begin mrbayes;

outgroup 1;

	CHARSET  Fib5 = 1-609;
	CHARSET  ATPase  =  610-1286;
	CHARSET  ND3 = 1307-1657;
	CHARSET  ND2 = 1682-2722;
	CHARSET  tRNA  =  1287-1306 1658-1681;
	CHARSET  first = 612-1284\3 1307-1655\3 1682-2720\3;
	CHARSET  second = 610-1285\3 1308-1656\3 1683-2721\3;
	CHARSET  third = 611-1286\3 1309-1657\3 1684-2722\3;

partition genes = 5: Fib5, ATPase, ND3, ND2, tRNA;
partition codons = 5: Fib5, tRNA, first, second, third;

end;


begin mrbayes;

set autoclose=yes;

log start filename=Run1_log;

set partition = genes;

prset applyto=(all) ratepr=variable;

lset applyto=(1,2,3,4) nst=6 rates=invgamma ngammacat=4;

lset applyto=(5) nst=2 rates=gamma;

unlink shape=(all) pinvar=(1,2,3,4) statefreq=(all) revmat=(all);

mcmcp ngen=1000 printfreq=100 samplefreq=10 nchains=4 startingtree=random;
report tree=brlens;
mcmc;
	sump burnin=5;
	sumt burnin=5 contype=halfcompat;
end;

quit;