Tree likelihood

= Computing the likelihood of a sequence alignment =

Note: This chapter describes the new likelihood framework, under active development, available only under the "newlik" branch for the GIT repository. The code described here IS NOT YET available in the stable version of Bio++ !

Simple or double recursive algorithm
Two algorithms exist for computing the likelihood of a sequence alignment given a phylogenetic tree and model of sequence evolution. These algorithms are called "simple recursive" (R) and "double recursive" (DR). They are described in detail in Felsenstein's book