[Bioperl-l] Phyloxml <alignment>
arlin.stoltzfus at nist.gov
Wed Jul 30 09:58:09 EDT 2008
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
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.
On Jul 29, 2008, at 12:45 PM, Jason Stajich wrote:
> Mira -
> I've not thought too clearly about how this should go, certainly
> Bio::AlignIO should be reused for the parsing aspect, although I'm
> not clear what format the alignment is in?
> At some point this is might need to be unified with the NEXUS-type
> objects that the Bio::NEXUS group has worked on. We may have to
> work with them to define the proper object here that holds both
> tree and alignment data and allows slicing out either from the object.
> So a super-object is probably going to have to be created to
> marshall out the trees and alignment data. I didn't realize the
> spec was going as far as to encapsulate all of the alignment data
> as well. We may need to think about whether we can support all of
> the aspects of the spec at this time as well.
> I hope other people have input here as well.
> On Jul 29, 2008, at 9:20 AM, Han, Mira wrote:
>> Sorry for bombarding the list
>> Thought this would be better on a separate thread.
>> Phyloxml documents have <phylogeny></phylogeny>s.
>> But also <align:alignment></align:alignment>s.
>> What would be the standard approach for parsing,
>> I guess TreeIO->next_tree
>> shouldn't take care of the alignments.
>> Would I need to make a AlignIO->next_aln for the phyloxml document
>> as well?
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
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Arlin Stoltzfus (arlin.stoltzfus at nist.gov), Research Biologist, NIST
Fellow, CARB, 9600 Gudelsky Drive, Rockville, Maryland 20850
tel 240 314 6208, fax 240 314 6255, www.molevol.org/camel
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