This is the end part of the nexus file:

begin mrbayes;

charset 18S = 1-307;

charset co1_1 = 308-967\3;

charset co1_2 = 309-967\3;

charset co1_3 = 310-967\3;

charset co1_4_co1_5 = 968-1297\3 969-1297\3;

charset co1_6 = 970-1297\3;

partition mymodels = 6: 18S, co1_1, co1_2, co1_3, co1_4_co1_5, co1_6;

set partition = mymodels;

lset applyto=(1) nst=2 rates=gamma;

prset applyto=(1) pinvarpr=uniform(0,1);

lset applyto=(2,3,4,6) nst=6 rates=gamma;

prset applyto=(2,3,4,6) pinvarpr=uniform(0,1);

lset applyto=(5) nst=1 rates=gamma;

prset applyto=(5) statefreqpr=fixed(equal);

prset applyto=(5) pinvarpr=uniform(0,1);

unlink statefreq=(all) revmat=(all) shape=(all) pinvar=(all);

mcmc ngen=10000000 printfreq=1000 samplefreq=1000 nchains=4 nruns=2;

sump;

sumt;

end;