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Rutger Vos > Bio-Phylo > Bio::Phylo::Models::Substitution::Dna::JC69

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Bio-Phylo-v2.0.1.tar.gz

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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

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