added several options (MAP, symq, red)
added several options (MAP, symq, red)

-A 3 to run approximate Maximum a Posteriori optimization (very
preliminary implementation)
-hp to estimate rate prior using Gamma hyper prior (by default fixed to
1)
-red removes all taxa that are sampled in a single area
-symq forces q rates to be symmetrical

dsilvestro/PyRate,dsilvestro/PyRate,dsilvestro/PyRate,dsilvestro/PyRate