Applying a discrete-time, non-stationary nucleotide model¶
We fit a discrete-time Markov nucleotide model. This corresponds to a Barry and Hartigan 1987 model.
NOTE: DLC stands for diagonal largest in column and the value is a
check on the identifiability of the model. unique_Q
is not
applicable to a discrete-time model and so remains as None
.
Looking at the likelihood function, you will
Get a tree with branch lengths as paralinear¶
This is the only possible length metric for a discrete-time process.
Getting parameter estimates¶
For a discrete-time model, aside from the root motif probabilities, everything is edge specific. But note that the tabular_result
has different keys from the continuous-time case, as demonstrated below.