We've ignored phi_0 and phi_1 (the two ends in Gibbs measure) so far, because the sequence is usually long enough. However if we analyze multi-species data, the boundaries of blocks cannot be ignored anymore. We might need to find a way to parameterize duplet rates but I'm not sure if it's the best way, because it introduces more parameters (something similar to "baseline" parameters).
We've ignored
phi_0andphi_1(the two ends in Gibbs measure) so far, because the sequence is usually long enough. However if we analyze multi-species data, the boundaries of blocks cannot be ignored anymore. We might need to find a way to parameterize duplet rates but I'm not sure if it's the best way, because it introduces more parameters (something similar to "baseline" parameters).