[Bioperl-l] Phyloxml <alignment>

Rutger Vos rutgeraldo at gmail.com
Thu Jul 31 10:27:15 EDT 2008

The Bio::Phylo approach is as follows:

- Bio::Phylo objects masquerade as BioPerl objects by implementing
(and inheriting from) their respective interfaces (e.g.
Bio::Phylo::Forest::Tree <-> Bio::Tree::TreeI)

- BioPerl objects can be unpacked in a new_from_bioperl constructor
which returns a Bio::Phylo object

On Wed, Jul 30, 2008 at 11:44 AM, Chris Fields <cjfields at uiuc.edu> wrote:
> On Jul 30, 2008, at 8:58 AM, Arlin Stoltzfus wrote:
>> Jason, et al--
>> In regard to the Bio::NEXUS objects, we (Bio::NEXUS team) have the
>> aspiration to integrate with BioPerl objects via some coordinated CDAT
>> (character-data-and-trees object) super-object that would allow coordinated
>> operations like slicing OTUs X, Y and Z out of both the tree and the
>> alignment.
>> But it hasn't really happened.  Aaron suggests that there might be a
>> lesson here, and maybe its about the folly of designing one great object
>> ("One Thing to rule them all; One Thing to find them; One Thing to gather
>> all, and in the darkness, bind them").  Anyway, Aaron suggests we should opt
>> for a "dumber" (his words) approach such as treating an alignment as an
>> "annotation" of a tree.  He and Weigang have done some of that.
>> Yet, I think Rutger might have worked out a smarter approach in
>> Bio::Phylo, which (as I understand it) *does* have bindings to BioPerl
>> objects.
>> It might be worth having a summit meeting to work out some strategy to
>> solve this problem.  We might be able to get support for a meeting or
>> hackathon via NESCent if we write a White Paper that lays out a plan aimed
>> at 1) object bindings between Bio::Phylo, BioPerl and Bio::NEXUS and 2) some
>> coordinated operations, with or without a super-object.  The purpose would
>> be to expand the power of these Perl libraries to facilitate evolutionary
>> analyses.
>> Any takers?
>> Arlin
> A hackathon sounds like a good idea.  Would NESCent be up for hosting this?
> chris

Dr. Rutger A. Vos
Department of zoology
University of British Columbia

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