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Stephen Smith edited this page Mar 3, 2017 · 15 revisions

see Installation page

and the more detailed Run Options page

For information on the theory behind these methods please see

Smith, SA, and BC O'Meara. 2012. Divergence time estimation using penalized likelihood for large phylogenies. Bioinformatics 28 (20): 2689-2690.

and

Sanderson, MJ. 2002. Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach. Mol Biol Evol. 19 (1): 101-109.