
Output from mraic.pl version 1.4.4 by Johan Nylander
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13:12 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/chr8_4075.phylip" (19 taxa, 623 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	-2662.0511	5418.9534	0.7116	0.7116
GTRIG	45	-2662.0230	5421.2211	0.2290	0.9405
HKYG	40	-2669.5250	5424.6858	0.0405	0.9810
HKYIG	41	-2669.4989	5426.9256	0.0132	0.9942
GTRI	44	-2667.0222	5428.8957	0.0049	0.9992
HKYI	40	-2673.4285	5432.4927	0.0008	1.0000
K2PG	37	-2692.3655	5463.5379	0.0000	1.0000
K2PIG	38	-2692.3153	5465.7060	0.0000	1.0000
SYMG	41	-2690.1827	5468.2930	0.0000	1.0000
K2PI	37	-2695.4401	5469.6871	0.0000	1.0000
SYMIG	42	-2690.1408	5470.5091	0.0000	1.0000
SYMI	41	-2693.3645	5474.6567	0.0000	1.0000
GTR	43	-2701.8063	5496.1481	0.0000	1.0000
HKY	39	-2708.5329	5500.4173	0.0000	1.0000
K2P	36	-2732.5210	5541.5882	0.0000	1.0000
SYM	40	-2730.0424	5545.7206	0.0000	1.0000
F81G	39	-2750.9508	5585.2532	0.0000	1.0000
F81IG	40	-2750.8863	5587.4084	0.0000	1.0000
F81I	39	-2753.9581	5591.2679	0.0000	1.0000
JC69G	36	-2767.5373	5611.6208	0.0000	1.0000
JC69IG	37	-2767.4697	5613.7462	0.0000	1.0000
JC69I	36	-2770.1661	5616.8783	0.0000	1.0000
F81	38	-2788.7203	5658.5159	0.0000	1.0000
JC69	35	-2805.4836	5685.2603	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2662.0511	5412.1021	0.7000	0.7000
GTRIG	45	-2662.0230	5414.0461	0.2648	0.9648
HKYG	40	-2669.5250	5419.0500	0.0217	0.9865
HKYIG	41	-2669.4989	5420.9979	0.0082	0.9947
GTRI	44	-2667.0222	5422.0444	0.0049	0.9996
HKYI	40	-2673.4285	5426.8569	0.0004	1.0000
K2PG	37	-2692.3655	5458.7311	0.0000	1.0000
K2PIG	38	-2692.3153	5460.6307	0.0000	1.0000
SYMG	41	-2690.1827	5462.3653	0.0000	1.0000
SYMIG	42	-2690.1408	5464.2815	0.0000	1.0000
K2PI	37	-2695.4401	5464.8803	0.0000	1.0000
SYMI	41	-2693.3645	5468.7290	0.0000	1.0000
GTR	43	-2701.8063	5489.6127	0.0000	1.0000
HKY	39	-2708.5329	5495.0657	0.0000	1.0000
K2P	36	-2732.5210	5537.0421	0.0000	1.0000
SYM	40	-2730.0424	5540.0849	0.0000	1.0000
F81G	39	-2750.9508	5579.9015	0.0000	1.0000
F81IG	40	-2750.8863	5581.7726	0.0000	1.0000
F81I	39	-2753.9581	5585.9163	0.0000	1.0000
JC69G	36	-2767.5373	5607.0747	0.0000	1.0000
JC69IG	37	-2767.4697	5608.9393	0.0000	1.0000
JC69I	36	-2770.1661	5612.3322	0.0000	1.0000
F81	38	-2788.7203	5653.4405	0.0000	1.0000
JC69	35	-2805.4836	5680.9673	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2669.5250	5596.4319	0.9380	0.9380
HKYIG	41	-2669.4989	5602.8143	0.0386	0.9766
HKYI	40	-2673.4285	5604.2388	0.0189	0.9955
GTRG	44	-2662.0511	5607.2222	0.0043	0.9998
GTRIG	45	-2662.0230	5613.6007	0.0002	1.0000
GTRI	44	-2667.0222	5617.1645	0.0000	1.0000
K2PG	37	-2692.3655	5622.8093	0.0000	1.0000
K2PI	37	-2695.4401	5628.9585	0.0000	1.0000
K2PIG	38	-2692.3153	5629.1434	0.0000	1.0000
SYMG	41	-2690.1827	5644.1817	0.0000	1.0000
SYMIG	42	-2690.1408	5650.5325	0.0000	1.0000
SYMI	41	-2693.3645	5650.5454	0.0000	1.0000
HKY	39	-2708.5329	5668.0130	0.0000	1.0000
GTR	43	-2701.8063	5680.2982	0.0000	1.0000
K2P	36	-2732.5210	5696.6858	0.0000	1.0000
SYM	40	-2730.0424	5717.4667	0.0000	1.0000
F81G	39	-2750.9508	5752.8489	0.0000	1.0000
F81I	39	-2753.9581	5758.8636	0.0000	1.0000
F81IG	40	-2750.8863	5759.1545	0.0000	1.0000
JC69G	36	-2767.5373	5766.7184	0.0000	1.0000
JC69I	36	-2770.1661	5771.9759	0.0000	1.0000
JC69IG	37	-2767.4697	5773.0176	0.0000	1.0000
F81	38	-2788.7203	5821.9533	0.0000	1.0000
JC69	35	-2805.4836	5836.1764	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/chr8_4075.phylip = 1 - 623;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_4075.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/chr8_4075.phylip = 1 - 623;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_4075.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/chr8_4075.phylip = 1 - 623;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_4075.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

