[Biopython-dev] [Wg-phyloinformatics] GSoC Weekly Update 9: PhyloXML for Biopython

Christian M Zmasek czmasek at burnham.org
Tue Jul 21 18:05:25 UTC 2009

> But referring to or identifying a clade must be referring to an entire 
> group of nodes, not only one. So attaching something to the clade 
> semantically has to attach it to all nodes in the clade. 

Good point!
Predefined phyloXML elements are defined to either apply to the whole 
clade, as long as they are not "overwritten" by values in descendant 
clades (for example Taxonomy) or are defined to only apply to the clade 
("node" in this case) they are in, "branch_length" for example.
The property element (used for "custom" data), has a "applies_to" 
attribute to indicate where to data should be attached to (values are: 
"phylogeny", "clade", "node", "parent_branch", ...).


> -hilmar
> -- 
> ===========================================================
> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
> ===========================================================

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