adh.nex

功能强大的bayes算法源码

end;

begin mrbayes;
	[The following lines define three character sets, each corresponding to a codon position.
	 Note the use of \3 to include every third character in the set]
	charset 1st_pos = 1-771\3;
	charset 2nd_pos = 2-771\3;
	charset 3rd_pos = 3-771\3;
	
	[The following line defines a partition called "by_codon" that divides the sites into three
	 sets corresponding to the first, second, and third codon position]
	partition by_codon = 3:1st_pos,2nd_pos,3rd_pos;

	[The following line sets the current partition to the one we just defined above. If we do not
         explicitly set the partition to the one we defined, MrBayes will use the default partition.
         The default partition divides the characters into sets based on their data type (DNA, amino acid, etc)]
	set partition=by_codon;
	
	[The following line allows the codon positions to have different rates. Without the following
         line, all codon positions will be assumed to evolve at the same rate]
	prset ratepr=variable; 
	
	[The last line defines a usertree, which can be used as a startingtree to speed up convergence.
	 Unless you set startingtree=user in mcmc, however, a random starting tree will be used instead
	 when the chain is run.]
	usertree = ((((((((D.persimilis,(D.pseudoobscura1,D.pseudoobscura2)),D.miranda),D.ambigua),(D.subobscura,D.madeirensis)),((((D.melanogaster,((D.simulans,D.sechellia),D.mauritiana)),(D.teissieri,D.yakuba)),D.orena),D.tsacasi)),D.willistoni),D.lebanonensis),(((D.crassifemur,Sc.albovittata),((((((D.montana,D.lacicola),D.borealis),D.flavomontana),(((D.texana,D.americana),D.lummei),(D.virilis_1,D.virilis_2))),(((D.buzzatii_1,D.buzzatii_2),((((D.arizonae_2,D.mojavensis_2),(((D.mulleri_1,D.mulleri_2),D.navojoa),D.wheeleri)),D.mayaguana),D.mojavensis_1)),(D.mettleri,(D.hydei_1,D.hydei_2)))),((((((D.silvestris,D.heteroneura),(D.planitibia,D.differens)),((D.grimshawi,D.hawaiiensis),D.affinidisjuncta)),D.picticornis),(D.mimica,D.adiastola)),D.nigra))),(D.immigrans,Z.tuberculatus)));
	
end;