Given that determining substitution costs in sequence analysis is such a bone of contention, many researchers look for a way for the data to generate the costs. The typical way to do this is, is by pooling transition rates and defining the substitution cost to be:

2 – p(ij) – p(ji)

where p(ij) is the transition rate from state i to state j. Intuitively, states that are closer to each other will have higher transitions, and vice versa. Continue reading Substitution costs from transition rates →