We would like to be able to apply our method to multiple sequences, thus extrapolating more information where possible. We could of course devise a multiple alignment indel model, and develop a new likelihood function from which to maximize over all tree branches simultaneously. This however would be of computational much higher demand, runtime increasing exponentially with the addition of each new sequence. Instead, we therefore opt to work with a multiple pairwise alignment under the assumption of a star shaped tree, with the reference sequence as the root in the star topology. This implies viewing the evolution of the pairwise sequences as independent, which is an approximation which we wish to address in future work. This merely requires per additional sequence an extra transition and transversion parameter, since selection is acting on the gene in the ancestor and we assume this to be constant over all branches. The modification to our program is thus trivial, with only a linear increase in runtime.