
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:30 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/chr3_7394.phylip" (19 taxa, 550 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	-2269.2290	4634.2996	0.6865	0.6865
HKYG	40	-2275.2774	4636.9988	0.1780	0.8645
HKYIG	41	-2274.6199	4638.0192	0.1069	0.9714
GTRIG	45	-2271.7615	4641.7373	0.0167	0.9881
GTRI	44	-2273.8076	4643.4568	0.0070	0.9951
HKYI	40	-2278.8830	4644.2101	0.0048	1.0000
SYMG	41	-2283.7244	4656.2284	0.0000	1.0000
SYMIG	42	-2283.1141	4657.3525	0.0000	1.0000
K2PG	37	-2292.4053	4664.3028	0.0000	1.0000
SYMI	41	-2288.0373	4664.8541	0.0000	1.0000
K2PIG	38	-2291.5909	4664.9821	0.0000	1.0000
K2PI	37	-2295.4641	4670.4205	0.0000	1.0000
GTR	43	-2331.9446	4757.3675	0.0000	1.0000
HKY	39	-2338.1472	4760.4121	0.0000	1.0000
SYM	40	-2348.0644	4782.5729	0.0000	1.0000
K2P	36	-2357.2020	4791.5969	0.0000	1.0000
F81G	39	-2376.8300	4837.7777	0.0000	1.0000
F81IG	40	-2376.4059	4839.2559	0.0000	1.0000
F81I	39	-2379.7260	4843.5697	0.0000	1.0000
JC69G	36	-2393.6230	4864.4391	0.0000	1.0000
JC69I	36	-2396.7733	4870.7397	0.0000	1.0000
JC69IG	37	-2397.1917	4873.8755	0.0000	1.0000
F81	38	-2437.3760	4956.5524	0.0000	1.0000
JC69	35	-2454.5690	4984.0407	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2269.2290	4626.4580	0.7914	0.7914
HKYG	40	-2275.2774	4630.5548	0.1020	0.8935
HKYIG	41	-2274.6199	4631.2397	0.0725	0.9660
GTRIG	45	-2271.7615	4633.5230	0.0231	0.9891
GTRI	44	-2273.8076	4635.6152	0.0081	0.9972
HKYI	40	-2278.8830	4637.7661	0.0028	1.0000
SYMG	41	-2283.7244	4649.4489	0.0000	1.0000
SYMIG	42	-2283.1141	4650.2282	0.0000	1.0000
SYMI	41	-2288.0373	4658.0746	0.0000	1.0000
K2PG	37	-2292.4053	4658.8106	0.0000	1.0000
K2PIG	38	-2291.5909	4659.1817	0.0000	1.0000
K2PI	37	-2295.4641	4664.9283	0.0000	1.0000
GTR	43	-2331.9446	4749.8892	0.0000	1.0000
HKY	39	-2338.1472	4754.2945	0.0000	1.0000
SYM	40	-2348.0644	4776.1289	0.0000	1.0000
K2P	36	-2357.2020	4786.4039	0.0000	1.0000
F81G	39	-2376.8300	4831.6600	0.0000	1.0000
F81IG	40	-2376.4059	4832.8119	0.0000	1.0000
F81I	39	-2379.7260	4837.4520	0.0000	1.0000
JC69G	36	-2393.6230	4859.2461	0.0000	1.0000
JC69I	36	-2396.7733	4865.5467	0.0000	1.0000
JC69IG	37	-2397.1917	4868.3833	0.0000	1.0000
F81	38	-2437.3760	4950.7520	0.0000	1.0000
JC69	35	-2454.5690	4979.1379	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2275.2774	4802.9516	0.8997	0.8997
HKYIG	41	-2274.6199	4807.9464	0.0740	0.9738
HKYI	40	-2278.8830	4810.1628	0.0244	0.9982
GTRG	44	-2269.2290	4816.0944	0.0013	0.9995
K2PG	37	-2292.4053	4818.2776	0.0004	0.9999
K2PIG	38	-2291.5909	4822.9586	0.0000	1.0000
K2PI	37	-2295.4641	4824.3953	0.0000	1.0000
GTRI	44	-2273.8076	4825.2516	0.0000	1.0000
SYMG	41	-2283.7244	4826.1555	0.0000	1.0000
GTRIG	45	-2271.7615	4827.4694	0.0000	1.0000
SYMIG	42	-2283.1141	4831.2448	0.0000	1.0000
SYMI	41	-2288.0373	4834.7812	0.0000	1.0000
HKY	39	-2338.1472	4922.3813	0.0000	1.0000
GTR	43	-2331.9446	4935.2157	0.0000	1.0000
K2P	36	-2357.2020	4941.5610	0.0000	1.0000
SYM	40	-2348.0644	4948.5256	0.0000	1.0000
F81G	39	-2376.8300	4999.7469	0.0000	1.0000
F81IG	40	-2376.4059	5005.2086	0.0000	1.0000
F81I	39	-2379.7260	5005.5388	0.0000	1.0000
JC69G	36	-2393.6230	5014.4031	0.0000	1.0000
JC69I	36	-2396.7733	5020.7037	0.0000	1.0000
JC69IG	37	-2397.1917	5027.8503	0.0000	1.0000
F81	38	-2437.3760	5114.5289	0.0000	1.0000
JC69	35	-2454.5690	5129.9851	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/chr3_7394.phylip = 1 - 550;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_7394.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/chr3_7394.phylip = 1 - 550;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_7394.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/chr3_7394.phylip = 1 - 550;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_7394.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

