Assigning different Q matrices to different morphological characters

[JMoysiuk]

Dear Klaus,

I am hoping to perform ML tree inference with a morphological dataset consisting of characters with varying numbers of states (from 2-5). I would like to be able to assign a Q matrix to each character according to its number of states. To clarify, I can generate a list of Q vectors (one vector corresponding to each character), but am unsure how to associate these with the characters in the pml function (it seems to only accept one Q matrix). Would you be able to suggest a way that this can be accomplished?

Appreciate any help you can provide.
Joe