Make halPhyloPTrain.py run in multithreaded mode (w/ PhyloFit)

[brantfaircloth]

This is a feature request, because (I think) you can work around this externally...

PhyloFit within halPhyloPTrain.py currently functions in single-threaded mode. And, for very large alignments, PhyloFit takes a very long time to run. However it seems that somewhere around Phast 1.9.4, a multithreaded mode was added to PhyloFit . And, I was hoping that it would not be too painful to (eventually) incorporate this.

In the meantime, I'm running the multithreaded PhyloFit outside of hal tools using the sufficient statistics file produced by halPhyloPTrain.py.

[glennhickey]

The whole phast integration in HAL is sadly out of date. I definitely recommend running the latest phast tools / best practices directly on the MAF for now.

[brantfaircloth]

Thanks! And, sounds good - that's my plan for the time being!