I think I saw this answered before but cannot find the post.
I was wondering what is a publishable approach in using these 2 methods. What I used to do before, is run the analysis using both methods and employing the same model. Then I would pick the better supported tree and compare the tree side by side copying the support values.
I now have a problem since I have 100 taxa, and the trees are somewhat different. I like my bayesian tree, gives better support. Can I force this tree onto phyml and construct BS values based on the bayesian tree? Then I know my ML tree is the same as the bayesian one and I just have to copy the values over.