I am not into the field of phylogeny, but I need some advice for a particular task in my research. My excuses beforehand if my question is naive.
Briefly, I downloaded orthologs of a protein sequence from OMA Browser, and I need to obtain a phylogenetic tree of the fetched orthologs. What I have done so far is a multiple sequence alignment (MSA), followed by some MSA curation and, finally, I have built a gene tree using PhyML 3.0.
Still, I'd like to perform a final gene/species tree reconciliation step. I know that many algorithms exist for such a purpose, but to be honest I do not know where to get the species tree from. In practice, I need a species tree that, potentially, includes all species in OMA Browser. In other words, were can I find a comprehensive species tree? Which one would you trust the most?
Thanks a lot!