[Bioperl-l] Phyloxml <alignment>

Chris Fields 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?
> Arlin

A hackathon sounds like a good idea.  Would NESCent be up for hosting  


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