Hello there, Good day. I hope it is okay for me to ask for some clarification character weighting when carrying out Maximum Parsimony.
Based on my data, I have no non-synonymous mutations. All SNPS are synonymous. I have higher first codon substitution than 2nd codon which is also more than 3rd codon substitutions. The frequencies of substitutions are 15:8:2 for 1st 2nd and 3rd codon positions respectively. In case I need to carry out a weighted Maximum Parsimony, how will you advise I weight each codon position?
I look forward to suggestions and or help from you. Kind regards, Nabi