Hello,
Does anyone knows how to get actual substitution matrices for codon ? I can get the amino-acid substitution matrices through the GiPhy website (https://giphy.pasteur.fr/empirical-models-of-amino-acid-substitution/) , but I do not find anything similar for codon based substitution matrices.
The IQ-tree software package has a complete list of them, but I don't know how to make it print the substitution matrix. Most of the papers in the literature don't give the codon matrix they use in supplementary information.
Help will be much appreciated.
P.S. I'm developing a fast algorithm to compute, for a given substitution matrix Q, its exponential exp(tQ), and I need to test it on an exhaustive set of substitution matrices.