
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:25 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/chr5_11219.phylip" (19 taxa, 766 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	-2791.8416	5677.1756	0.9822	0.9822
GTRIG	45	-2794.8559	5685.4618	0.0156	0.9978
GTRI	44	-2798.4495	5690.3914	0.0013	0.9991
HKYG	40	-2803.3845	5691.2932	0.0008	0.9999
HKYIG	41	-2804.7564	5696.2697	0.0001	1.0000
HKYI	40	-2808.0118	5700.5477	0.0000	1.0000
F81G	39	-2831.7807	5745.8588	0.0000	1.0000
F81IG	40	-2834.3662	5753.2565	0.0000	1.0000
F81I	39	-2835.8607	5754.0188	0.0000	1.0000
SYMG	41	-2842.7762	5772.3092	0.0000	1.0000
SYMIG	42	-2844.1374	5777.2707	0.0000	1.0000
SYMI	41	-2846.5276	5779.8120	0.0000	1.0000
K2PG	37	-2855.0343	5787.9313	0.0000	1.0000
K2PIG	38	-2855.7196	5791.5162	0.0000	1.0000
K2PI	37	-2857.5353	5792.9333	0.0000	1.0000
GTR	43	-2859.4722	5810.1854	0.0000	1.0000
HKY	39	-2870.5843	5823.4662	0.0000	1.0000
JC69G	36	-2875.4882	5826.6308	0.0000	1.0000
JC69IG	37	-2874.9800	5827.8227	0.0000	1.0000
JC69I	36	-2879.4295	5834.5133	0.0000	1.0000
F81	38	-2896.1151	5872.3072	0.0000	1.0000
SYM	40	-2902.6548	5889.8337	0.0000	1.0000
K2P	36	-2916.2436	5908.1414	0.0000	1.0000
JC69	35	-2936.8005	5947.0530	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2791.8416	5671.6832	0.9804	0.9804
GTRIG	45	-2794.8559	5679.7118	0.0177	0.9981
GTRI	44	-2798.4495	5684.8991	0.0013	0.9994
HKYG	40	-2803.3845	5686.7691	0.0005	0.9999
HKYIG	41	-2804.7564	5691.5128	0.0000	1.0000
HKYI	40	-2808.0118	5696.0236	0.0000	1.0000
F81G	39	-2831.7807	5741.5613	0.0000	1.0000
F81IG	40	-2834.3662	5748.7324	0.0000	1.0000
F81I	39	-2835.8607	5749.7213	0.0000	1.0000
SYMG	41	-2842.7762	5767.5523	0.0000	1.0000
SYMIG	42	-2844.1374	5772.2749	0.0000	1.0000
SYMI	41	-2846.5276	5775.0551	0.0000	1.0000
K2PG	37	-2855.0343	5784.0687	0.0000	1.0000
K2PIG	38	-2855.7196	5787.4392	0.0000	1.0000
K2PI	37	-2857.5353	5789.0706	0.0000	1.0000
GTR	43	-2859.4722	5804.9444	0.0000	1.0000
HKY	39	-2870.5843	5819.1686	0.0000	1.0000
JC69G	36	-2875.4882	5822.9764	0.0000	1.0000
JC69IG	37	-2874.9800	5823.9600	0.0000	1.0000
JC69I	36	-2879.4295	5830.8590	0.0000	1.0000
F81	38	-2896.1151	5868.2302	0.0000	1.0000
SYM	40	-2902.6548	5885.3096	0.0000	1.0000
K2P	36	-2916.2436	5904.4871	0.0000	1.0000
JC69	35	-2936.8005	5943.6010	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2803.3845	5872.4163	0.8367	0.8367
GTRG	44	-2791.8416	5875.8952	0.1469	0.9837
HKYI	40	-2808.0118	5881.6709	0.0082	0.9919
HKYIG	41	-2804.7564	5881.8013	0.0077	0.9995
GTRIG	45	-2794.8559	5888.5650	0.0003	0.9998
GTRI	44	-2798.4495	5889.1111	0.0002	1.0000
F81G	39	-2831.7807	5922.5674	0.0000	1.0000
F81I	39	-2835.8607	5930.7274	0.0000	1.0000
F81IG	40	-2834.3662	5934.3797	0.0000	1.0000
K2PG	37	-2855.0343	5955.7924	0.0000	1.0000
SYMG	41	-2842.7762	5957.8408	0.0000	1.0000
K2PI	37	-2857.5353	5960.7944	0.0000	1.0000
K2PIG	38	-2855.7196	5963.8041	0.0000	1.0000
SYMI	41	-2846.5276	5965.3436	0.0000	1.0000
SYMIG	42	-2844.1374	5967.2045	0.0000	1.0000
JC69G	36	-2875.4882	5990.0590	0.0000	1.0000
JC69IG	37	-2874.9800	5995.6838	0.0000	1.0000
JC69I	36	-2879.4295	5997.9415	0.0000	1.0000
HKY	39	-2870.5843	6000.1747	0.0000	1.0000
GTR	43	-2859.4722	6004.5153	0.0000	1.0000
F81	38	-2896.1151	6044.5951	0.0000	1.0000
SYM	40	-2902.6548	6070.9569	0.0000	1.0000
K2P	36	-2916.2436	6071.5697	0.0000	1.0000
JC69	35	-2936.8005	6106.0424	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/chr5_11219.phylip = 1 - 766;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_11219.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/chr5_11219.phylip = 1 - 766;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_11219.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/chr5_11219.phylip = 1 - 766;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_11219.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

