NAME

Bio::Phylo::Models::Substitution::Dna::JC69 - Jukes, Cantor (1969)

DESCRIPTION

See Bio::Phylo::Models::Substitution::Dna

METHODS

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_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_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.

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