This question is exactly what I need, How to test for convergent/parallel evolution in a group of homologous proteins?, but surprisingly, it hasn't received any response for over two years.
I'm at a point where I want to test whether convergent changes between the two unrelated lineages are random or not. This paper kind of established the method: Zhang, Jianzhi, and Sudhir Kumar. "Detection of convergent and parallel evolution at the amino acid sequence level." Molecular Biology and Evolution 14.5 (1997): 527-536.
Is there an R package that could make test for significance of molecular convergence rather straightforward?
Thanks all and look forward your responses.