I'd like to double check my interpretation of the output for SubtreeSelectionComparison (SSC) with someone who can confirm for certain whether I'm right.

the SSC batchfile asks the user to specify a 'node' to designate 'subtree' that will be tested for a specific difference in dN relative to branches outside that subtree.  

SSC then produces an output table with the following headers:

dN Tree,dN Clade,dS,dN/dS Tree,dN/dS Clade,dN Tree = dN Clade,Joint dS,Joint dN/dS,LRT,p-value

My question is about what is indicated by 'Tree' vs. 'Clade' relative to what I've specified as the 'subtree' as input.  I assume that 'Clade' in the table is associated with the 'subtree' I give as input and 'Tree' values are for the branches outside of that 'subtree'.  

Am I correct?  My concern is that it *might* be the otherway 'round.

Thanks,

Jamie

Hi Jamie,

I looked at the source of SSC.bf and it appears that dN Clade refers to the subtree rooted at the node you select, and dN Tree -- to everywhere else in the tree.

Sergei