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Bio-Phylo-v2.0.1
River stage two • 8 direct dependents • 17 total dependents
/ Bio::Phylo::Models::Substitution::Dna

NAME

Bio::Phylo::Models::Substitution::Dna - DNA substitution model

SYNOPSIS


            

              
              
use Bio::Phylo::Models::Substitution::Dna;
# create a DNA substitution model from scratch
my $model = Bio::Phylo::Models::Substitution::Dna->new(
    '-type'   => 'GTR',
    '-pi'     => [ 0.23, 0.27, 0.24, 0.26 ],
    '-kappa'  => 2,
    '-alpha'  => 0.9,
    '-pinvar' => 0.5,
    '-ncat'   => 6,
    '-median' => 1,
    '-rate'   => [
        [ 0.23, 0.23, 0.23, 0.23 ],
        [ 0.23, 0.26, 0.26, 0.26 ],
        [ 0.27, 0.26, 0.26, 0.26 ],
        [ 0.24, 0.26, 0.26, 0.26 ]
    ]
);
# get substitution rate from A to C
my $rate = $model->get_rate('A', 'C');
# get model representation that can be used by Garli
my $modelstr = $model->to_string( '-format' => 'garli' )

DESCRIPTION

This is a superclass for models of DNA evolution. Classes that inherit from this class provide methods for retreiving general parameters such as substitution rates or the number of states as well as model-specific parameters. Currently most of the popular models are implemented. The static function modeltest determines the substitution model from a Bio::Phylo::Matrices::Matrix object and returns the appropriate instance of the subclass. This class also provides serialization of a model to standard phylogenetics file formats.

METHODS

CONSTRUCTOR

new

Dna model constructor.


            

              
              
Type    : Constructor
Title   : new
Usage   : my $model = Bio::Phylo::Models::Substitution::Dna->new(%args);
Function: Instantiates a Bio::Phylo::Models::Substitution::Dna object.
Returns : A Bio::Phylo::Models::Substitution::Dna object.
Args    : Optional:
           -type       => type of model, one of GTR, F81, HKY85, JC69, K80
           -pi         => base frequencies of bases A, C, G, T
           -kappa      => ratio transitions/transversions
           -alpha      => shape parameter (for models of GTR family)
           -mu         => overall mutation rate
           -pinvar     => proportion of invariant sites
           -ncat       => number of distinct rate categories
           -median     => median for gamma-modeled rate categories
           -rate       => Array of Arrays (4x4) giving substitution rates betwen A, C, T, G
           -catweights => weights for rate categories
get_catrates

Getter for rate categories, implemented by child classes.


            

              
              
Type    : method
Title   : get_catrates
Usage   : $model->get_catrates;
Function: Getter for rate categories.
Returns : scalar or array
Args    : None.
get_nst

Getter for number of transition rate parameters.


            

              
              
Type    : method
Title   : get_nst
Usage   : $model->get_nst;
Function: Getter for number of transition rate parameters.
Returns : scalar
Args    : None.
get_rate

Getter for substitution rate. If bases are given as arguments, returns corresponding rate. If no arguments given, returns rate matrix or overall rate, dependent on model.


            

              
              
Type    : method
Title   : get_rate
Usage   : $model->get_rate('A', 'C');
Function: Getter for transition rate between nucleotides.
Returns : scalar or array
Args    : Optional:
          base1: scalar
          base2: scalar
get_nstates

Getter for number of states (bases).


            

              
              
Type    : method
Title   : get_nstates
Usage   : $model->get_nstates;
Function: Getter for transition rate between nucleotides.
Returns : scalar
Args    : None
get_ncat

Getter for number of rate categories.


            

              
              
Type    : method
Title   : get_ncat
Usage   : $model->get_ncat;
Function: Getter for number of rate categories.
Returns : scalar
Args    : None
get_catweights

Getter for weights on rate categories.


            

              
              
Type    : method
Title   : get_catweights
Usage   : $model->get_catweights;
Function: Getter for number of rate categories.
Returns : array
Args    : None
get_kappa

Getter for transition/transversion ratio.


            

              
              
Type    : method
Title   : get_kappa
Usage   : $model->get_kappa;
Function: Getter for transition/transversion ratio.
Returns : scalar
Args    : None
get_alpha

Getter for shape parameter.


            

              
              
Type    : method
Title   : get_alpha
Usage   : $model->get_alpha;
Function: Getter for shape parameter.
Returns : scalar
Args    : None
get_mu

Getter for overall mutation rate.


