
Output from mraic.pl version 1.4.4 by Johan Nylander
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13:05 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/chr9_6343.phylip" (19 taxa, 776 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	-2611.6679	5316.7530	0.5485	0.5485
GTRIG	45	-2611.0932	5317.8575	0.3157	0.8642
GTRI	44	-2613.4041	5320.2254	0.0966	0.9608
HKYG	40	-2619.3176	5323.0978	0.0230	0.9838
HKYIG	41	-2618.7753	5324.2426	0.0130	0.9968
HKYI	40	-2621.2791	5327.0209	0.0032	1.0000
GTR	43	-2650.0527	5391.2749	0.0000	1.0000
K2PG	37	-2659.1027	5396.0158	0.0000	1.0000
K2PIG	38	-2658.6325	5397.2867	0.0000	1.0000
HKY	39	-2657.6364	5397.5120	0.0000	1.0000
SYMG	41	-2655.9736	5398.6393	0.0000	1.0000
SYMIG	42	-2655.5289	5399.9855	0.0000	1.0000
K2PI	37	-2661.5319	5400.8740	0.0000	1.0000
SYMI	41	-2658.1484	5402.9888	0.0000	1.0000
F81G	39	-2681.3329	5444.9049	0.0000	1.0000
F81IG	40	-2680.9378	5446.3383	0.0000	1.0000
F81I	39	-2683.4430	5449.1251	0.0000	1.0000
K2P	36	-2697.7339	5471.0726	0.0000	1.0000
SYM	40	-2694.3050	5473.0726	0.0000	1.0000
JC69G	36	-2713.6467	5502.8982	0.0000	1.0000
JC69IG	37	-2713.2717	5504.3537	0.0000	1.0000
JC69I	36	-2716.0127	5507.6303	0.0000	1.0000
F81	38	-2715.9599	5511.9415	0.0000	1.0000
JC69	35	-2748.9524	5571.3102	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2611.6679	5311.3357	0.5331	0.5331
GTRIG	45	-2611.0932	5312.1863	0.3484	0.8815
GTRI	44	-2613.4041	5314.8082	0.0939	0.9754
HKYG	40	-2619.3176	5318.6353	0.0139	0.9893
HKYIG	41	-2618.7753	5319.5505	0.0088	0.9981
HKYI	40	-2621.2791	5322.5583	0.0019	1.0000
GTR	43	-2650.0527	5386.1055	0.0000	1.0000
K2PG	37	-2659.1027	5392.2055	0.0000	1.0000
K2PIG	38	-2658.6325	5393.2650	0.0000	1.0000
HKY	39	-2657.6364	5393.2728	0.0000	1.0000
SYMG	41	-2655.9736	5393.9472	0.0000	1.0000
SYMIG	42	-2655.5289	5395.0578	0.0000	1.0000
K2PI	37	-2661.5319	5397.0637	0.0000	1.0000
SYMI	41	-2658.1484	5398.2967	0.0000	1.0000
F81G	39	-2681.3329	5440.6657	0.0000	1.0000
F81IG	40	-2680.9378	5441.8757	0.0000	1.0000
F81I	39	-2683.4430	5444.8859	0.0000	1.0000
K2P	36	-2697.7339	5467.4677	0.0000	1.0000
SYM	40	-2694.3050	5468.6101	0.0000	1.0000
JC69G	36	-2713.6467	5499.2933	0.0000	1.0000
JC69IG	37	-2713.2717	5500.5434	0.0000	1.0000
JC69I	36	-2716.0127	5504.0254	0.0000	1.0000
F81	38	-2715.9599	5507.9198	0.0000	1.0000
JC69	35	-2748.9524	5567.9048	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2619.3176	5504.8014	0.8287	0.8287
HKYI	40	-2621.2791	5508.7244	0.1166	0.9452
HKYIG	41	-2618.7753	5510.3708	0.0512	0.9964
GTRG	44	-2611.6679	5516.1185	0.0029	0.9993
GTRI	44	-2613.4041	5519.5909	0.0005	0.9998
GTRIG	45	-2611.0932	5521.6232	0.0002	1.0000
K2PG	37	-2659.1027	5564.4091	0.0000	1.0000
K2PI	37	-2661.5319	5569.2674	0.0000	1.0000
K2PIG	38	-2658.6325	5570.1228	0.0000	1.0000
HKY	39	-2657.6364	5574.7848	0.0000	1.0000
SYMG	41	-2655.9736	5584.7675	0.0000	1.0000
GTR	43	-2650.0527	5586.2340	0.0000	1.0000
SYMI	41	-2658.1484	5589.1170	0.0000	1.0000
SYMIG	42	-2655.5289	5590.5322	0.0000	1.0000
F81G	39	-2681.3329	5622.1777	0.0000	1.0000
F81I	39	-2683.4430	5626.3979	0.0000	1.0000
F81IG	40	-2680.9378	5628.0418	0.0000	1.0000
K2P	36	-2697.7339	5635.0172	0.0000	1.0000
SYM	40	-2694.3050	5654.7762	0.0000	1.0000
JC69G	36	-2713.6467	5666.8428	0.0000	1.0000
JC69I	36	-2716.0127	5671.5749	0.0000	1.0000
JC69IG	37	-2713.2717	5672.7471	0.0000	1.0000
F81	38	-2715.9599	5684.7776	0.0000	1.0000
JC69	35	-2748.9524	5730.8001	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/chr9_6343.phylip = 1 - 776;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_6343.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/chr9_6343.phylip = 1 - 776;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_6343.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/chr9_6343.phylip = 1 - 776;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_6343.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

