
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:12 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/chr13_710.phylip" (19 taxa, 557 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	-1336.4769	2759.3103	0.3728	0.3728
HKYI	40	-1336.5527	2759.4620	0.3456	0.7184
GTRG	44	-1333.2031	2762.1406	0.0906	0.8090
GTRI	44	-1333.3094	2762.3532	0.0814	0.8904
HKYIG	41	-1336.8438	2762.3750	0.0805	0.9709
GTRIG	45	-1333.1554	2764.4126	0.0291	1.0000
HKY	39	-1349.3597	2782.7542	0.0000	1.0000
K2PG	37	-1353.2853	2785.9888	0.0000	1.0000
K2PI	37	-1353.4593	2786.3366	0.0000	1.0000
K2PIG	38	-1353.0214	2787.7648	0.0000	1.0000
GTR	43	-1347.1963	2787.7689	0.0000	1.0000
SYMG	41	-1351.1638	2791.0151	0.0000	1.0000
SYMI	41	-1351.3395	2791.3663	0.0000	1.0000
SYMIG	42	-1350.9162	2792.8596	0.0000	1.0000
F81G	39	-1356.2369	2796.5087	0.0000	1.0000
F81I	39	-1356.3696	2796.7740	0.0000	1.0000
F81IG	40	-1356.1496	2798.6558	0.0000	1.0000
K2P	36	-1368.2138	2813.5507	0.0000	1.0000
SYM	40	-1366.0783	2818.5132	0.0000	1.0000
JC69G	36	-1371.6312	2820.3855	0.0000	1.0000
F81	38	-1369.4084	2820.5387	0.0000	1.0000
JC69I	36	-1371.8115	2820.7461	0.0000	1.0000
JC69IG	37	-1371.4528	2822.3236	0.0000	1.0000
JC69	35	-1385.3808	2845.5985	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-1336.4769	2752.9537	0.3042	0.3042
HKYI	40	-1336.5527	2753.1054	0.2820	0.5862
GTRG	44	-1333.2031	2754.4063	0.1472	0.7334
GTRI	44	-1333.3094	2754.6188	0.1323	0.8657
HKYIG	41	-1336.8438	2755.6877	0.0775	0.9432
GTRIG	45	-1333.1554	2756.3108	0.0568	1.0000
HKY	39	-1349.3597	2776.7194	0.0000	1.0000
GTR	43	-1347.1963	2780.3927	0.0000	1.0000
K2PG	37	-1353.2853	2780.5707	0.0000	1.0000
K2PI	37	-1353.4593	2780.9185	0.0000	1.0000
K2PIG	38	-1353.0214	2782.0428	0.0000	1.0000
SYMG	41	-1351.1638	2784.3277	0.0000	1.0000
SYMI	41	-1351.3395	2784.6789	0.0000	1.0000
SYMIG	42	-1350.9162	2785.8323	0.0000	1.0000
F81G	39	-1356.2369	2790.4739	0.0000	1.0000
F81I	39	-1356.3696	2790.7391	0.0000	1.0000
F81IG	40	-1356.1496	2792.2992	0.0000	1.0000
K2P	36	-1368.2138	2808.4276	0.0000	1.0000
SYM	40	-1366.0783	2812.1566	0.0000	1.0000
F81	38	-1369.4084	2814.8167	0.0000	1.0000
JC69G	36	-1371.6312	2815.2624	0.0000	1.0000
JC69I	36	-1371.8115	2815.6230	0.0000	1.0000
JC69IG	37	-1371.4528	2816.9055	0.0000	1.0000
JC69	35	-1385.3808	2840.7616	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1336.4769	2925.8563	0.5108	0.5108
HKYI	40	-1336.5527	2926.0080	0.4735	0.9843
HKYIG	41	-1336.8438	2932.9128	0.0150	0.9992
K2PG	37	-1353.2853	2940.5056	0.0003	0.9996
K2PI	37	-1353.4593	2940.8534	0.0003	0.9999
GTRG	44	-1333.2031	2944.5991	0.0000	0.9999
GTRI	44	-1333.3094	2944.8117	0.0000	0.9999
HKY	39	-1349.3597	2945.2994	0.0000	1.0000
K2PIG	38	-1353.0214	2946.3003	0.0000	1.0000
GTRIG	45	-1333.1554	2950.8263	0.0000	1.0000
F81G	39	-1356.2369	2959.0539	0.0000	1.0000
F81I	39	-1356.3696	2959.3192	0.0000	1.0000
SYMG	41	-1351.1638	2961.5529	0.0000	1.0000
SYMI	41	-1351.3395	2961.9041	0.0000	1.0000
K2P	36	-1368.2138	2964.0400	0.0000	1.0000
F81IG	40	-1356.1496	2965.2018	0.0000	1.0000
GTR	43	-1347.1963	2966.2630	0.0000	1.0000
SYMIG	42	-1350.9162	2967.3801	0.0000	1.0000
JC69G	36	-1371.6312	2970.8748	0.0000	1.0000
JC69I	36	-1371.8115	2971.2354	0.0000	1.0000
JC69IG	37	-1371.4528	2976.8404	0.0000	1.0000
F81	38	-1369.4084	2979.0742	0.0000	1.0000
SYM	40	-1366.0783	2985.0592	0.0000	1.0000
JC69	35	-1385.3808	2992.0514	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/chr13_710.phylip = 1 - 557;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr13_710.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/chr13_710.phylip = 1 - 557;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr13_710.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/chr13_710.phylip = 1 - 557;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr13_710.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

