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comparing substitution rate/divergence of two different genes

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.

phylogenetic tree

2 answers

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

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