
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:22 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/chr1_5468.phylip" (19 taxa, 436 characters)

Minimum AIC  model: GTRG
Minimum AICc model: HKYG
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
HKYG	40	-1317.1000	2722.5038	0.3403	0.3403
GTRG	44	-1312.4430	2723.0138	0.2637	0.6039
HKYIG	41	-1316.5869	2723.9150	0.1680	0.7720
GTRIG	45	-1311.9400	2724.4954	0.1257	0.8977
HKYI	40	-1318.8084	2725.9207	0.0616	0.9593
GTRI	44	-1314.3115	2726.7508	0.0407	1.0000
K2PG	37	-1332.8949	2746.8552	0.0000	1.0000
K2PIG	38	-1332.5316	2748.5292	0.0000	1.0000
K2PI	37	-1334.0071	2749.0794	0.0000	1.0000
SYMG	41	-1331.2547	2753.2505	0.0000	1.0000
SYMIG	42	-1330.7229	2754.6367	0.0000	1.0000
SYMI	41	-1332.6970	2756.1350	0.0000	1.0000
HKY	39	-1339.5785	2765.0359	0.0000	1.0000
GTR	43	-1334.7154	2765.0839	0.0000	1.0000
K2P	36	-1356.1002	2790.8770	0.0000	1.0000
F81G	39	-1353.9382	2793.7551	0.0000	1.0000
F81IG	40	-1353.4859	2795.2755	0.0000	1.0000
F81I	39	-1355.5126	2796.9040	0.0000	1.0000
SYM	40	-1354.9439	2798.1915	0.0000	1.0000
JC69G	36	-1368.3049	2815.2865	0.0000	1.0000
JC69IG	37	-1367.7809	2816.6272	0.0000	1.0000
JC69I	36	-1369.8994	2818.4756	0.0000	1.0000
F81	38	-1375.3572	2834.1803	0.0000	1.0000
JC69	35	-1390.6924	2857.6848	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1312.4430	2712.8859	0.3713	0.3713
GTRIG	45	-1311.9400	2713.8800	0.2259	0.5971
HKYG	40	-1317.1000	2714.2000	0.1925	0.7896
HKYIG	41	-1316.5869	2715.1738	0.1183	0.9078
GTRI	44	-1314.3115	2716.6229	0.0573	0.9651
HKYI	40	-1318.8084	2717.6169	0.0349	1.0000
K2PG	37	-1332.8949	2739.7898	0.0000	1.0000
K2PIG	38	-1332.5316	2741.0632	0.0000	1.0000
K2PI	37	-1334.0071	2742.0141	0.0000	1.0000
SYMG	41	-1331.2547	2744.5094	0.0000	1.0000
SYMIG	42	-1330.7229	2745.4459	0.0000	1.0000
SYMI	41	-1332.6970	2747.3939	0.0000	1.0000
GTR	43	-1334.7154	2755.4309	0.0000	1.0000
HKY	39	-1339.5785	2757.1571	0.0000	1.0000
K2P	36	-1356.1002	2784.2003	0.0000	1.0000
F81G	39	-1353.9382	2785.8764	0.0000	1.0000
F81IG	40	-1353.4859	2786.9717	0.0000	1.0000
F81I	39	-1355.5126	2789.0252	0.0000	1.0000
SYM	40	-1354.9439	2789.8877	0.0000	1.0000
JC69G	36	-1368.3049	2808.6098	0.0000	1.0000
JC69IG	37	-1367.7809	2809.5619	0.0000	1.0000
JC69I	36	-1369.8994	2811.7989	0.0000	1.0000
F81	38	-1375.3572	2826.7143	0.0000	1.0000
JC69	35	-1390.6924	2851.3848	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1317.1000	2877.3057	0.7914	0.7914
HKYI	40	-1318.8084	2880.7226	0.1434	0.9348
HKYIG	41	-1316.5869	2882.3572	0.0633	0.9981
K2PG	37	-1332.8949	2890.6626	0.0010	0.9991
GTRG	44	-1312.4430	2892.3022	0.0004	0.9995
K2PI	37	-1334.0071	2892.8869	0.0003	0.9998
K2PIG	38	-1332.5316	2896.0136	0.0001	0.9999
GTRI	44	-1314.3115	2896.0392	0.0001	1.0000
GTRIG	45	-1311.9400	2897.3739	0.0000	1.0000
SYMG	41	-1331.2547	2911.6927	0.0000	1.0000
SYMI	41	-1332.6970	2914.5773	0.0000	1.0000
HKY	39	-1339.5785	2916.1851	0.0000	1.0000
SYMIG	42	-1330.7229	2916.7068	0.0000	1.0000
GTR	43	-1334.7154	2930.7695	0.0000	1.0000
K2P	36	-1356.1002	2930.9954	0.0000	1.0000
F81G	39	-1353.9382	2944.9044	0.0000	1.0000
F81I	39	-1355.5126	2948.0532	0.0000	1.0000
F81IG	40	-1353.4859	2950.0774	0.0000	1.0000
SYM	40	-1354.9439	2952.9934	0.0000	1.0000
JC69G	36	-1368.3049	2955.4049	0.0000	1.0000
JC69I	36	-1369.8994	2958.5940	0.0000	1.0000
JC69IG	37	-1367.7809	2960.4346	0.0000	1.0000
F81	38	-1375.3572	2981.6647	0.0000	1.0000
JC69	35	-1390.6924	2994.1022	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/chr1_5468.phylip = 1 - 436;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_5468.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 (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_5468.phylip = 1 - 436;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_5468.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;


[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/chr1_5468.phylip = 1 - 436;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_5468.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

