if no alignment ID is set, it is set by reading it from the alignment file
if no taxa names are set, these are set by reading these from the alignment file
A FASTA filename.
a Bayesian phylogenetic inference model. An inference model is the complete model setup in which a site model, clock model, tree prior and more are specified. Use create_inference_model to create an inference model. Use check_inference_model to check if an inference model is valid. Use rename_inference_model_filenames to rename the files in an inference model.
an initialized MRCA prior
Richèl J.C. Bilderbeek