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Can GARLI output site-likelihoods for use in a program like CONSEL?

April 26, 2017garli output program

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Can GARLI output site-likelihoods for use in a program like CONSEL?

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Currently there is no easy way to do this (but there will be in the next version). However, if you have access to PAUP* you can easily get the site likelihood values for nucleotide models that are exactly equivalent to what GARLI calculates internally. To do this: • Perform a normal GARLI run • Load your dataset into PAUP*. • Execute the .best.tre file (for the single best tree found) or the .best.all.tre file (for the best trees found in each individual search replicate). You should not use gettrees, but actually execute the treefile. This is because there is a PAUP* block in the treefile that will tell PAUP* to fix exactly the parameter values and branch lengths inferred by GARLI. • Now tell PAUP* to score the tree(s) and output the site likelihoods, e.g.