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lib/Bio/Phylo/Models/Substitution/Dna.pm  view on Meta::CPAN

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.

=cut

sub modeltest {
	my ($self, %args) = @_;

	my $matrix = $args{'-matrix'};
	my $tree = $args{'-tree'};
	my $timeout = $args{'-timeout'};