
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:13 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_32333.phylip" (19 taxa, 462 characters)

Minimum AIC  model: HKYG
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	-1238.8535	2565.4980	0.4268	0.4268
HKYIG	41	-1238.2395	2566.6790	0.2365	0.6633
HKYI	40	-1239.5094	2566.8097	0.2215	0.8848
GTRG	44	-1236.0173	2569.5309	0.0568	0.9417
GTRIG	45	-1235.4513	2570.8545	0.0293	0.9710
GTRI	44	-1236.6898	2570.8760	0.0290	1.0000
K2PG	37	-1253.0608	2586.7536	0.0000	1.0000
K2PIG	38	-1252.3389	2587.6849	0.0000	1.0000
K2PI	37	-1253.6927	2588.0174	0.0000	1.0000
SYMG	41	-1251.8272	2593.8544	0.0000	1.0000
SYMIG	42	-1251.1430	2594.9065	0.0000	1.0000
SYMI	41	-1252.4649	2595.1298	0.0000	1.0000
HKY	39	-1257.6240	2600.6413	0.0000	1.0000
GTR	43	-1253.9973	2603.0472	0.0000	1.0000
F81G	39	-1260.8162	2607.0258	0.0000	1.0000
F81I	39	-1261.4090	2608.2114	0.0000	1.0000
F81IG	40	-1260.3046	2608.4002	0.0000	1.0000
K2P	36	-1273.1000	2624.4682	0.0000	1.0000
JC69G	36	-1273.7645	2625.7973	0.0000	1.0000
JC69I	36	-1274.3601	2626.9883	0.0000	1.0000
JC69IG	37	-1273.1917	2627.0154	0.0000	1.0000
SYM	40	-1271.2429	2630.2768	0.0000	1.0000
F81	38	-1279.8342	2642.6755	0.0000	1.0000
JC69	35	-1293.4057	2662.7269	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-1238.8535	2557.7071	0.3481	0.3481
HKYIG	41	-1238.2395	2558.4790	0.2366	0.5847
HKYI	40	-1239.5094	2559.0187	0.1807	0.7654
GTRG	44	-1236.0173	2560.0345	0.1087	0.8741
GTRIG	45	-1235.4513	2560.9026	0.0704	0.9445
GTRI	44	-1236.6898	2561.3796	0.0555	1.0000
K2PG	37	-1253.0608	2580.1215	0.0000	1.0000
K2PIG	38	-1252.3389	2580.6778	0.0000	1.0000
K2PI	37	-1253.6927	2581.3854	0.0000	1.0000
SYMG	41	-1251.8272	2585.6544	0.0000	1.0000
SYMIG	42	-1251.1430	2586.2860	0.0000	1.0000
SYMI	41	-1252.4649	2586.9298	0.0000	1.0000
HKY	39	-1257.6240	2593.2480	0.0000	1.0000
GTR	43	-1253.9973	2593.9946	0.0000	1.0000
F81G	39	-1260.8162	2599.6325	0.0000	1.0000
F81IG	40	-1260.3046	2600.6093	0.0000	1.0000
F81I	39	-1261.4090	2600.8180	0.0000	1.0000
K2P	36	-1273.1000	2618.1999	0.0000	1.0000
JC69G	36	-1273.7645	2619.5290	0.0000	1.0000
JC69IG	37	-1273.1917	2620.3833	0.0000	1.0000
JC69I	36	-1274.3601	2620.7201	0.0000	1.0000
SYM	40	-1271.2429	2622.4858	0.0000	1.0000
F81	38	-1279.8342	2635.6684	0.0000	1.0000
JC69	35	-1293.4057	2656.8114	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1238.8535	2723.1297	0.6188	0.6188
HKYI	40	-1239.5094	2724.4413	0.3212	0.9400
HKYIG	41	-1238.2395	2728.0371	0.0532	0.9932
K2PG	37	-1253.0608	2733.1374	0.0042	0.9973
K2PI	37	-1253.6927	2734.4013	0.0022	0.9995
K2PIG	38	-1252.3389	2737.8293	0.0004	0.9999
GTRG	44	-1236.0173	2741.9994	0.0000	1.0000
GTRI	44	-1236.6898	2743.3445	0.0000	1.0000
GTRIG	45	-1235.4513	2747.0030	0.0000	1.0000
HKY	39	-1257.6240	2754.5350	0.0000	1.0000
SYMG	41	-1251.8272	2755.2126	0.0000	1.0000
SYMI	41	-1252.4649	2756.4879	0.0000	1.0000
SYMIG	42	-1251.1430	2759.9797	0.0000	1.0000
F81G	39	-1260.8162	2760.9195	0.0000	1.0000
F81I	39	-1261.4090	2762.1051	0.0000	1.0000
F81IG	40	-1260.3046	2766.0319	0.0000	1.0000
K2P	36	-1273.1000	2767.0803	0.0000	1.0000
JC69G	36	-1273.7645	2768.4094	0.0000	1.0000
JC69I	36	-1274.3601	2769.6004	0.0000	1.0000
GTR	43	-1253.9973	2771.8239	0.0000	1.0000
JC69IG	37	-1273.1917	2773.3992	0.0000	1.0000
SYM	40	-1271.2429	2787.9084	0.0000	1.0000
F81	38	-1279.8342	2792.8198	0.0000	1.0000
JC69	35	-1293.4057	2801.5562	0.0000	1.0000



To specify default values for best AIC, AICc, or BIC models in MrBayes:

[Mrbayes block for the best AIC model (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_32333.phylip = 1 - 462;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_32333.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 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_32333.phylip = 1 - 462;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_32333.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_32333.phylip = 1 - 462;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_32333.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;


-------------------------------------------------------------
End of Output

