## This folder contains all relevant raxml output files. ## ## Contatenated runs, each with a different outgroup configuration: RAxML_bipartitionsBranchLabels.EjaC.Ckot.DP5.GQ20.MAXMISS0.9.MAF0.01.GTRCAT.bootstrap100 # C. kottae as outgroup RAxML_bipartitionsBranchLabels.EjaC.Ckot.Dstat.DP5.GQ20.MAXMISS0.9.MAF0.01.GTRCAT.bootstrap100 # C. kottae and S. galilaeus as outgroup RAxML_bipartitionsBranchLabels.EjaC.Dstat.DP5.GQ20.MAXMISS0.9.MAF0.01.GTRCAT.bootstrap100 # S. galilaeus as outgroup ## Gene trees from window-based tree building, each with a different outgroup configuration: raxml_EjaC.Cgal.Cgui.DP5.GQ20.MAXMISS0.9.MAF0.01.minsites250.Window100kb_allGeneTrees.tre # No outgroups raxml_EjaC.Ckot.DP5.GQ20.MAXMISS0.9.MAF0.01.minsites250.Window100kb_allGeneTrees.tre # C. kottae as outgroup raxml_EjaC.Ckot.Dstat.DP5.GQ20.MAXMISS0.9.MAF0.01.minsites250.Window100kb_allGeneTrees.tre # C. kottae and S. galilaeus as outgroup raxml_EjaC.Dstat.DP5.GQ20.MAXMISS0.9.MAF0.01.minsites250.Window100kb_allGeneTrees.tre # S. galilaeus as outgroup ## Trees with ICA scores, each with a different outgroup configuration: RAxML_IC_Score_BranchLabels.EjaC.Ckot.DP5.GQ20.MAXMISS0.9.MAF0.01.minsites250.ICAscores.MLtree # C. kottae as outgroup RAxML_IC_Score_BranchLabels.EjaC.Ckot.Dstat.DP5.GQ20.MAXMISS0.9.MAF0.01.minsites250.ICAscores.MLtree # C. kottae and S. galilaeus as outgroup RAxML_IC_Score_BranchLabels.EjaC.Dstat.DP5.GQ20.MAXMISS0.9.MAF0.01.minsites250.ICAscores.MLtree # S. galilaeus as outgroup