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Creating a custom substitution matrix from multiple alignments/trees?

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.

alignment substitution matrix
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written by Genayng • Genayng

1 answer

You can use BayesTraits in Multistate mode

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written by Asaf Asaf

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