[Bioperl-l] Phyloxml <alignment>

aaron.j.mackey at gsk.com aaron.j.mackey at gsk.com
Tue Jul 29 12:59:59 EDT 2008


The "super-object" approach is hard, based on the experience of the NEXUS 
working group.  I recommend the "dumber" approach of linking things 
together with "has-a" annotation relationships (tree is an annotation of 
an alignment, and vice versa), without worrying about coordinated slicing 
or other "joint" manipulations.  We already do similar things with 
sequences and features (i.e. manipulation of the sequence does not affect 
the features, or vice versa).

-Aaron

bioperl-l-bounces at lists.open-bio.org wrote on 07/29/2008 12:45:06 PM:

> 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.
> 
> -jason
> 
> 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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> 
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