Hi,
HyPhy is a great tool for quickly calculating (pair-wise) relative rates in protein alignments (Standard Analysis -> PairwiseRelativeRate.bf). This method however requires to define an outgroup. Is there any way to calculate these rates without outgroups, but by using mid-point rooting instead?
Thanks

Hi Sergei,
I am trying to identify phylogenetically old genes in a symbiotic fungal species, by looking at reduced evolutionary rates, compared to homologues in a defined group of related fungal taxa. One of these reference taxa is more distant and used as outgroup. I considered a gene of my fungal species with a reduced rate, if it constantly showed the lowest rate in all triplet comparisons within the HyPhy rate test (I processed several thousand alignments, with exactly one sequence per species).  That worked well and let me identify a small number of genes.

The biological idea behind this approach is that symbiosis was acquired early in evolution, and some (not all) key genes haven't much evolved since then, in order to maintain the symbiotic lifestyle.

In a second approach I am now working with MCL clustered gene families, instead of well conserved homologue groups. These gene families are naturally more diverse, with usually more than one, non monophyletic outgroup sequence, and can therefore not be rooted. My idea was now to identify different path lengths (as you described it above) for each two species in an unrooted tree instead.

Since I have several thousand alignments it would be very helpful if a test existed, which could perform this mid-point path length calculation, without the need of building a tree first.

Olaf