Each sequence model estimates the probability of emitting column X[k] using a phylogenetic tree. Figure 4 shows a schematic of the phylogenetic tree for four Drosophila species used in testing. The goal is to compute the probability of the observed column having evolved from a common ancestral sequence. For the tree in Figure 4, assume the ancestral base at the root ("Ancestor 1") to be A and the descendant node ("Ancestor 2") to be C. The probability of A evolving to C is computed using a nucleotide substitution model. The HYK model [32] was chosen for the use of three features: distinguished transition/transversion mutation events (assumed to be a fixed parameter), a nucleotide equilibrium model, and the evolutionary time interval defined by the tree branch length. The probability of emitting column X[k] is found by computing, in linear time with respect to the number of nodes in the tree, the probability of all possible ancestral sequences having evolved into the observed column using the Felsenstein phylogenetic tree scoring procedure [33].