
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:11 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/chr11_1746.phylip" (19 taxa, 339 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	-1213.4932	2528.4557	0.5005	0.5005
HKYG	40	-1219.5527	2530.1122	0.2186	0.7191
GTRIG	45	-1213.3730	2530.8758	0.1492	0.8684
HKYIG	41	-1219.5044	2532.6048	0.0629	0.9312
GTRI	44	-1215.9286	2533.3267	0.0438	0.9751
HKYI	40	-1221.7808	2534.5683	0.0236	0.9986
SYMG	41	-1224.1556	2541.9071	0.0006	0.9992
K2PG	37	-1229.7470	2542.8361	0.0004	0.9996
SYMIG	42	-1224.0386	2544.2799	0.0002	0.9998
K2PIG	38	-1229.6838	2545.2476	0.0001	0.9999
SYMI	41	-1226.3043	2546.2046	0.0001	1.0000
K2PI	37	-1231.8089	2546.9600	0.0000	1.0000
F81G	39	-1238.8490	2566.1328	0.0000	1.0000
F81IG	40	-1238.7851	2568.5769	0.0000	1.0000
F81I	39	-1240.2674	2568.9695	0.0000	1.0000
JC69G	36	-1247.8047	2576.4307	0.0000	1.0000
JC69I	36	-1249.0733	2578.9678	0.0000	1.0000
JC69IG	37	-1248.0029	2579.3480	0.0000	1.0000
HKY	39	-1249.2677	2586.9701	0.0000	1.0000
GTR	43	-1245.1847	2589.1965	0.0000	1.0000
K2P	36	-1259.7158	2600.2528	0.0000	1.0000
SYM	40	-1255.7134	2602.4335	0.0000	1.0000
F81	38	-1268.4429	2622.7658	0.0000	1.0000
JC69	35	-1277.5351	2633.3870	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1213.4932	2514.9863	0.5904	0.5904
GTRIG	45	-1213.3730	2516.7461	0.2449	0.8353
HKYG	40	-1219.5527	2519.1054	0.0753	0.9106
GTRI	44	-1215.9286	2519.8573	0.0517	0.9623
HKYIG	41	-1219.5044	2521.0089	0.0291	0.9914
HKYI	40	-1221.7808	2523.5616	0.0081	0.9995
SYMG	41	-1224.1556	2530.3112	0.0003	0.9998
SYMIG	42	-1224.0386	2532.0772	0.0001	0.9999
K2PG	37	-1229.7470	2533.4939	0.0001	0.9999
SYMI	41	-1226.3043	2534.6087	0.0000	1.0000
K2PIG	38	-1229.6838	2535.3676	0.0000	1.0000
K2PI	37	-1231.8089	2537.6178	0.0000	1.0000
F81G	39	-1238.8490	2555.6980	0.0000	1.0000
F81IG	40	-1238.7851	2557.5702	0.0000	1.0000
F81I	39	-1240.2674	2558.5347	0.0000	1.0000
JC69G	36	-1247.8047	2567.6095	0.0000	1.0000
JC69IG	37	-1248.0029	2570.0058	0.0000	1.0000
JC69I	36	-1249.0733	2570.1466	0.0000	1.0000
GTR	43	-1245.1847	2576.3693	0.0000	1.0000
HKY	39	-1249.2677	2576.5353	0.0000	1.0000
SYM	40	-1255.7134	2591.4268	0.0000	1.0000
K2P	36	-1259.7158	2591.4316	0.0000	1.0000
F81	38	-1268.4429	2612.8858	0.0000	1.0000
JC69	35	-1277.5351	2625.0701	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1219.5527	2672.1454	0.6915	0.6915
K2PG	37	-1229.7470	2675.0559	0.1614	0.8528
HKYI	40	-1221.7808	2676.6016	0.0745	0.9273
HKYIG	41	-1219.5044	2677.8749	0.0394	0.9667
K2PI	37	-1231.8089	2679.1798	0.0205	0.9873
K2PIG	38	-1229.6838	2680.7556	0.0093	0.9966
GTRG	44	-1213.4932	2683.3303	0.0026	0.9992
SYMG	41	-1224.1556	2687.1772	0.0004	0.9995
GTRI	44	-1215.9286	2688.2013	0.0002	0.9998
GTRIG	45	-1213.3730	2688.9161	0.0002	0.9999
SYMI	41	-1226.3043	2691.4747	0.0000	1.0000
SYMIG	42	-1224.0386	2692.7692	0.0000	1.0000
F81G	39	-1238.8490	2704.9120	0.0000	1.0000
JC69G	36	-1247.8047	2705.3455	0.0000	1.0000
F81I	39	-1240.2674	2707.7487	0.0000	1.0000
JC69I	36	-1249.0733	2707.8826	0.0000	1.0000
F81IG	40	-1238.7851	2710.6102	0.0000	1.0000
JC69IG	37	-1248.0029	2711.5678	0.0000	1.0000
HKY	39	-1249.2677	2725.7493	0.0000	1.0000
K2P	36	-1259.7158	2729.1676	0.0000	1.0000
GTR	43	-1245.1847	2740.8873	0.0000	1.0000
SYM	40	-1255.7134	2744.4668	0.0000	1.0000
F81	38	-1268.4429	2758.2738	0.0000	1.0000
JC69	35	-1277.5351	2758.9801	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/chr11_1746.phylip = 1 - 339;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_1746.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/chr11_1746.phylip = 1 - 339;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_1746.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/chr11_1746.phylip = 1 - 339;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_1746.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

