#MESQUITEINIT BATCHFILE 1
 name = GTR_Model_Test
 explanation = 'This template produces a batch file to request PAUP to quickly find a tree using neighbor joining.  It asks PAUP to calculate the likelihood value for the tree, estimating any parameters specified in the snippet''s lset command, and then write the results to a score file.  '
 start1 = '#NEXUS^nbegin paup;^n	log file=''<name>.log'';^n	set autoclose nowarnreset tcompress torder=right;^n	dset distance=hky85;^n	lset basefreq=empirical nst=6 rmatrix=estimate pinvar=0 rates=equal;'
 repeat1 = '	execute ''<name><number>.nex'';^n	nj;^n 	lscore 1/scorefile=''<name>Score.scr'' append;^n'
 end1 = '	log stop;^nend;'
 batchFileName1 = PaupCommands.nex
 start2 = 'MesquiteInstructions^nnumVariables = 5^nnumFiles = 1^nfile1 = ''itemsPerRecord=14 v1=10 v2=11 v3=12 v4=13 v5=14''^nrecordLabel = ''Replicates''^nlabel1 = ''R(a)''^nlabel2 = ''R(b)''^nlabel3 = ''R(c)''^nlabel4 = ''R(d)''^nlabel5 = ''R(e)''^n'
 batchFileName2 = MesquiteInstructions
 matrixExportFormat =  NEXUS_file