[Bioperl-l] Phylo::PAML::Codeml

Jason Stajich jason at cgt.duhs.duke.edu
Tue May 25 20:39:52 EDT 2004

Where do you see it documented that you can call get_model_params.

The Codeml Parser is Bio::Tools::Phylo::PAML
and you get back a Bio::Tools::Phylo::PAML::Result object

Bio::Tools::Run::Phylo::PAML::Codeml is the wrapper module for running

Which NSSites params do you want?  You can get the model results like this

# get a ModelResult from a PAML::Result object
use Bio::Tools::Phylo::PAML;
my $paml = new Bio::Tools::Phylo::PAML(-file => 'mlc');
my $result = $paml->next_result;
foreach my $model ( $result->get_model_results ) {
    print $model->model_num, " ", $mode->model_description, "\n";
    print $model->kappa, "\n";
    print $model->run_time, "\n";

But there may be things that don't work - let us know more specifically
what you need to get out so can make sure it works.

On Tue, 25 May 2004, Olin Silander wrote:

> I'm having trouble getting results from Bio::Tools::Phylo::PAML::Codeml.
>   I'm not sure how to get the parameters back out.  The documentation
> seems to claim you can use get_model_params, but this routine doesn't
> seem to be coded.  How do I get out paramters for NSsites?
> Olin
> UCSD Division of Biology
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Jason Stajich
Duke University
jason at cgt.mc.duke.edu

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