
Output from mraic.pl version 1.4.4 by Johan Nylander
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13:23 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/chrZ_532.phylip" (19 taxa, 892 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	-2721.2471	5535.1695	0.9193	0.9193
GTRIG	45	-2722.6373	5540.1682	0.0755	0.9948
HKYIG	41	-2730.0741	5546.1999	0.0037	0.9985
HKYG	40	-2732.1211	5548.0966	0.0014	0.9999
GTRI	44	-2730.6488	5553.9729	0.0001	1.0000
HKYI	40	-2739.2807	5562.4157	0.0000	1.0000
F81IG	40	-2775.9106	5635.6755	0.0000	1.0000
SYMG	41	-2775.7014	5637.4545	0.0000	1.0000
K2PIG	38	-2779.3318	5638.1384	0.0000	1.0000
F81G	39	-2779.0754	5639.8128	0.0000	1.0000
K2PG	37	-2782.2533	5641.7994	0.0000	1.0000
SYMIG	42	-2779.0935	5646.4414	0.0000	1.0000
F81I	39	-2785.3790	5652.4200	0.0000	1.0000
K2PI	37	-2789.6927	5656.6781	0.0000	1.0000
SYMI	41	-2789.1637	5664.3791	0.0000	1.0000
GTR	43	-2804.3717	5699.2056	0.0000	1.0000
HKY	39	-2812.2596	5706.1811	0.0000	1.0000
JC69IG	37	-2824.4016	5726.0959	0.0000	1.0000
JC69G	36	-2826.5887	5728.2932	0.0000	1.0000
JC69I	36	-2834.2768	5743.6693	0.0000	1.0000
SYM	40	-2856.5240	5796.9023	0.0000	1.0000
F81	38	-2862.3005	5804.0759	0.0000	1.0000
K2P	36	-2864.6903	5804.4964	0.0000	1.0000
JC69	35	-2910.3992	5893.7424	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2721.2471	5530.4941	0.9127	0.9127
GTRIG	45	-2722.6373	5535.2746	0.0836	0.9963
HKYIG	41	-2730.0741	5542.1481	0.0027	0.9990
HKYG	40	-2732.1211	5544.2423	0.0009	0.9999
GTRI	44	-2730.6488	5549.2976	0.0001	1.0000
HKYI	40	-2739.2807	5558.5615	0.0000	1.0000
F81IG	40	-2775.9106	5631.8212	0.0000	1.0000
SYMG	41	-2775.7014	5633.4027	0.0000	1.0000
K2PIG	38	-2779.3318	5634.6636	0.0000	1.0000
F81G	39	-2779.0754	5636.1509	0.0000	1.0000
K2PG	37	-2782.2533	5638.5067	0.0000	1.0000
SYMIG	42	-2779.0935	5642.1870	0.0000	1.0000
F81I	39	-2785.3790	5648.7580	0.0000	1.0000
K2PI	37	-2789.6927	5653.3853	0.0000	1.0000
SYMI	41	-2789.1637	5660.3274	0.0000	1.0000
GTR	43	-2804.3717	5694.7434	0.0000	1.0000
HKY	39	-2812.2596	5702.5191	0.0000	1.0000
JC69IG	37	-2824.4016	5722.8032	0.0000	1.0000
JC69G	36	-2826.5887	5725.1774	0.0000	1.0000
JC69I	36	-2834.2768	5740.5535	0.0000	1.0000
SYM	40	-2856.5240	5793.0480	0.0000	1.0000
F81	38	-2862.3005	5800.6011	0.0000	1.0000
K2P	36	-2864.6903	5801.3806	0.0000	1.0000
JC69	35	-2910.3992	5890.7985	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2732.1211	5735.9809	0.7536	0.7536
HKYIG	41	-2730.0741	5738.6802	0.1954	0.9490
GTRG	44	-2721.2471	5741.4066	0.0500	0.9990
HKYI	40	-2739.2807	5750.3001	0.0006	0.9996
GTRIG	45	-2722.6373	5750.9805	0.0004	1.0000
GTRI	44	-2730.6488	5760.2101	0.0000	1.0000
K2PG	37	-2782.2533	5815.8649	0.0000	1.0000
K2PIG	38	-2779.3318	5816.8153	0.0000	1.0000
F81G	39	-2779.0754	5823.0960	0.0000	1.0000
F81IG	40	-2775.9106	5823.5598	0.0000	1.0000
SYMG	41	-2775.7014	5829.9349	0.0000	1.0000
K2PI	37	-2789.6927	5830.7436	0.0000	1.0000
F81I	39	-2785.3790	5835.7032	0.0000	1.0000
SYMIG	42	-2779.0935	5843.5126	0.0000	1.0000
SYMI	41	-2789.1637	5856.8595	0.0000	1.0000
HKY	39	-2812.2596	5889.4643	0.0000	1.0000
JC69G	36	-2826.5887	5897.7422	0.0000	1.0000
JC69IG	37	-2824.4016	5900.1614	0.0000	1.0000
GTR	43	-2804.3717	5900.8624	0.0000	1.0000
JC69I	36	-2834.2768	5913.1183	0.0000	1.0000
K2P	36	-2864.6903	5973.9454	0.0000	1.0000
F81	38	-2862.3005	5982.7528	0.0000	1.0000
SYM	40	-2856.5240	5984.7867	0.0000	1.0000
JC69	35	-2910.3992	6058.5698	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/chrZ_532.phylip = 1 - 892;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_532.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/chrZ_532.phylip = 1 - 892;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_532.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/chrZ_532.phylip = 1 - 892;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_532.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

