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