
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:04 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_3174.phylip" (19 taxa, 694 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	-3874.7029	7843.5075	0.7537	0.7537
GTRIG	45	-3874.7031	7845.7950	0.2401	0.9939
HKYG	40	-3884.3349	7853.6928	0.0046	0.9985
HKYIG	41	-3884.3350	7855.9521	0.0015	1.0000
SYMG	41	-3891.3267	7869.9356	0.0000	1.0000
K2PG	37	-3896.5063	7871.2991	0.0000	1.0000
SYMIG	42	-3891.3267	7872.2018	0.0000	1.0000
K2PIG	38	-3896.5064	7873.5379	0.0000	1.0000
GTRI	44	-3892.1847	7878.4712	0.0000	1.0000
HKYI	40	-3902.3414	7889.7057	0.0000	1.0000
SYMI	41	-3910.7973	7908.8769	0.0000	1.0000
K2PI	37	-3917.7635	7913.8137	0.0000	1.0000
GTR	43	-3939.5082	7970.8379	0.0000	1.0000
HKY	39	-3953.2655	7989.3016	0.0000	1.0000
SYM	40	-3963.2365	8011.4960	0.0000	1.0000
K2P	36	-3972.6212	8021.2971	0.0000	1.0000
F81G	39	-4018.2303	8119.2312	0.0000	1.0000
F81IG	40	-4018.2304	8121.4838	0.0000	1.0000
JC69G	36	-4030.6797	8137.4142	0.0000	1.0000
JC69IG	37	-4030.6799	8139.6463	0.0000	1.0000
F81I	39	-4034.7192	8152.2090	0.0000	1.0000
JC69I	36	-4047.4686	8170.9920	0.0000	1.0000
F81	38	-4083.3633	8247.2519	0.0000	1.0000
JC69	35	-4097.4217	8268.6732	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-3874.7029	7837.4058	0.7285	0.7285
GTRIG	45	-3874.7031	7839.4062	0.2679	0.9964
HKYG	40	-3884.3349	7848.6698	0.0026	0.9990
HKYIG	41	-3884.3350	7850.6699	0.0010	1.0000
SYMG	41	-3891.3267	7864.6534	0.0000	1.0000
SYMIG	42	-3891.3267	7866.6534	0.0000	1.0000
K2PG	37	-3896.5063	7867.0126	0.0000	1.0000
K2PIG	38	-3896.5064	7869.0127	0.0000	1.0000
GTRI	44	-3892.1847	7872.3695	0.0000	1.0000
HKYI	40	-3902.3414	7884.6827	0.0000	1.0000
SYMI	41	-3910.7973	7903.5947	0.0000	1.0000
K2PI	37	-3917.7635	7909.5271	0.0000	1.0000
GTR	43	-3939.5082	7965.0163	0.0000	1.0000
HKY	39	-3953.2655	7984.5310	0.0000	1.0000
SYM	40	-3963.2365	8006.4730	0.0000	1.0000
K2P	36	-3972.6212	8017.2423	0.0000	1.0000
F81G	39	-4018.2303	8114.4606	0.0000	1.0000
F81IG	40	-4018.2304	8116.4608	0.0000	1.0000
JC69G	36	-4030.6797	8133.3594	0.0000	1.0000
JC69IG	37	-4030.6799	8135.3598	0.0000	1.0000
F81I	39	-4034.7192	8147.4383	0.0000	1.0000
JC69I	36	-4047.4686	8166.9372	0.0000	1.0000
F81	38	-4083.3633	8242.7267	0.0000	1.0000
JC69	35	-4097.4217	8264.8434	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-3884.3349	8030.3687	0.8554	0.8554
K2PG	37	-3896.5063	8035.0840	0.0810	0.9363
HKYIG	41	-3884.3350	8036.9113	0.0325	0.9688
GTRG	44	-3874.7029	8037.2745	0.0271	0.9959
K2PIG	38	-3896.5064	8041.6266	0.0031	0.9989
GTRIG	45	-3874.7031	8043.8174	0.0010	1.0000
SYMG	41	-3891.3267	8050.8947	0.0000	1.0000
SYMIG	42	-3891.3267	8057.4372	0.0000	1.0000
HKYI	40	-3902.3414	8066.3816	0.0000	1.0000
GTRI	44	-3892.1847	8072.2382	0.0000	1.0000
K2PI	37	-3917.7635	8077.5985	0.0000	1.0000
SYMI	41	-3910.7973	8089.8360	0.0000	1.0000
GTR	43	-3939.5082	8160.3426	0.0000	1.0000
HKY	39	-3953.2655	8161.6874	0.0000	1.0000
K2P	36	-3972.6212	8180.7713	0.0000	1.0000
SYM	40	-3963.2365	8188.1719	0.0000	1.0000
F81G	39	-4018.2303	8291.6170	0.0000	1.0000
JC69G	36	-4030.6797	8296.8884	0.0000	1.0000
F81IG	40	-4018.2304	8298.1597	0.0000	1.0000
JC69IG	37	-4030.6799	8303.4312	0.0000	1.0000
F81I	39	-4034.7192	8324.5947	0.0000	1.0000
JC69I	36	-4047.4686	8330.4662	0.0000	1.0000
F81	38	-4083.3633	8415.3406	0.0000	1.0000
JC69	35	-4097.4217	8423.8299	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_3174.phylip = 1 - 694;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_3174.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_3174.phylip = 1 - 694;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_3174.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_3174.phylip = 1 - 694;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_3174.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

