
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:49 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_10618.phylip" (19 taxa, 575 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	-1301.5197	2698.5111	0.4179	0.4179
GTRI	44	-1301.7904	2699.0525	0.3188	0.7367
GTRIG	45	-1301.3275	2700.4811	0.1561	0.8928
HKYG	40	-1308.3352	2702.8126	0.0486	0.9415
HKYI	40	-1308.5085	2703.1592	0.0409	0.9824
HKYIG	41	-1308.1907	2704.8429	0.0176	1.0000
GTR	43	-1313.0514	2719.2290	0.0000	1.0000
HKY	39	-1319.5428	2722.9174	0.0000	1.0000
F81G	39	-1328.0598	2739.9513	0.0000	1.0000
F81I	39	-1328.1823	2740.1963	0.0000	1.0000
F81IG	40	-1327.9921	2742.1264	0.0000	1.0000
F81	38	-1338.7495	2759.0289	0.0000	1.0000
K2PG	37	-1349.8439	2778.9243	0.0000	1.0000
K2PI	37	-1349.9260	2779.0884	0.0000	1.0000
K2PIG	38	-1349.7797	2781.0892	0.0000	1.0000
SYMG	41	-1346.5859	2781.6333	0.0000	1.0000
SYMI	41	-1346.6684	2781.7983	0.0000	1.0000
SYMIG	42	-1346.5418	2783.8731	0.0000	1.0000
K2P	36	-1361.3853	2799.7222	0.0000	1.0000
SYM	40	-1357.7954	2801.7332	0.0000	1.0000
JC69G	36	-1365.7095	2808.3707	0.0000	1.0000
JC69I	36	-1365.7938	2808.5393	0.0000	1.0000
JC69IG	37	-1365.6656	2810.5676	0.0000	1.0000
JC69	35	-1376.6135	2827.9023	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1301.5197	2691.0394	0.4266	0.4266
GTRI	44	-1301.7904	2691.5808	0.3254	0.7519
GTRIG	45	-1301.3275	2692.6551	0.1902	0.9421
HKYG	40	-1308.3352	2696.6703	0.0255	0.9677
HKYI	40	-1308.5085	2697.0169	0.0215	0.9891
HKYIG	41	-1308.1907	2698.3813	0.0109	1.0000
GTR	43	-1313.0514	2712.1029	0.0000	1.0000
HKY	39	-1319.5428	2717.0856	0.0000	1.0000
F81G	39	-1328.0598	2734.1195	0.0000	1.0000
F81I	39	-1328.1823	2734.3645	0.0000	1.0000
F81IG	40	-1327.9921	2735.9841	0.0000	1.0000
F81	38	-1338.7495	2753.4990	0.0000	1.0000
K2PG	37	-1349.8439	2773.6878	0.0000	1.0000
K2PI	37	-1349.9260	2773.8519	0.0000	1.0000
SYMG	41	-1346.5859	2775.1717	0.0000	1.0000
SYMI	41	-1346.6684	2775.3367	0.0000	1.0000
K2PIG	38	-1349.7797	2775.5594	0.0000	1.0000
SYMIG	42	-1346.5418	2777.0836	0.0000	1.0000
K2P	36	-1361.3853	2794.7705	0.0000	1.0000
SYM	40	-1357.7954	2795.5909	0.0000	1.0000
JC69G	36	-1365.7095	2803.4190	0.0000	1.0000
JC69I	36	-1365.7938	2803.5876	0.0000	1.0000
JC69IG	37	-1365.6656	2805.3311	0.0000	1.0000
JC69	35	-1376.6135	2823.2270	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1308.3352	2870.8451	0.5279	0.5279
HKYI	40	-1308.5085	2871.1917	0.4439	0.9718
HKYIG	41	-1308.1907	2876.9105	0.0254	0.9972
GTRG	44	-1301.5197	2882.6317	0.0015	0.9986
GTRI	44	-1301.7904	2883.1730	0.0011	0.9998
HKY	39	-1319.5428	2886.9061	0.0002	0.9999
GTRIG	45	-1301.3275	2888.6017	0.0001	1.0000
GTR	43	-1313.0514	2899.3408	0.0000	1.0000
F81G	39	-1328.0598	2903.9400	0.0000	1.0000
F81I	39	-1328.1823	2904.1850	0.0000	1.0000
F81IG	40	-1327.9921	2910.1589	0.0000	1.0000
F81	38	-1338.7495	2918.9651	0.0000	1.0000
K2PG	37	-1349.8439	2934.7995	0.0000	1.0000
K2PI	37	-1349.9260	2934.9636	0.0000	1.0000
K2PIG	38	-1349.7797	2941.0254	0.0000	1.0000
K2P	36	-1361.3853	2951.5279	0.0000	1.0000
SYMG	41	-1346.5859	2953.7009	0.0000	1.0000
SYMI	41	-1346.6684	2953.8659	0.0000	1.0000
SYMIG	42	-1346.5418	2959.9671	0.0000	1.0000
JC69G	36	-1365.7095	2960.1764	0.0000	1.0000
JC69I	36	-1365.7938	2960.3449	0.0000	1.0000
JC69IG	37	-1365.6656	2966.4428	0.0000	1.0000
SYM	40	-1357.7954	2969.7657	0.0000	1.0000
JC69	35	-1376.6135	2975.6299	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_10618.phylip = 1 - 575;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10618.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_10618.phylip = 1 - 575;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10618.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_10618.phylip = 1 - 575;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10618.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

