
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
13:27 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/chr9_2502.phylip" (19 taxa, 886 characters)

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


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	-2731.8029	5556.3144	0.5274	0.5274
GTRIG	45	-2730.9474	5556.8234	0.4089	0.9364
GTRI	44	-2733.9179	5560.5445	0.0636	1.0000
HKYG	40	-2749.9855	5583.8527	0.0000	1.0000
HKYIG	41	-2749.7137	5585.5080	0.0000	1.0000
HKYI	40	-2751.1853	5586.2522	0.0000	1.0000
SYMG	41	-2764.6551	5615.3907	0.0000	1.0000
SYMIG	42	-2764.4823	5617.2493	0.0000	1.0000
SYMI	41	-2765.6545	5617.3895	0.0000	1.0000
K2PG	37	-2774.2929	5625.9019	0.0000	1.0000
K2PI	37	-2775.2344	5627.7848	0.0000	1.0000
K2PIG	38	-2774.1532	5627.8057	0.0000	1.0000
F81G	39	-2798.5602	5678.8083	0.0000	1.0000
F81IG	40	-2798.4103	5680.7022	0.0000	1.0000
F81I	39	-2799.6135	5680.9150	0.0000	1.0000
GTR	43	-2811.5307	5713.5554	0.0000	1.0000
JC69G	36	-2819.4056	5713.9489	0.0000	1.0000
JC69I	36	-2820.2918	5715.7214	0.0000	1.0000
JC69IG	37	-2819.3236	5715.9632	0.0000	1.0000
HKY	39	-2827.3918	5736.4715	0.0000	1.0000
SYM	40	-2842.0516	5767.9850	0.0000	1.0000
K2P	36	-2851.7430	5778.6237	0.0000	1.0000
F81	38	-2873.7395	5826.9785	0.0000	1.0000
JC69	35	-2894.5312	5862.0272	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2731.8029	5551.6057	0.5035	0.5035
GTRIG	45	-2730.9474	5551.8948	0.4357	0.9393
GTRI	44	-2733.9179	5555.8358	0.0607	1.0000
HKYG	40	-2749.9855	5579.9710	0.0000	1.0000
HKYIG	41	-2749.7137	5581.4275	0.0000	1.0000
HKYI	40	-2751.1853	5582.3706	0.0000	1.0000
SYMG	41	-2764.6551	5611.3101	0.0000	1.0000
SYMIG	42	-2764.4823	5612.9646	0.0000	1.0000
SYMI	41	-2765.6545	5613.3090	0.0000	1.0000
K2PG	37	-2774.2929	5622.5858	0.0000	1.0000
K2PIG	38	-2774.1532	5624.3063	0.0000	1.0000
K2PI	37	-2775.2344	5624.4688	0.0000	1.0000
F81G	39	-2798.5602	5675.1204	0.0000	1.0000
F81IG	40	-2798.4103	5676.8206	0.0000	1.0000
F81I	39	-2799.6135	5677.2270	0.0000	1.0000
GTR	43	-2811.5307	5709.0613	0.0000	1.0000
JC69G	36	-2819.4056	5710.8111	0.0000	1.0000
JC69I	36	-2820.2918	5712.5836	0.0000	1.0000
JC69IG	37	-2819.3236	5712.6472	0.0000	1.0000
HKY	39	-2827.3918	5732.7836	0.0000	1.0000
SYM	40	-2842.0516	5764.1033	0.0000	1.0000
K2P	36	-2851.7430	5775.4859	0.0000	1.0000
F81	38	-2873.7395	5823.4791	0.0000	1.0000
JC69	35	-2894.5312	5859.0625	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
GTRG	44	-2731.8029	5762.2213	0.8244	0.8244
GTRI	44	-2733.9179	5766.4513	0.0994	0.9238
GTRIG	45	-2730.9474	5767.2971	0.0652	0.9890
HKYG	40	-2749.9855	5771.4397	0.0082	0.9972
HKYI	40	-2751.1853	5773.8393	0.0025	0.9996
HKYIG	41	-2749.7137	5777.6829	0.0004	1.0000
K2PG	37	-2774.2929	5799.6944	0.0000	1.0000
K2PI	37	-2775.2344	5801.5773	0.0000	1.0000
K2PIG	38	-2774.1532	5806.2015	0.0000	1.0000
SYMG	41	-2764.6551	5807.5655	0.0000	1.0000
SYMI	41	-2765.6545	5809.5644	0.0000	1.0000
SYMIG	42	-2764.4823	5814.0068	0.0000	1.0000
F81G	39	-2798.5602	5861.8024	0.0000	1.0000
F81I	39	-2799.6135	5863.9090	0.0000	1.0000
F81IG	40	-2798.4103	5868.2892	0.0000	1.0000
JC69G	36	-2819.4056	5883.1330	0.0000	1.0000
JC69I	36	-2820.2918	5884.9054	0.0000	1.0000
JC69IG	37	-2819.3236	5889.7557	0.0000	1.0000
GTR	43	-2811.5307	5914.8901	0.0000	1.0000
HKY	39	-2827.3918	5919.4655	0.0000	1.0000
K2P	36	-2851.7430	5947.8078	0.0000	1.0000
SYM	40	-2842.0516	5955.5720	0.0000	1.0000
F81	38	-2873.7395	6005.3743	0.0000	1.0000
JC69	35	-2894.5312	6026.5976	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/chr9_2502.phylip = 1 - 886;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_2502.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/chr9_2502.phylip = 1 - 886;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_2502.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 (GTRG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_2502.phylip = 1 - 886;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_2502.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;


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End of Output

