
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
13:13 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/chr7_4896.phylip" (19 taxa, 519 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	-1391.2934	2878.9412	0.4760	0.4760
GTRI	44	-1391.8607	2880.0758	0.2699	0.7459
GTRIG	45	-1391.2348	2881.2223	0.1521	0.8980
HKYG	40	-1398.2794	2883.4207	0.0507	0.9487
HKYI	40	-1398.6471	2884.1560	0.0351	0.9838
HKYIG	41	-1398.2448	2885.7098	0.0161	0.9999
GTR	43	-1401.6903	2897.3470	0.0000	1.0000
HKY	39	-1408.7984	2902.1103	0.0000	1.0000
K2PG	37	-1417.6255	2915.0971	0.0000	1.0000
K2PI	37	-1417.9387	2915.7235	0.0000	1.0000
F81G	39	-1416.2390	2916.9915	0.0000	1.0000
K2PIG	38	-1417.5962	2917.3673	0.0000	1.0000
F81I	39	-1416.5531	2917.6198	0.0000	1.0000
SYMG	41	-1414.2079	2917.6358	0.0000	1.0000
SYMI	41	-1414.5929	2918.4060	0.0000	1.0000
F81IG	40	-1416.2162	2919.2944	0.0000	1.0000
SYMIG	42	-1414.1769	2919.9420	0.0000	1.0000
K2P	36	-1428.5158	2934.5585	0.0000	1.0000
SYM	40	-1424.3725	2935.6070	0.0000	1.0000
F81	38	-1426.8985	2935.9721	0.0000	1.0000
JC69G	36	-1433.7462	2945.0193	0.0000	1.0000
JC69I	36	-1434.0461	2945.6192	0.0000	1.0000
JC69IG	37	-1433.7210	2947.2882	0.0000	1.0000
JC69	35	-1444.6530	2964.5235	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1391.2934	2870.5867	0.4850	0.4850
GTRI	44	-1391.8607	2871.7214	0.2750	0.7600
GTRIG	45	-1391.2348	2872.4697	0.1892	0.9492
HKYG	40	-1398.2794	2876.5588	0.0245	0.9737
HKYI	40	-1398.6471	2877.2941	0.0170	0.9906
HKYIG	41	-1398.2448	2878.4897	0.0093	1.0000
GTR	43	-1401.6903	2889.3807	0.0000	1.0000
HKY	39	-1408.7984	2895.5967	0.0000	1.0000
K2PG	37	-1417.6255	2909.2510	0.0000	1.0000
K2PI	37	-1417.9387	2909.8773	0.0000	1.0000
SYMG	41	-1414.2079	2910.4157	0.0000	1.0000
F81G	39	-1416.2390	2910.4780	0.0000	1.0000
F81I	39	-1416.5531	2911.1062	0.0000	1.0000
SYMI	41	-1414.5929	2911.1859	0.0000	1.0000
K2PIG	38	-1417.5962	2911.1923	0.0000	1.0000
SYMIG	42	-1414.1769	2912.3538	0.0000	1.0000
F81IG	40	-1416.2162	2912.4325	0.0000	1.0000
SYM	40	-1424.3725	2928.7451	0.0000	1.0000
K2P	36	-1428.5158	2929.0316	0.0000	1.0000
F81	38	-1426.8985	2929.7971	0.0000	1.0000
JC69G	36	-1433.7462	2939.4923	0.0000	1.0000
JC69I	36	-1434.0461	2940.0922	0.0000	1.0000
JC69IG	37	-1433.7210	2941.4420	0.0000	1.0000
JC69	35	-1444.6530	2959.3061	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1398.2794	3046.6349	0.5731	0.5731
HKYI	40	-1398.6471	3047.3703	0.3968	0.9698
HKYIG	41	-1398.2448	3052.8177	0.0260	0.9959
GTRG	44	-1391.2934	3057.6705	0.0023	0.9982
GTRI	44	-1391.8607	3058.8052	0.0013	0.9995
HKY	39	-1408.7984	3061.4210	0.0004	0.9998
GTRIG	45	-1391.2348	3063.8053	0.0001	1.0000
K2PG	37	-1417.6255	3066.5714	0.0000	1.0000
K2PI	37	-1417.9387	3067.1977	0.0000	1.0000
GTR	43	-1401.6903	3072.2125	0.0000	1.0000
K2PIG	38	-1417.5962	3072.7646	0.0000	1.0000
F81G	39	-1416.2390	3076.3022	0.0000	1.0000
F81I	39	-1416.5531	3076.9305	0.0000	1.0000
K2P	36	-1428.5158	3082.1001	0.0000	1.0000
F81IG	40	-1416.2162	3082.5086	0.0000	1.0000
SYMG	41	-1414.2079	3084.7438	0.0000	1.0000
SYMI	41	-1414.5929	3085.5139	0.0000	1.0000
SYMIG	42	-1414.1769	3090.9337	0.0000	1.0000
F81	38	-1426.8985	3091.3694	0.0000	1.0000
JC69G	36	-1433.7462	3092.5609	0.0000	1.0000
JC69I	36	-1434.0461	3093.1608	0.0000	1.0000
JC69IG	37	-1433.7210	3098.7625	0.0000	1.0000
SYM	40	-1424.3725	3098.8212	0.0000	1.0000
JC69	35	-1444.6530	3108.1227	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/chr7_4896.phylip = 1 - 519;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_4896.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/chr7_4896.phylip = 1 - 519;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_4896.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/chr7_4896.phylip = 1 - 519;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_4896.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

