4.6 years ago by
I used the p-distance for obtaining the tree topology that then I used in order to contrast the different models for detecting positive selection.
If you are fixing the tree (i.e., not letting codeml optimize topology/branch lengths), I would recommend using a more sophisticated means of estimating the tree. I would expect to see, at the very least, corrected p-distances if I was a reviewer. Likelihood-based approaches are better. Remember to transform your tree from units of substitutions/site to substitutions/codon.
Think of the branch lengths as your data for these analyses. The longer the branch lengths among your taxa, the more power you will have to infer positive selection; this is why it's hard to confidently infer positive selection acting on codons in closely-related lineages. Therefore, if your branch lengths are problematic, you might be drawing incorrect conclusions.