
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:40 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/chr6_9640.phylip" (19 taxa, 396 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
Minimum BIC  model: GTRG


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	-1258.7754	2616.8329	0.6529	0.6529
GTRIG	45	-1258.5183	2618.8651	0.2363	0.8892
GTRI	44	-1260.5532	2620.3884	0.1103	0.9996
HKYG	40	-1271.5858	2632.4111	0.0003	0.9998
HKYIG	41	-1271.3851	2634.4991	0.0001	0.9999
HKYI	40	-1272.8725	2634.9844	0.0001	1.0000
SYMG	41	-1278.4272	2648.5832	0.0000	1.0000
SYMIG	42	-1278.2613	2650.7549	0.0000	1.0000
SYMI	41	-1279.6557	2651.0403	0.0000	1.0000
GTR	43	-1277.9875	2652.7249	0.0000	1.0000
K2PG	37	-1286.0352	2653.9251	0.0000	1.0000
K2PIG	38	-1285.8720	2656.0466	0.0000	1.0000
K2PI	37	-1287.1975	2656.2498	0.0000	1.0000
HKY	39	-1288.6512	2664.0665	0.0000	1.0000
SYM	40	-1295.3843	2680.0080	0.0000	1.0000
K2P	36	-1302.5456	2684.5117	0.0000	1.0000
F81G	39	-1304.2740	2695.3119	0.0000	1.0000
F81IG	40	-1303.1900	2695.6195	0.0000	1.0000
F81I	39	-1305.3981	2697.5602	0.0000	1.0000
JC69G	36	-1315.0273	2709.4752	0.0000	1.0000
JC69I	36	-1316.1074	2711.6355	0.0000	1.0000
JC69IG	37	-1314.8949	2711.6445	0.0000	1.0000
F81	38	-1320.3327	2724.9679	0.0000	1.0000
JC69	35	-1331.0089	2739.0179	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1258.7754	2605.5508	0.6079	0.6079
GTRIG	45	-1258.5183	2607.0365	0.2892	0.8971
GTRI	44	-1260.5532	2609.1064	0.1027	0.9998
HKYG	40	-1271.5858	2623.1716	0.0001	0.9999
HKYIG	41	-1271.3851	2624.7703	0.0000	1.0000
HKYI	40	-1272.8725	2625.7450	0.0000	1.0000
SYMG	41	-1278.4272	2638.8544	0.0000	1.0000
SYMIG	42	-1278.2613	2640.5226	0.0000	1.0000
SYMI	41	-1279.6557	2641.3115	0.0000	1.0000
GTR	43	-1277.9875	2641.9749	0.0000	1.0000
K2PG	37	-1286.0352	2646.0703	0.0000	1.0000
K2PIG	38	-1285.8720	2647.7440	0.0000	1.0000
K2PI	37	-1287.1975	2648.3950	0.0000	1.0000
HKY	39	-1288.6512	2655.3024	0.0000	1.0000
SYM	40	-1295.3843	2670.7685	0.0000	1.0000
K2P	36	-1302.5456	2677.0911	0.0000	1.0000
F81IG	40	-1303.1900	2686.3801	0.0000	1.0000
F81G	39	-1304.2740	2686.5479	0.0000	1.0000
F81I	39	-1305.3981	2688.7961	0.0000	1.0000
JC69G	36	-1315.0273	2702.0546	0.0000	1.0000
JC69IG	37	-1314.8949	2703.7898	0.0000	1.0000
JC69I	36	-1316.1074	2704.2149	0.0000	1.0000
F81	38	-1320.3327	2716.6654	0.0000	1.0000
JC69	35	-1331.0089	2732.0179	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
GTRG	44	-1258.7754	2780.7330	0.5526	0.5526
HKYG	40	-1271.5858	2782.4282	0.2368	0.7894
GTRI	44	-1260.5532	2784.2886	0.0934	0.8828
HKYI	40	-1272.8725	2785.0015	0.0654	0.9482
GTRIG	45	-1258.5183	2786.2002	0.0359	0.9841
HKYIG	41	-1271.3851	2788.0083	0.0145	0.9986
K2PG	37	-1286.0352	2793.3827	0.0010	0.9996
K2PI	37	-1287.1975	2795.7073	0.0003	0.9999
K2PIG	38	-1285.8720	2799.0378	0.0001	1.0000
SYMG	41	-1278.4272	2802.0924	0.0000	1.0000
SYMI	41	-1279.6557	2804.5495	0.0000	1.0000
SYMIG	42	-1278.2613	2807.7420	0.0000	1.0000
HKY	39	-1288.6512	2810.5776	0.0000	1.0000
GTR	43	-1277.9875	2813.1758	0.0000	1.0000
K2P	36	-1302.5456	2820.4220	0.0000	1.0000
SYM	40	-1295.3843	2830.0251	0.0000	1.0000
F81G	39	-1304.2740	2841.8231	0.0000	1.0000
F81I	39	-1305.3981	2844.0713	0.0000	1.0000
JC69G	36	-1315.0273	2845.3855	0.0000	1.0000
F81IG	40	-1303.1900	2845.6366	0.0000	1.0000
JC69I	36	-1316.1074	2847.5458	0.0000	1.0000
JC69IG	37	-1314.8949	2851.1021	0.0000	1.0000
F81	38	-1320.3327	2867.9591	0.0000	1.0000
JC69	35	-1331.0089	2871.3674	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/chr6_9640.phylip = 1 - 396;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_9640.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/chr6_9640.phylip = 1 - 396;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_9640.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 (GTRG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_9640.phylip = 1 - 396;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_9640.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;


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End of Output

