comparing substitution rate/divergence of two different genes

Question

[Pappu]

I want to compare the divergence or substitution rate of two genes among pair of organisms in two trees by comparing the branch lengths that separe them. I am wondering if there is any software for it and I can use a more sophisticated statistical model. Thanks.

Answer 1

[Jean-Karim Heriche]

You could try TreeBest (from Li Heng) or its Ensembl Compara variant.