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