Probably a very easy question, but I could’t find a straightforward answer for 
I have a posterior distribution of trees all rooted with a 
not-so-closely-related outgroup. I’d like to perform some diversification 
analyses (LTT, etc.) just for the ingroup, obviating the outgroup. Is there an 
easy way to extract the ingroup (or remove the outgroup) from all the trees 
before performing the analyses? I have tried to do it ‘manually’, deleting the 
outgroup taxa in Mesquite, but it looks to me that the LTT plots are still 
considering some branch lengths from the ingroup to the outgroup clade (kind of 
considering a stem-origin, not a crown-origin for the ingroup clade…).

Sorry if the question is too naïve…



David Buckley
Dpt. Biodiversity and Evolutionary Biology
Museo Nacional de Ciencias Naturales, MNCN-CSIC
c/José Gutiérrez Abascal 2
Phone: +34 91 411 13 28 ext. 1126 

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