Creating a custom substitution matrix from multiple alignments/trees?

Question

[Genayng]

Hello. I have several alignments from different trees that I would like to use to estimate a single substitution matrix. Does there exist an efficient way to do this? If you could point me in the right direction, that would be much appreciated. Thank you.

Answer 1

[Asaf]

You can use BayesTraits in Multistate mode