We have recently released the first version of RPHAST, an interface to PHAST from the R programming environment, but only a portion of PHAST's functionality is currently supported within RPHAST. Work is underway to expand access to the PHAST libraries from within RPHAST.
Dennis Kostka in Katie Pollard's lab has recently developed methods modeling biased conversion (BGC) in the framework of continuous-time Markov models of DNA substitution, and work is in progress to implement these models in PHAST. We also plan to support likelihood ratio tests that allow one to distinguish between BGC and accelerated substitution rates, in a lineage-specific manner.
Improvements to the API documentation are planned.