Analytic solutions for three taxon ML trees with variable rates across sites Original Research Article

We consider the problem of finding the maximum likelihood rooted tree of three species under a molecular clock symmetric model of substitution of 2-state characters. For identically distributed rates per site this is probably the simplest phylogenetic estimation problem, and it is readily solved numerically. Analytic solutions, on the other hand, were obtained only recently by Yang [Complexity of the simplest phylogenetic estimation problem, Proc. Roy Soc. London Ser. B 267 (2000) 109–119].