When doing MLE with the R package ape or phangorn, is it possible to set the substitution model to Mk? If so, how does one do this?
From reading though the documentation, the Mk model does not appear available.
Although the JC69 model is, which this source describes as a slightly less generalized form as Mk. The JC69 model still assumes equal substitution rates and equal base frequencies. To use the JC69 model in phangorn set the model to "JC" and in ape set the model to "JC69".
The R package diversitree has a large range of models including functions to optimise under Mk. Perhaps have a look at that.