Modelling sequence evolution

cogent3 possesses unique capabilities for molecular evolutionary analyses. Of particular significance are our non-stationary model classes and the associated measurement of genetic distance from these. That said, we also implement most of the conventional substitution models. See cogent3.available_models() for a display of the built-in models.

You can use these models either through the general model app, or some task specific apps. Both are described in the following “how-tos”.

• Apply a non-stationary nucleotide model to an alignment with 3 sequences
• Apply a non-stationary nucleotide model to an alignment with a tree
• Specifying a non-stationary model with time-heterogeneous parameters
• Extracting maximum likelihood estimates from a model_result
• Reconstructing ancestral states
• Applying a discrete-time, non-stationary nucleotide model
• Applying a time-reversible nucleotide model
• Applying GNC, a non-stationary codon model
• Applying a time-reversible codon model