[Bioperl-l] Which interfaces to use for phylogenetics?

[Rutger Vos]

Hi all,

I am working on the next release of Bio::Phylo. Not part of BioPerl - 
the reasons why make a longish story - maybe the BioPerl gurus would 
like to discuss a timeline for merging and extending bioperl's 
phylogenetics capabilities? For the time being, though, I'd like to be 
as interoperable as possible with BioPerl. Hence, the following works:

#######################################
use Bio::Phylo::Forest::Tree;
use Bio::TreeIO;

my $bp_tree = Bio::TreeIO->new( '-format' => 'newick', '-file' => 
'intree.dnd' )->next_tree;
my $newtree = Bio::Phylo::Forest::Tree->new_from_bioperl( $bp_tree );
#######################################

In the opposite direction, Bio::Phylo::Forest::Tree objects and 
Bio::Phylo::Forest::Node will implement the Bio::Tree::TreeI and 
Bio::Tree::NodeI interfaces respectively (and push them in their @ISA), 
if BioPerl is installed on the system.

I'd like to do the same for data matrices. Hence, I'll implement a 
new_from_bioperl constructor for the Bio::Phylo::Matrices::Matrix and 
Bio::Phylo::Matrices::Datum objects. However, from which BioPerl 
interfaces should I inherit? Which objects are most handy as argument to 
the constructor from BioPerl's perspective? Note that the Matrix object 
behaves either as a sequence alignment or a categorical or continuous 
character state matrix. Bio::Align::AlignI doesn't seem entirely 
appropriate, at least in that it is entirely 
molecular-sequence-oriented. Is there a more generic matrix interface? 
Maybe Bio::Matrix::MatrixI? Obviously, I'm looking for an interface that 
will be readily accepted by the Bio::Tools::Run::* phylogenetics modules.

On a related note - I'm writing a wrapper around MrBayes which I'd like 
to contribute as Bio::Tools::Run::MrBayes. I posted the code as an 
attachment to the list but I think it got blocked (okay, I can see why) 
so whom would I send this to for consideration? (Or, how does one get a 
cvs commit bit?)

Thanks!

Rutger

-- 
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Rutger Vos, PhD. candidate
Department of Biological Sciences
Simon Fraser University
8888 University Drive
Burnaby, BC, V5A1S6
Phone: 604-291-5625 
Fax: 604-291-3496
Personal site: http://www.sfu.ca/~rvosa
FAB* lab: http://www.sfu.ca/~fabstar
Bio::Phylo: http://search.cpan.org/~rvosa/Bio-Phylo/
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