We wish to eliminate the bias in parameter estimation created by the use of a fixed alignment. For this, we work with a probabilistic alignment, which instead of producing an 'optimal' alignment, handles the set of all possible alignments and their likelihood. It computes posterior probabilities for each state at every nucleotide position. We thus are considering all possible sequence alignments and weighing them appropriately (see [23] ), according to our indel model. This method has been previously used and described in further detail in [9, 10] . Note, that when referring to the insertion and deletion states, the related posteriors are added together so that we obtain the posterior probability of a certain nucleotide not being aligned, as opposed to belonging to a particular gap.