NAME

Bio::Phylo::Models::Substitution::Binary - Binary character substitution model

SYNOPSIS

use Bio::Phylo::Models::Substitution::Binary;

# create a binary substitution model # by doing a modeltest my $model = Bio::Phylo::Models::Substitution::Binary->modeltest( -tree => $tree, # phylogeny -matrix => $matrix, # character state matrix, standard categorical data -model => 'ARD', # ace model -char => 'c1', # column ID in $matrix );

# after model test, forward and reverse instantaneous transition # rates are available, e.g. for simulation print $model->forward, "\n"; print $model->reverse, "\n";

DESCRIPTION

This is a class that encapsulates an instantaneous transition model for a binary character. The model is asymmetrical in that the forward and reverse rates (can) differ. The rates can be inferred from a character in a character state matrix by modeltesting. This is done by delegation to the R package ape. For this to work, you therefore need to have R and ape installed, as well as the bridge that allows Perl to communicate with R, which is done by the optional package Statistics::R.

METHODS

CONSTRUCTOR

new

Binary character model constructor.

            

              
              
Type    : Constructor
Title   : new
Usage   : my $model = Bio::Phylo::Models::Substitution::Binary->new(%args);
Function: Instantiates a Bio::Phylo::Models::Substitution::Binary object.
Returns : A Bio::Phylo::Models::Substitution::Binary object.
Args    : Optional:
       -forward => sets forward rate
       -reverse => sets reverse rate
            
          

set_forward

Setter for forward transition rate

            

              
              
Type    : method
Title   : set_forward
Usage   : $model->set_forward($rate);
Function: Setter for forward transition rate
Returns : $self
Args    : A rate (floating point number)
            
          

set_reverse

Setter for reverse transition rate

            

              
              
Type    : method
Title   : set_reverse
Usage   : $model->set_reverse($rate);
Function: Setter for reverse transition rate
Returns : $self
Args    : A rate (floating point number)
            
          

get_forward

Setter for forward transition rate

            

              
              
Type    : method
Title   : get_forward
Usage   : my $rate = $model->get_forward;
Function: Getter for forward transition rate
Returns : A rate (floating point number)
Args    : NONE
            
          

get_reverse

Setter for reverse transition rate

            

              
              
Type    : method
Title   : get_reverse
Usage   : my $rate = $model->get_reverse;
Function: Getter for reverse transition rate
Returns : A rate (floating point number)
Args    : NONE
            
          

modeltest

Performs a model test to infer transition rates

            

              
              
Type    : method
Title   : modeltest
Usage   : my $model = $package->modeltest;
Function: Performs a model test to infer transition rates
Returns : A populated $model object
Args    : All required:
                -tree   => $tree,   # phylogeny
                -matrix => $matrix, # character state matrix, standard categorical data
                -model  => 'ARD',   # ace model
                -char   => 'c1',    # column ID in $matrix
            
          

SEE ALSO

There is a mailing list at https://groups.google.com/forum/#!forum/bio-phylo for any user or developer questions and discussions.

Bio::Phylo::Manual

Also see the manual: Bio::Phylo::Manual and http://rutgervos.blogspot.com.

CITATION

If you use Bio::Phylo in published research, please cite it:

Rutger A Vos, Jason Caravas, Klaas Hartmann, Mark A Jensen and Chase Miller, 2011. Bio::Phylo - phyloinformatic analysis using Perl. BMC Bioinformatics 12:63. http://dx.doi.org/10.1186/1471-2105-12-63