Get probability values for ASR about treetime HOT 4 CLOSED

are you interested in sequence reconstructions, or discrete trait reconstruction. for the latter, this is possible via

treetime mugration --confidence ...

probabilities for regular sequence reconstructions are available if you use treetime in a script and do marginal ancestral inference. each node will have an attribute marginal_profile which has the probability of each state.

from treetime.

Ancestral sequence reconstruction, thanks. You're referring to this script, yes? https://github.com/neherlab/treetime_examples/blob/master/scripts/ancestral_sequence_inference.py. thank you-

from treetime.

Any chance of same for joint reconstruction - would be handy to be able to check the actual probability that lead to a particular call (indication of support or otherwise for the particular call).

from treetime.

For a joint reconstruction, you can't specify the probability of an individual state. Only the most like global configuration is calculated along with its probability.

from treetime.