
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:50 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/chr2_7512.phylip" (19 taxa, 378 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	-1277.4406	2654.7731	0.9000	0.9000
GTRIG	45	-1279.1166	2660.7032	0.0464	0.9464
HKYG	40	-1285.5420	2660.8170	0.0438	0.9903
GTRI	44	-1282.5319	2664.9557	0.0055	0.9958
HKYIG	41	-1286.6959	2665.6419	0.0039	0.9997
HKYI	40	-1290.6485	2671.0300	0.0003	1.0000
SYMG	41	-1297.1184	2686.4867	0.0000	1.0000
K2PG	37	-1302.2564	2686.7833	0.0000	1.0000
K2PIG	38	-1301.2918	2687.3270	0.0000	1.0000
SYMIG	42	-1296.5399	2687.8619	0.0000	1.0000
SYMI	41	-1299.3401	2690.9301	0.0000	1.0000
K2PI	37	-1304.9740	2692.2185	0.0000	1.0000
GTR	43	-1301.3492	2700.0277	0.0000	1.0000
HKY	39	-1311.2131	2709.6569	0.0000	1.0000
F81G	39	-1317.3977	2722.0262	0.0000	1.0000
F81IG	40	-1316.6660	2723.0650	0.0000	1.0000
F81I	39	-1319.9575	2727.1458	0.0000	1.0000
JC69G	36	-1330.1610	2740.1343	0.0000	1.0000
JC69IG	37	-1329.3955	2741.0615	0.0000	1.0000
JC69I	36	-1332.6206	2745.0535	0.0000	1.0000
SYM	40	-1327.8905	2745.5139	0.0000	1.0000
K2P	36	-1334.1354	2748.0832	0.0000	1.0000
F81	38	-1343.1411	2771.0256	0.0000	1.0000
JC69	35	-1360.4636	2798.2956	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1277.4406	2642.8812	0.9144	0.9144
GTRIG	45	-1279.1166	2648.2333	0.0629	0.9774
HKYG	40	-1285.5420	2651.0840	0.0151	0.9925
GTRI	44	-1282.5319	2653.0638	0.0056	0.9982
HKYIG	41	-1286.6959	2655.3919	0.0018	0.9999
HKYI	40	-1290.6485	2661.2970	0.0001	1.0000
SYMG	41	-1297.1184	2676.2367	0.0000	1.0000
SYMIG	42	-1296.5399	2677.0798	0.0000	1.0000
K2PG	37	-1302.2564	2678.5127	0.0000	1.0000
K2PIG	38	-1301.2918	2678.5836	0.0000	1.0000
SYMI	41	-1299.3401	2680.6801	0.0000	1.0000
K2PI	37	-1304.9740	2683.9479	0.0000	1.0000
GTR	43	-1301.3492	2688.6984	0.0000	1.0000
HKY	39	-1311.2131	2700.4261	0.0000	1.0000
F81G	39	-1317.3977	2712.7955	0.0000	1.0000
F81IG	40	-1316.6660	2713.3321	0.0000	1.0000
F81I	39	-1319.9575	2717.9150	0.0000	1.0000
JC69G	36	-1330.1610	2732.3220	0.0000	1.0000
JC69IG	37	-1329.3955	2732.7910	0.0000	1.0000
SYM	40	-1327.8905	2735.7810	0.0000	1.0000
JC69I	36	-1332.6206	2737.2412	0.0000	1.0000
K2P	36	-1334.1354	2740.2709	0.0000	1.0000
F81	38	-1343.1411	2762.2822	0.0000	1.0000
JC69	35	-1360.4636	2790.9272	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1285.5420	2808.4798	0.9558	0.9558
GTRG	44	-1277.4406	2816.0165	0.0221	0.9779
HKYIG	41	-1286.6959	2816.7225	0.0155	0.9934
HKYI	40	-1290.6485	2818.6928	0.0058	0.9992
K2PG	37	-1302.2564	2824.1038	0.0004	0.9996
GTRIG	45	-1279.1166	2825.3035	0.0002	0.9998
GTRI	44	-1282.5319	2826.1991	0.0001	0.9999
K2PIG	38	-1301.2918	2828.1096	0.0001	1.0000
K2PI	37	-1304.9740	2829.5390	0.0000	1.0000
SYMG	41	-1297.1184	2837.5674	0.0000	1.0000
SYMI	41	-1299.3401	2842.0108	0.0000	1.0000
SYMIG	42	-1296.5399	2842.3454	0.0000	1.0000
HKY	39	-1311.2131	2853.8870	0.0000	1.0000
GTR	43	-1301.3492	2857.8988	0.0000	1.0000
F81G	39	-1317.3977	2866.2564	0.0000	1.0000
F81IG	40	-1316.6660	2870.7278	0.0000	1.0000
F81I	39	-1319.9575	2871.3759	0.0000	1.0000
JC69G	36	-1330.1610	2873.9782	0.0000	1.0000
JC69IG	37	-1329.3955	2878.3820	0.0000	1.0000
JC69I	36	-1332.6206	2878.8974	0.0000	1.0000
K2P	36	-1334.1354	2881.9271	0.0000	1.0000
SYM	40	-1327.8905	2893.1767	0.0000	1.0000
F81	38	-1343.1411	2911.8082	0.0000	1.0000
JC69	35	-1360.4636	2928.6485	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/chr2_7512.phylip = 1 - 378;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_7512.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/chr2_7512.phylip = 1 - 378;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_7512.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/chr2_7512.phylip = 1 - 378;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_7512.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

