#nexus

[begins PAUP*]
begin paup;
	
set 
autoclose     [closes the status window automatically]
nowarntree    [turns off the feature that prompts you to save trees in memory]
nowarnreset   [turns off feature that asks "do you really want to reset the data file"]
torder=right  [specifies the tree order to be ladderized to the right]
flush         [flushes the file buffer]
tcompress=yes [prints trees in a compressed format, which allows you to view large trees in a single page]
defaultmode;  [tells paup to use the default option when a dialog box is opened]




	[start writing to log file; replace "your_log" with your log file name]
	log file=your_log.log;
	
	[execute your data file; replace "your_data" with your data file name]
	exec your_data.nex;

	[get first tree(s); replace "your_tree1" with your first tree file name]
	gettrees file=your_tree1.tre;

	[get second file tree(s), and keep all trees that are different; replace "your_tree2" with your second tree file name]
	gettrees file=your_tree2.tre mode= 5;

	[set criterion to maximum likelihood]
	set criterion=likelihood;

	[set likelihood model and estimate all parameters; this is GTR+I+G]
	lset nst=6 rmatrix=estimate basefreq=estimate pinv=estimate rates=gamma shape=estimate;

	[calculate likelihood parameters for all trees and test for significant differences between trees using Kishino-Hasegawa test]
	lscores all /khtest;

	[display trees]
	describe all/plot=phylogram labelnode=no;

	[stop writing to log file]
	log stop;

	[quit paup]
	quit;

end;