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Rutger Vos > Bio-Phylo > Bio::Phylo::Models::Substitution::Binary

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Bio-Phylo-v2.0.1.tar.gz

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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

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