contributed Perl DocumenBio::Tools::Run::Simprot(3)

NAME
       Bio::Tools::Run::Simprot	- Wrapper around the Simprot program. Wrapper
       for the calculation of a	multiple sequence alignment from a
       phylogenetic tree

SYNOPSIS
	 use Bio::Tools::Run::Simprot;
	 use Bio::TreeIO;

	 my $treeio = Bio::TreeIO->new(
	     -format =>	'nh', -file => 't/data/tree.nh');

	 my $tree = $treeio->next_tree;

	 my $simprot = Bio::Tools::Run::Simprot->new();
	 $simprot->tree($tree);
	 my ($rc,$aln,$seq) = $simprot->run();

DESCRIPTION
       This is a wrapper around	the Simprot program by Andy Pang, Andrew D
       Smith, Paulo AS Nuin and	Elisabeth RM Tillier.

       Simprot allows for several models of amino acid substitution (PAM, JTT
       and PMB), allows	for gamma distributed sites rates according to Yang's
       model, and implements a parameterised Qian and Goldstein	distribution
       model for insertion and deletion.

       See http://www.uhnres.utoronto.ca/labs/tillier/software.htm for more
       information.

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

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

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

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 $simprot =	Bio::Tools::Run::Simprot->new();
	Function: Builds a new Bio::Tools::Run::Simprot
	Returns	: Bio::Tools::Run::Simprot
	Args	: -alignment =>	the Bio::Align::AlignI object
		  -tree	=> the Bio::Tree::TreeI	object
		  -save_tempfiles => boolean to	save the generated tempfiles and
				     NOT cleanup after onesself	(default FALSE)
		  -executable => where the simprot executable resides
						-params	=> A reference to a hash where keys are	parameter names
							   and hash values are the associated parameter	values

       See also: Bio::Tree::TreeI, Bio::Align::AlignI

   set_parameters
	Title	: set_parameters
	Usage	: $codeml->set_parameters($parameter, $value);
	Function: (Re)set the SimProt parameters
	Returns	: none
	Args	: First	argument is the	parameter name
		  Second argument is the parameter value

   set_default_parameters
	Title	: set_default_parameters
	Usage	: $codeml->set_default_parameters(0);
	Function: (Re)set the default parameters from the defaults
		  (the first value in each array in the
		   %VALIDVALUES	class variable)
	Returns	: none
	Args	: boolean: keep	existing parameter values

   get_parameters
	Title	: get_parameters
	Usage	: my %params = $self->get_parameters();
	Function: returns the list of parameters as a hash
	Returns	: associative array keyed on parameter names
	Args	: none

   prepare
	Title	: prepare
	Usage	: my $rundir = $simprot->prepare();
	Function: prepare the simprot analysis using the default or updated parameters
		  the alignment	parameter and species tree must	have been set
	Returns	: value	of rundir
	Args	: L<Bio::Align::AlignI>	object,
		  L<Bio::Tree::TreeI> object [optional]

   run
	Title	: run
	Usage	: my $nhx_tree = $simprot->run();
	Function: run the simprot analysis using the default or	updated	parameters
		  the alignment	parameter must have been set
	Returns	: L<Bio::Tree::TreeI> object [optional]
	Args	: L<Bio::Align::AlignI>	object
		  L<Bio::Tree::TreeI> object

   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

   alignment
	Title	: alignment
	Usage	: $simprot->align($aln);
	Function: Get/Set the L<Bio::Align::AlignI> object
	Returns	: L<Bio::Align::AlignI>	object
	Args	: [optional] L<Bio::Align::AlignI>
	Comment	: We could potentially add support for running directly	on a file
		  but we shall keep it simple
	See also: L<Bio::SimpleAlign>

   tree
	Title	: tree
	Usage	: $simprot->tree($tree,	%params);
	Function: Get/Set the L<Bio::Tree::TreeI> object
	Returns	: L<Bio::Tree::TreeI>
	Args	: [optional] $tree => L<Bio::Tree::TreeI>,
		  [optional] %parameters => hash of tree-specific parameters

	Comment	: We could potentially add support for running directly	on a file
		  but we shall keep it simple
	See also: L<Bio::Tree::Tree>

Bio::Tools::Run::BaseWrapper methods
   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 =	$simprot->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	: $simprot->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 v5.24.1			  2017-07-08	   Bio::Tools::Run::Simprot(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Albert Vilella | APPENDIX | Bio::Tools::Run::BaseWrapper methods

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