[PAUP* block to make a ML phylogenetic tree]

BEGIN PAUP;
set autoclose=yes criterion=likelihood notifybeep=yes;
log file=***.log;
<<<<ADD MODELTEST PARAMETERS HERE>>>>>;
Hsearch addseq=random nreps=10;
savetrees format=nexus brlens=yes append=yes file=***.nex;
savetrees format=phylip brlens=yes append=yes  file=***.phy;
lscores 1/scorefile=***.sf append=yes;
END;

[ Version 2.3 (7 January 2006) 
 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]