Hello all!

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!

Nancy
If you are familiar with Python you can convert a rooted tree into ultrametric topology (all leaves will have the same distance to root) using [ETE Toolkit 2-3][1]. 

    from ete2 import Tree
    
    t = Tree('(A:1,(B:1,(C:1,D:1):0.5):0.5);')
    # Root tree at B node.
    t.set_outgroup('B')  
    
    print('Non-ultrametric rooted tree:')
    print(t.write())
        
    t.convert_to_ultrametric()
    print('Ultrametric rooted tree:')
    print(t.write())

Output:

    Non-ultrametric rooted tree:
    (B:0.5,((C:1,D:1)1:0.5,A:1.5)1:0.5);

    Ultrametric rooted tree:
    (B:2,((C:0.666667,D:0.666667)1:0.666667,A:1.33333)1:0.666667);


  [1]: http://etetoolkit.org