Updated make file in UNIX version. Version 1.2 - Invariable Sites model. Different trees for different partitions of the data. This allows simulation of recombinant histories. Can specify the random number seed.
Full details are in the manual .
This will reduce the amount of variability in a set of simulations. Version 1.06 - Added ability to load an alignment of sequences and use one of them as an ancestral sequence. Version 1.04 - Fixed problem with Makefile. Version 1.03 - Fixed problem calculating Kappa in HKY model for unequal base frequencies. Version 1.02 - Added the discrete approximation to the gamma rate heterogeneity model.