//use the simulation MSA burnin=50. inference=4000 calibration=100. thinnin=3
-tTrees/6_tree.txt -ORuns/Oct26_1.0Alpha_6Tree/ -sRuns/Oct26_1.0Alpha_6Tree/msa/simulateMSA.txt -b50 -i4000 -c100 -e3
h-tTrees/6_tree.txt -ORuns\\Oct30_1.0Alpha_6Tree -sRuns/Oct30_1.0Alpha_6Tree/msa/simulateMSA.txt -b50 -i4000 -c100 -e3


-ORuns -tTrees/6_tree.txt -sRuns/Oct26_1.0Alpha_6Tree/msa/simulateMSA.txt -qm -b50 -i4000 -c100   -e3 




//works!
-tTrees/6_tree2.txt -ORuns/Nov17_1.0Alpha_6Tree -sRuns/Nov17_1.0Alpha_6Tree/msa/simulateMSA.txt -b3000 -i3000 -c100 -e10