Dear HYPHY team,

Some questions about the tree topology inference:
1. Is TBR branch swapping method implemented in HYPHY? If not, how difficult would it be to implement it?

2. Are topology inference methods parallelized using MPI?

Thanks,
Luobin

Dear Luobin,

HyPhy does not presently implement TBR. It is not terrible difficult but rather tedious to add it (a lot of book-keeping). It has been on my list of things to do for a while.

Most of HyPhy topology search analyses have been parallelized to run on MPI.

However, it is worth noting, that HyPhy is not primarily a phylogeny package (it is geared towards quantifying and testing the evolutionary process, e.g. rates, selection, recombination etc), and many of the methods are slow compared to state-of-the-art packages like PAUP* and PhyML. NJ and NNI branch swapping can be quite fast, on the other hand.

Cheers,
Sergei