How to statistically test significance of molecular convergence in two unrelated lineages

Question

[ishengomae]

Hi Biostars,

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.

Answer 1

[ddiez]

Have you taken a look in the Phylogenetics task view at CRAN? There is a package, convevol, that might be what you are looking for, as it is described as:

Quantifies and assesses the significance of convergent evolution.

There might be other (I guess many), non-R options.

[ishengomae]

This looks like what I want. Thanks.