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

[Christian M Zmasek]

Hi, Hilmar:

Hilmar Lapp wrote:

> 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

Actually, that is how clade is being used.
Like so:

<phylogeny rooted="true">
   <clade>
     <clade branch_length="0.06">
       <clade branch_length="0.102">
         <name>A</name>
       </clade>
       <clade branch_length="0.23">
         <name>B</name>
       </clade>
     </clade>
     <clade branch_length="0.4">
       <name>C</name>
     </clade>
   </clade>
</phylogeny>

The difference is, a clade can contain other clades, wheres as node cannot.

Chris