TODO

TODO:

* Data parallelization

    MrBayes currently uses MPI to run different chains in parallel
    on different processors.  However, data sets are becoming a lot
    larger now with respect to number of sites, so it is becoming
    important also to distribute likelihood computations on data across
    processors.  This would require some programming but it is not a
    huge challenge.

* Native AVX and FMA code

    I have added native AVX and FMA code for the 4by4 nucleotide models.
    It would be straightforward to add native AVX and FMA code for the
    other models.  Particularly the AA-model would probably benefit from
    this code (when not using the beagle library).

* Dynamic scaling

    Scaling of likelihoods take a surprisingly large amount of time when
    using the standard 4by4 nucleotide models.  Maxim added dynamic
    scaling code for the Beagle implementation but not for the native
    likelihoood calculators, which are faster.  The dynamic scaling
    code adjusts the rescaling frequency so that you do not rescale
    likelihoods more often than needed to avoid numerical exceptions and
    achieve a reasonable level of precision.  For typical-size trees
    and the 4by4 model, no rescaling is often needed.  I added the
    infrastructure needed to support dynamic scaling for both Beagle and
    native calculators in December 2015.  In principle, it should be
    straightforward now to rewrite Maxim's dynamic scaling code (which
    is not so pretty C code) so that it works for both Beagle and native
    likelihood calculators.