HyPhy branch language sequence simulation scripts for the FUBAR3D model.
To generate settings files from csvs in subdirectory "data" (within this directory):
./genSets.sh data
To generate fasta files from these settings files:
./runSets.sh data
To change the number of taxa in a tree, edit the genSets.sh file and change the integer passed to simsetgen.py (it can be any number, but will be unrooted).
To change the distributions from which syns and nonsyns are drawn, change the parameters to simsetgen.py in genSets.sh to include
--nonsyn mu1 sigma1 mu2 sigma2
and
--syn mu1 sigma1 mu2 sigma2