[Bioperl-l] Phyloxml <alignment>

Jason Stajich jason at bioperl.org
Tue Jul 29 12:45:06 EDT 2008

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:

> Hi,
> 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?
> Mira
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