When I'm using the probabilistic alignment (CATG file), it doesn't care about the probability value for each nucleotide; in all scenarios, the branch lengths are 0.1. Also, it doesn't matter what is the model option (--opt-branches on/off, --blopt: anything), the output tree is the same all the time.
amkozlov
commented
2 years ago
When I'm using the probabilistic alignment (CATG file), it doesn't care about the probability value for each nucleotide; in all scenarios, the branch lengths are 0.1. Also, it doesn't matter what is the model option (--opt-branches on/off, --blopt: anything), the output tree is the same all the time.