I have used OrthoFinder to identify orthogroups among five species. Part of the output is a rooted phylogenetic tree, but I think it is not ultrametric?
I would like to use the tree as part of the input for a CAFE analysis. The CAFE tutorial described using the program r8s to make a tree ultrametric, but I don't know the number of sites in the alignment used to estimate the species tree. TimeTree has approximate divergence time for some of the species in my tree, which I can use to calibrate the tree?
Any suggestions on how I can create an ultrametric phylogenetic tree would be greatly appreciated!