Adding mask to R file generated by sump after cpo analysis that shows where in the alignment the most poorly predicted sites are located
Adding file keyword argument to TreeCollection because I can never remember to use filename (file and filename are now synonymous)
Simplified scriptgen command by forcing users to choose just one analysis (e.g. cpo, ss, mcmc, etc.) - it was too complicated to try to combine disparate types of analysis into one script reliably