            

              
              
Type    : method
Title   : get_mu
Usage   : $model->get_mu;
Function: Getter for overall mutation rate.
Returns : scalar
Args    : None
get_pinvar

Getter for proportion of invariant sites.


            

              
              
Type    : method
Title   : get_pinvar
Usage   : $model->get_pinvar;
Function: Getter for proportion of invariant sites.
Returns : scalar
Args    : None
get_pi

Getter for base frequencies.


            

              
              
Type    : method
Title   : get_pi
Usage   : $model->get_pi;
Function: Getter for base frequencies.
Returns : array
Args    : Optional:
          Base (A, C, T or G)
get_median

Getter for median for gamma-modeled rate categories.


            

              
              
Type    : method
Title   : get_median
Usage   : $model->get_median;
Function: Getter for median.
Returns : scalar
Args    : None
set_rate

Setter for substitution rate.


            

              
              
Type    : method
Title   : set_rate
Usage   : $model->set_rate(1);
Function: Set nucleotide transition rates.
Returns : A Bio::Phylo::Models::Substitution::Dna object.
Args    : scalar or array of arrays (4x4)
set_ncat

Setter for number of rate categories.


            

              
              
Type    : method
Title   : set_ncat
Usage   : $model->set_ncat(6);
Function: Set the number of rate categoeries.
Returns : A Bio::Phylo::Models::Substitution::Dna object.
Args    : scalar
set_catweights

Setter for weights on rate categories.


            

              
              
Type    : method
Title   : set_catweights
Usage   : $model->get_catweights;
Function: Set number of rate categories.
Returns : A Bio::Phylo::Models::Substitution::Dna object.
Args    : array
set_kappa

Setter for weights on rate categories.


            

              
              
Type    : method
Title   : set_kappa
Usage   : $model->set_kappa(2);
Function: Set transition/transversion ratio.
Returns : A Bio::Phylo::Models::Substitution::Dna object.
Args    : scalar
set_alpha

Setter for shape parameter.


            

              
              
Type    : method
Title   : set_alpha
Usage   : $model->set_alpha(1);
Function: Set shape parameter.
Returns : A Bio::Phylo::Models::Substitution::Dna object.
Args    : scalar
set_mu

Setter for overall mutation rate.


            

              
              
Type    : method
Title   : set_mu
Usage   : $model->set_mu(0.5);
Function: Set overall mutation rate.
Returns : A Bio::Phylo::Models::Substitution::Dna object.
Args    : scalar
set_pinvar

Set for proportion of invariant sites.


            

              
              
Type    : method
Title   : set_pinvar
Usage   : $model->set_pinvar(0.1);
Function: Set proportion of invariant sites.
Returns : A Bio::Phylo::Models::Substitution::Dna object.
Args    : scalar
set_pi

Setter for base frequencies.


            

              
              
Type    : method
Title   : get_pi
Usage   : $model->set_pi((0.2, 0.2, 0.3, 0.3));
Function: Set base frequencies.
Returns : A Bio::Phylo::Models::Substitution::Dna object.
Args    : array of four base frequencies (A, C, G, T)
Comments: Base frequencies must sum to one
set_median

Setter for median for gamma-modeled rate categories.


            

              
              
Type    : method
Title   : set_median
Usage   : $model->set_median(1);
Function: Setter for median.
Returns : A Bio::Phylo::Models::Substitution::Dna object.
Args    : scalar
modeltest

Performing a modeltest using the package 'phangorn' in R (Schliep, Bioinformatics (2011) 27 (4): 592-593) from an DNA alignment. If no tree is given as argument, a neighbor-joining tree is generated from the alignment to perform model testing. Selects the model with the minimum AIC.


            

              
              
Type    : method
Title   : modeltest
Usage   : $model->modeltest(-matrix=>$matrix);
Function: Determine DNA substitution model from alignment.
Returns : An object which is subclass of Bio::Phylo::Models::Substitution::Dna.
Args    : -matrix: A Bio::Phylo::Matrices::Matrix object
          Optional:
          -tree: A Bio::Phylo::Forest::Tree object
          -timeout: Timeout in seconds to prevent getting stuck in an R process.
Comments: Prerequisites: Statistics::R, R, and the R package phangorn.
to_string

Get string representation of model in specified format (paup, phyml, mrbayes or garli)


            

              
              
Type    : method
Title   : to_string
Usage   : $model->to_string(-format=>'mrbayes');
Function: Write model to string.
Returns : scalar
Args    : scalar
Comments: format must be either paup, phyml, mrbayes or garli

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