Estimating phylogenetic trees from pairwise likelihoods and posterior probabilities of substitution counts

► We investigated two new criteria for estimating phylogenetic trees. ► Estimating trees from pairwise likelihoods is shown to be statistically consistent. ► We also investigated jointly estimating the tree and the number of substitutions. ► We derive formulae for the posterior probability of the number of substitutions along a path between two sequences.