[Bioperl-l] Phyloxml <alignment>
cjfields at uiuc.edu
Wed Jul 30 11:44:16 EDT 2008
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?
A hackathon sounds like a good idea. Would NESCent be up for hosting
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