begin mrbayes;

set autoclose=yes nowarn=yes;

log start filename=basal.12.txt replace;


outgroup Callorhin [Chimaera Amblyraja Squalus Scyliorhi];


[MODIFY WITH DIFFERENT FRAGMENTS]


charset 12S =	1-1111;
charset 16S  =	1112-2850;
charset COX1 =	2851-4440;
charset COX2 =	4441-5131;
charset COX3 =	5132-5922;
charset nd1 =	5923-6900;
charset nd2 =	6901-7950;
charset nd3 =	7951-8299;
charset nd4L =	8300-8596;
charset nd4 =	8597-9983;
charset nd5 =	9984-11900;
charset nd6 =	11901-12441;
charset cytB =	12442-13608;
charset ATP6 =	13609-14280;
charset ATP8 =	14281-14448;
charset tRNAs =	14449-16128;

charset Cox1a = 2851-4440\3;
charset cox1b = 2852-4440\3;
charset cox1c = 2853-4440\3;

charset cox2a = 4441-5131\3;
charset cox2b = 4442-5131\3;
charset cox2c = 4443-5131\3;

charset cox3a = 5132-5922\3;
charset cox3b = 5133-5922\3;
charset cox3c = 5134-5922\3;

charset nd1a = 5923-6900\3;
charset nd1b = 5924-6900\3;
charset nd1c = 5925-6900\3;

charset nd2a = 6901-7950\3;
charset nd2b = 6902-7950\3;
charset nd2c = 6903-7950\3;

charset nd3a = 7951-8299\3;
charset nd3b = 7952-8299\3;
charset nd3c = 7953-8299\3;

charset nd4La = 8300-8596\3;
charset nd4Lb = 8301-8596\3;
charset nd4Lc = 8302-8596\3;

charset nd4a = 8597-9983\3;
charset nd4b = 8598-9983\3;
charset nd4c = 8599-9983\3;

charset nd5a = 9984-11900\3;
charset nd5b = 9985-11900\3;
charset nd5c = 9986-11900\3;

charset nd6a = 11901-12441\3;
charset nd6b = 11902-12441\3;
charset nd6c = 11903-12441\3;

charset cytBa = 12442-13608\3;
charset cytBb = 12443-13608\3;
charset cytBc = 12444-13608\3;

charset atp6a = 13609-14280\3;
charset atp6b = 13610-14280\3;
charset atp6c = 13611-14280\3;

charset atp8a = 14281-14448\3;
charset atp8b = 14282-14448\3;
charset atp8c = 14283-14448\3;


exclude atp8c atp6c cytBc nd6c nd5c nd4c nd4Lc nd3c nd2c 
         cox3c  cox2c cox1c;


	partition all = 13:12S 16S, COX1, COX2, COX3, nd1, nd2, nd3, nd4L nd4, nd5, nd6, cytB, ATP6 ATP8, tRNAs;

	set partition=all;

	Lset  applyto=(all) nst=6  rates=gamma;
	
	unlink statefreq=(all) revmat=(all) shape=(all) pinvar=(all);	
	

	mcmc ngen=1000000 printfreq=100 samplefreq=100 nchains=4 temp=0.2 swapfreq=1 savebrlens=yes;

	sump burnin=2000;

	sumt contype=allcompat burnin=2000;

	log stop;

end;