addprocs(55)

Pkg.checkout("PhyloNetworks")

Pkg.update("PhyloNetworks")

@everywhere using PhyloNetworks
 
homedir()
 
cd("$(homedir())/SNaQ")
 
pwd()

raxmltrees = joinpath("SNaQ_trees.tre")

genetrees = readMultiTopology(raxmltrees);

raxmlCF = readTrees2CF(raxmltrees, CFfile="tableCF.txt");
 
df_sp = mapAllelesCFtable("Bothriechis_mapping.csv", "tableCF.txt") 
 
d_sp = readTableCF!(df_sp)

tre = readTopology("StartingTree_Species.tre")

net0_100 = snaq!(tre, d_sp,runs=100,hmax=0, filename="net0_100runs")

net1_100 = snaq!(net0_100, d_sp,runs=100,hmax=1, filename="net1_100runs")

net2_100 = snaq!(net1_100, d_sp,runs=100,hmax=2, filename="net2_100runs")

net3_100 = snaq!(net2_100, d_sp,runs=100,hmax=3, filename="net3_100runs")

net4_100 = snaq!(net3_100, d_sp,runs=100,hmax=4, filename="net4_100runs")

net5_100 = snaq!(net4_100, d_sp,runs=100,hmax=5, filename="net5_100runs")

net6_100 = snaq!(net5_100, d_sp,runs=100,hmax=6, filename="net6_100runs")

net7_100 = snaq!(net6_100, d_sp,runs=100,hmax=7, filename="net7_100runs")

net8_100 = snaq!(net7_100, d_sp,runs=100,hmax=8, filename="net8_100runs")

net9_100 = snaq!(net2_100, d_sp,runs=100,hmax=3, filename="net9_100runs")
