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

Han, Mira mirhan at indiana.edu
Tue Jul 29 12:10:31 EDT 2008


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 nodes
by its id_src id by parsing the text.
I was wondering if you would have any other ideas.






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