I am working with certain programs in python. I want to use WAG matrix for phylogeny inference, but I am confused about the formula implemented by it.
For example, in phylogenetics study, when a sequence file is used to generate a distance based matrix, there is a formula called "p-distance" implemented and on the basis of this formula and some standard values for sequence data, a matrix is generated which is later used to construct a tree.
When a character based method for tree construction is used, "WAG" is one of the matrices used for likelihood tree construction. What I want to say is that if one wants to implement this matrix, then what is the formula basis for it?
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Does this help?
The 'WAG' matrix: a new amino acid replacement matrix for globular proteins
I have studied this article and the rest of the information given by it. But I find myself miserable saying that I am still unable to get the information I want to. (I meant the formula implemented by "WAG" matrix for calculating on amino acids) Can you elaborate for me to understand??