[PAUP* block to make a ML phylogenetic tree] BEGIN PAUP; set autoclose=yes criterion=likelihood notifybeep=yes; log file=***.log; <<<>>>>; Hsearch addseq=random nreps=100 start=stepwise savereps=yes swap=tbr multrees=yes; savetrees format=nexus brlens=yes append=yes file=***.all.nex; lscores 1/scorefile=***.sf append=yes; log stop; END; [ Version 3.1 (26 January 2009) This file written by Bevan Weir downloaded from http://www.rhizobia.co.nz Replace "***" above with your gene name Overwrite the 4th line with the MODELTEST parameters Every line must end with a " ; " Increase the number of nreps for more replications more replications will take longer but I recomend 10+ to examine the tree-island profile]