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

Hilmar Lapp hlapp at gmx.net
Tue Jul 21 17:12:00 UTC 2009

On Jul 20, 2009, at 10:57 AM, Eric Talevich wrote:

> the 'node' in Nexus and PhyloDB is called 'clade' in phyloXML

Really? A clade is *not* a node in the sense it is normally used in  
phylogenetics, and I would suggest that PhyloXML is using "clade"  
synonymously with "node" it needs to change b/c using established  
terminology in conflicting ways isn't a good idea.

A clade is a subtree of a tree, i.e., a node and all its descendent  
nodes (and the branches that connect them). Or more generally for an  
unrooted tree, it is any group of nodes (and branches connecting them)  
that can be completely separated from the rest of the tree by severing  
a single branch.


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

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