
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:27 02/24/2011

Input data from file "/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr12_5837.phylip" (19 taxa, 807 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
Minimum BIC  model: HKYG


Note: number of parameters compared to sample size
is low (Nchar/Nparams < 40). Consider the use of AICc.


(Output sorted by AICc. w: Akaike weight, cw: cumulative w.)

Model	df	lnL		AICc		wAICc	cwAICc
GTRG	44	-2272.9434	4639.0837	0.5393	0.5393
GTRI	44	-2273.7004	4640.5977	0.2530	0.7923
GTRIG	45	-2272.7825	4641.0052	0.2063	0.9986
HKYG	40	-2283.9758	4652.2336	0.0008	0.9994
HKYIG	41	-2283.7339	4653.9697	0.0003	0.9997
HKYI	40	-2284.9026	4654.0873	0.0003	1.0000
SYMG	41	-2287.7511	4662.0041	0.0000	1.0000
SYMI	41	-2288.4936	4663.4891	0.0000	1.0000
SYMIG	42	-2287.6042	4663.9361	0.0000	1.0000
K2PG	37	-2296.8876	4671.4318	0.0000	1.0000
K2PI	37	-2297.6629	4672.9825	0.0000	1.0000
K2PIG	38	-2296.7344	4673.3283	0.0000	1.0000
GTR	43	-2312.3690	4715.6973	0.0000	1.0000
HKY	39	-2322.8473	4727.7623	0.0000	1.0000
F81G	39	-2325.7857	4733.6393	0.0000	1.0000
F81I	39	-2326.4852	4735.0382	0.0000	1.0000
F81IG	40	-2325.6915	4735.6651	0.0000	1.0000
SYM	40	-2326.2860	4736.8540	0.0000	1.0000
K2P	36	-2335.2197	4745.8992	0.0000	1.0000
JC69G	36	-2340.0745	4755.6088	0.0000	1.0000
JC69I	36	-2340.7860	4757.0318	0.0000	1.0000
JC69IG	37	-2339.9774	4757.6115	0.0000	1.0000
F81	38	-2362.6840	4805.2274	0.0000	1.0000
JC69	35	-2376.4228	4826.1142	0.0000	1.0000



(Output sorted by AIC. w: Akaike weight, cw: cumulative w.)

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2272.9434	4633.8868	0.5255	0.5255
GTRI	44	-2273.7004	4635.4008	0.2465	0.7720
GTRIG	45	-2272.7825	4635.5650	0.2271	0.9991
HKYG	40	-2283.9758	4647.9516	0.0005	0.9996
HKYIG	41	-2283.7339	4649.4677	0.0002	0.9998
HKYI	40	-2284.9026	4649.8053	0.0002	1.0000
SYMG	41	-2287.7511	4657.5021	0.0000	1.0000
SYMI	41	-2288.4936	4658.9872	0.0000	1.0000
SYMIG	42	-2287.6042	4659.2083	0.0000	1.0000
K2PG	37	-2296.8876	4667.7751	0.0000	1.0000
K2PI	37	-2297.6629	4669.3258	0.0000	1.0000
K2PIG	38	-2296.7344	4669.4689	0.0000	1.0000
GTR	43	-2312.3690	4710.7379	0.0000	1.0000
HKY	39	-2322.8473	4723.6945	0.0000	1.0000
F81G	39	-2325.7857	4729.5715	0.0000	1.0000
F81I	39	-2326.4852	4730.9704	0.0000	1.0000
F81IG	40	-2325.6915	4731.3831	0.0000	1.0000
SYM	40	-2326.2860	4732.5720	0.0000	1.0000
K2P	36	-2335.2197	4742.4395	0.0000	1.0000
JC69G	36	-2340.0745	4752.1491	0.0000	1.0000
JC69I	36	-2340.7860	4753.5721	0.0000	1.0000
JC69IG	37	-2339.9774	4753.9548	0.0000	1.0000
F81	38	-2362.6840	4801.3680	0.0000	1.0000
JC69	35	-2376.4228	4822.8457	0.0000	1.0000



(Output sorted by BIC. w: Akaike weight, cw: cumulative w.)

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2283.9758	4835.6845	0.5987	0.5987
HKYI	40	-2284.9026	4837.5382	0.2370	0.8357
GTRG	44	-2272.9434	4840.3931	0.0569	0.8925
K2PG	37	-2296.8876	4841.4281	0.0339	0.9264
HKYIG	41	-2283.7339	4841.8940	0.0268	0.9533
GTRI	44	-2273.7004	4841.9071	0.0267	0.9799
K2PI	37	-2297.6629	4842.9788	0.0156	0.9955
GTRIG	45	-2272.7825	4846.7645	0.0024	0.9979
K2PIG	38	-2296.7344	4847.8152	0.0014	0.9993
SYMG	41	-2287.7511	4849.9284	0.0005	0.9998
SYMI	41	-2288.4936	4851.4135	0.0002	1.0000
SYMIG	42	-2287.6042	4856.3279	0.0000	1.0000
HKY	39	-2322.8473	4906.7342	0.0000	1.0000
K2P	36	-2335.2197	4911.3991	0.0000	1.0000
GTR	43	-2312.3690	4912.5509	0.0000	1.0000
F81G	39	-2325.7857	4912.6111	0.0000	1.0000
F81I	39	-2326.4852	4914.0100	0.0000	1.0000
F81IG	40	-2325.6915	4919.1160	0.0000	1.0000
SYM	40	-2326.2860	4920.3049	0.0000	1.0000
JC69G	36	-2340.0745	4921.1088	0.0000	1.0000
JC69I	36	-2340.7860	4922.5317	0.0000	1.0000
JC69IG	37	-2339.9774	4927.6078	0.0000	1.0000
F81	38	-2362.6840	4979.7143	0.0000	1.0000
JC69	35	-2376.4228	4987.1120	0.0000	1.0000



To specify default values for best AIC, AICc, or BIC models in MrBayes:

[Mrbayes block for the best AIC model (GTRG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr12_5837.phylip = 1 - 807;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr12_5837.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=gamma;
 Prset applyto=(1) revmatpr=Dirichlet(1.0,1.0,1.0,1.0,1.0,1.0) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


[Mrbayes block for the best AICc model (GTRG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr12_5837.phylip = 1 - 807;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr12_5837.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=gamma;
 Prset applyto=(1) revmatpr=Dirichlet(1.0,1.0,1.0,1.0,1.0,1.0) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


[Mrbayes block for the best BIC model (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr12_5837.phylip = 1 - 807;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr12_5837.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=gamma;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


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End of Output

