[Bioperl-l] Phyloxml parsing <clade_relation> <sequence_relation>

aaron.j.mackey at gsk.com aaron.j.mackey at gsk.com
Tue Jul 29 12:46:28 EDT 2008

use Annotations, and author a new 
Bio::Annotation::Tree::Node::Relationship::Pairwise (or somesuch) for 
typing the relationship.

-Aaron, a fan of AnnotatableI

bioperl-l-bounces at lists.open-bio.org wrote on 07/29/2008 12:10:31 PM:

> Hi,
> I'd like to get some opinions on how to design the phyloxml parsing.
> There are a couple of tags in phyloxml that doesn't have obvious bioperl
> implementations.
> 1. <clade_relation>
> This is for expressing network structures on the tree.
> <clade_relation id_ref_0="b" id_ref_1="c" type="network_connection"/>
> Will mean that c and b is connected even though they are not direct
> parent-daughters of each other.
> 2. <sequence_relation>
> Homology relationship between sequences.
> <sequence_relation id_ref_0="x" id_ref_1="y" type="paralogy"/>
> These tags are both used by the <phylogeny>.
> Right now I'm just saving the information in the tree as simple text by
> tags.
> So that if the user wants to follow the information he can look up the 
> by its id_src id by parsing the text.
> I was wondering if you would have any other ideas.
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