[Bioperl-l] Phyloxml <alignment>

aaron.j.mackey at gsk.com aaron.j.mackey at gsk.com
Tue Jul 29 12:43:02 EDT 2008

Personally, I'd like to see TreeIO::phyloxml provide trees that have 
alignments (if present) as annotations of the Tree (Bio::Tree's are 
AnnotatableI).  Weigang Qiu and I made a little progress on this for the 
Nexus parser, so all the bits and bobs are already in place for this to 

Whether a corresponding AlignIO::phyloxml would do the reverse (provide 
alignments with Tree's as annotations) would just be icing on the cake, 
but not very important, in my opinion (in fact, it seems like an 
AlignIO::phyloxml would just delegate the parsing to TreeIO::phyloxml, and 
then muck around with the objects to get the inside-out structure).


bioperl-l-bounces at lists.open-bio.org wrote on 07/29/2008 12:20:33 PM:

> 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 
> Mira
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