NAME

Bio::Phylo::Models::Substitution::Dna::HKY85 - Hasegawa, Kishino, Yano (1985) model

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

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>

NAME

DESCRIPTION

METHODS

SEE ALSO

CITATION