Very slow speed

Hello, 

reconstructR looks pretty neat, we are trying it out for the H5N1 influenza A outbreak in cattle. Is there a way to multithread run_mcmc? At the current rate it is going it will take 66 days to finish. There are 500 samples, so 500,000 iterations and 300 complete per hour. The alignment length is around 13,000 bp. 

Thanks!

Carl