Dear Jaime,
Thank you a lot for help!
I got some protein sequences expressed by orthologous genes from multiple species. These proteins are compared and grouped by OrthoMCL. I would like to infer the evolutionary history of these orthologous genes in the form of tree. I know that some gene trees can be constructed under the guide of associated species trees, since we know species phylogenies. Method used in TreeBest is one example of them, but I think it is a old program.
I also heard that some gene trees were built using PhyML with the help of ETE toolkit. It is easy for me to build a rooted tree using the latest version of PhyML, but I do not know how to improve tree topology under the guide of species phylogenies using ETE toolkit.
Could you offer me any suggestion and information?
Thanks again!
Yizi