Greetings,

I have added a standard analysis (under Miscellaneous), which enables to test whether two or more (non-nested) clades in a tree have different mean branch lengths or within-clade pairwise divergences. This analysis is available in builds from August 29th, 2005 onwards.

This analysis can be run with any standard HyPhy nucleotide/protein/codon models (including models with multiple parameters per branch, e.g. to test the differences in dS and dN, using Local codon models).

It requires that the roots of clades of interest be named 'CladeN' where N is a number, e.g.

Code:

(((a,b),c)Clade1, (d,e), ((f,g),(h,(i,j))Clade2)))
 

Cheers,
Sergei

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