3.3 Stochastic generation of initial multiple alignments

We incorporated the progressive alignment method to generate a starting population for the evolutionary algorithm. In order to obtain several such alignments, we have developed a process of randomly generating guide trees. We use a method akin to the NJ algorithm, where at each step a pair of clusters with the highest average similarity of their elements is joined. In our implementation, a pair to be joined is chosen randomly with a probability proportional to the average similarity of elements.