
Output from mraic.pl version 1.4.4 by Johan Nylander
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13:06 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/chr7_11479.phylip" (19 taxa, 719 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	-2717.8061	5529.4877	0.7824	0.7824
GTRIG	45	-2718.3095	5532.7706	0.1515	0.9339
HKYG	40	-2724.9492	5534.7362	0.0567	0.9906
HKYIG	41	-2725.6911	5538.4693	0.0088	0.9994
GTRI	44	-2725.1200	5544.1154	0.0005	0.9999
HKYI	40	-2731.3654	5547.5686	0.0001	1.0000
K2PG	37	-2761.2577	5600.6447	0.0000	1.0000
K2PIG	38	-2760.9642	5602.2873	0.0000	1.0000
SYMG	41	-2760.9472	5608.9816	0.0000	1.0000
SYMIG	42	-2760.6606	5610.6645	0.0000	1.0000
K2PI	37	-2767.3279	5612.7850	0.0000	1.0000
SYMI	41	-2766.9493	5620.9857	0.0000	1.0000
GTR	43	-2769.5995	5630.8049	0.0000	1.0000
HKY	39	-2774.3824	5631.3598	0.0000	1.0000
F81G	39	-2779.5671	5641.7291	0.0000	1.0000
F81IG	40	-2779.2513	5643.3404	0.0000	1.0000
F81I	39	-2785.4882	5653.5714	0.0000	1.0000
JC69G	36	-2808.0144	5691.9350	0.0000	1.0000
JC69IG	37	-2807.6903	5693.5098	0.0000	1.0000
K2P	36	-2810.5650	5697.0362	0.0000	1.0000
JC69I	36	-2813.9187	5703.7436	0.0000	1.0000
SYM	40	-2810.1649	5705.1676	0.0000	1.0000
F81	38	-2828.0214	5736.4017	0.0000	1.0000
JC69	35	-2856.5610	5786.8116	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2717.8061	5523.6123	0.7850	0.7850
GTRIG	45	-2718.3095	5526.6190	0.1746	0.9596
HKYG	40	-2724.9492	5529.8984	0.0339	0.9935
HKYIG	41	-2725.6911	5533.3822	0.0059	0.9994
GTRI	44	-2725.1200	5538.2401	0.0005	0.9999
HKYI	40	-2731.3654	5542.7308	0.0001	1.0000
K2PG	37	-2761.2577	5596.5154	0.0000	1.0000
K2PIG	38	-2760.9642	5597.9285	0.0000	1.0000
SYMG	41	-2760.9472	5603.8944	0.0000	1.0000
SYMIG	42	-2760.6606	5605.3213	0.0000	1.0000
K2PI	37	-2767.3279	5608.6558	0.0000	1.0000
SYMI	41	-2766.9493	5615.8986	0.0000	1.0000
GTR	43	-2769.5995	5625.1990	0.0000	1.0000
HKY	39	-2774.3824	5626.7648	0.0000	1.0000
F81G	39	-2779.5671	5637.1341	0.0000	1.0000
F81IG	40	-2779.2513	5638.5027	0.0000	1.0000
F81I	39	-2785.4882	5648.9764	0.0000	1.0000
JC69G	36	-2808.0144	5688.0289	0.0000	1.0000
JC69IG	37	-2807.6903	5689.3806	0.0000	1.0000
K2P	36	-2810.5650	5693.1300	0.0000	1.0000
JC69I	36	-2813.9187	5699.8374	0.0000	1.0000
SYM	40	-2810.1649	5700.3299	0.0000	1.0000
F81	38	-2828.0214	5732.0429	0.0000	1.0000
JC69	35	-2856.5610	5783.1220	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2724.9492	5713.0129	0.9786	0.9786
HKYIG	41	-2725.6911	5721.0745	0.0174	0.9959
GTRG	44	-2717.8061	5725.0382	0.0024	0.9983
HKYI	40	-2731.3654	5725.8453	0.0016	0.9999
GTRIG	45	-2718.3095	5732.6228	0.0001	1.0000
GTRI	44	-2725.1200	5739.6660	0.0000	1.0000
K2PG	37	-2761.2577	5765.8963	0.0000	1.0000
K2PIG	38	-2760.9642	5771.8872	0.0000	1.0000
K2PI	37	-2767.3279	5778.0366	0.0000	1.0000
SYMG	41	-2760.9472	5791.5868	0.0000	1.0000
SYMIG	42	-2760.6606	5797.5915	0.0000	1.0000
SYMI	41	-2766.9493	5803.5909	0.0000	1.0000
HKY	39	-2774.3824	5805.3014	0.0000	1.0000
F81G	39	-2779.5671	5815.6707	0.0000	1.0000
F81IG	40	-2779.2513	5821.6171	0.0000	1.0000
GTR	43	-2769.5995	5822.0470	0.0000	1.0000
F81I	39	-2785.4882	5827.5130	0.0000	1.0000
JC69G	36	-2808.0144	5852.8319	0.0000	1.0000
K2P	36	-2810.5650	5857.9330	0.0000	1.0000
JC69IG	37	-2807.6903	5858.7615	0.0000	1.0000
JC69I	36	-2813.9187	5864.6404	0.0000	1.0000
SYM	40	-2810.1649	5883.4443	0.0000	1.0000
F81	38	-2828.0214	5906.0016	0.0000	1.0000
JC69	35	-2856.5610	5943.3472	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/chr7_11479.phylip = 1 - 719;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_11479.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/chr7_11479.phylip = 1 - 719;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_11479.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/chr7_11479.phylip = 1 - 719;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_11479.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

