MLE estimation with Mk model in ape or phangorn?
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".