
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:56 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/chr3_17769.phylip" (19 taxa, 643 characters)

Minimum AIC  model: GTRIG
Minimum AICc model: GTRIG
Minimum BIC  model: HKYIG


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
GTRIG	45	-2467.9607	5032.8560	0.9993	0.9993
HKYIG	41	-2479.8624	5047.4552	0.0007	1.0000
GTRI	44	-2480.5912	5055.8045	0.0000	1.0000
GTRG	44	-2481.2028	5057.0276	0.0000	1.0000
HKYG	40	-2494.3117	5074.0720	0.0000	1.0000
SYMIG	42	-2501.6913	5093.4027	0.0000	1.0000
HKYI	40	-2508.0766	5101.6017	0.0000	1.0000
SYMI	41	-2509.6365	5107.0035	0.0000	1.0000
SYMG	41	-2514.7670	5117.2644	0.0000	1.0000
K2PIG	38	-2521.0172	5122.9416	0.0000	1.0000
K2PG	37	-2534.5863	5147.8206	0.0000	1.0000
K2PI	37	-2545.2681	5169.1841	0.0000	1.0000
F81IG	40	-2565.6083	5216.6651	0.0000	1.0000
GTR	43	-2562.7315	5217.7801	0.0000	1.0000
HKY	39	-2574.2148	5231.6037	0.0000	1.0000
F81I	39	-2577.6548	5238.4836	0.0000	1.0000
F81G	39	-2580.8923	5244.9587	0.0000	1.0000
SYM	40	-2590.5326	5266.5137	0.0000	1.0000
JC69IG	37	-2607.7530	5294.1540	0.0000	1.0000
K2P	36	-2612.2079	5300.8119	0.0000	1.0000
JC69I	36	-2616.0776	5308.5512	0.0000	1.0000
JC69G	36	-2622.2768	5320.9497	0.0000	1.0000
F81	38	-2659.6828	5400.2729	0.0000	1.0000
JC69	35	-2693.8372	5461.8259	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRIG	45	-2467.9607	5025.9213	0.9996	0.9996
HKYIG	41	-2479.8624	5041.7248	0.0004	1.0000
GTRI	44	-2480.5912	5049.1824	0.0000	1.0000
GTRG	44	-2481.2028	5050.4055	0.0000	1.0000
HKYG	40	-2494.3117	5068.6235	0.0000	1.0000
SYMIG	42	-2501.6913	5087.3827	0.0000	1.0000
HKYI	40	-2508.0766	5096.1532	0.0000	1.0000
SYMI	41	-2509.6365	5101.2730	0.0000	1.0000
SYMG	41	-2514.7670	5111.5340	0.0000	1.0000
K2PIG	38	-2521.0172	5118.0343	0.0000	1.0000
K2PG	37	-2534.5863	5143.1727	0.0000	1.0000
K2PI	37	-2545.2681	5164.5362	0.0000	1.0000
F81IG	40	-2565.6083	5211.2166	0.0000	1.0000
GTR	43	-2562.7315	5211.4629	0.0000	1.0000
HKY	39	-2574.2148	5226.4296	0.0000	1.0000
F81I	39	-2577.6548	5233.3095	0.0000	1.0000
F81G	39	-2580.8923	5239.7846	0.0000	1.0000
SYM	40	-2590.5326	5261.0652	0.0000	1.0000
JC69IG	37	-2607.7530	5289.5061	0.0000	1.0000
K2P	36	-2612.2079	5296.4159	0.0000	1.0000
JC69I	36	-2616.0776	5304.1552	0.0000	1.0000
JC69G	36	-2622.2768	5316.5537	0.0000	1.0000
F81	38	-2659.6828	5395.3656	0.0000	1.0000
JC69	35	-2693.8372	5457.6743	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYIG	41	-2479.8624	5224.8367	0.7370	0.7370
GTRIG	45	-2467.9607	5226.8978	0.2630	1.0000
GTRI	44	-2480.5912	5245.6928	0.0000	1.0000
GTRG	44	-2481.2028	5246.9159	0.0000	1.0000
HKYG	40	-2494.3117	5247.2692	0.0000	1.0000
HKYI	40	-2508.0766	5274.7990	0.0000	1.0000
SYMIG	42	-2501.6913	5274.9607	0.0000	1.0000
SYMI	41	-2509.6365	5284.3850	0.0000	1.0000
K2PIG	38	-2521.0172	5287.7478	0.0000	1.0000
SYMG	41	-2514.7670	5294.6459	0.0000	1.0000
K2PG	37	-2534.5863	5308.4200	0.0000	1.0000
K2PI	37	-2545.2681	5329.7835	0.0000	1.0000
F81IG	40	-2565.6083	5389.8623	0.0000	1.0000
HKY	39	-2574.2148	5400.6092	0.0000	1.0000
GTR	43	-2562.7315	5403.5071	0.0000	1.0000
F81I	39	-2577.6548	5407.4892	0.0000	1.0000
F81G	39	-2580.8923	5413.9643	0.0000	1.0000
SYM	40	-2590.5326	5439.7110	0.0000	1.0000
JC69IG	37	-2607.7530	5454.7535	0.0000	1.0000
K2P	36	-2612.2079	5457.1971	0.0000	1.0000
JC69I	36	-2616.0776	5464.9364	0.0000	1.0000
JC69G	36	-2622.2768	5477.3349	0.0000	1.0000
F81	38	-2659.6828	5565.0791	0.0000	1.0000
JC69	35	-2693.8372	5613.9894	0.0000	1.0000



To specify default values for best AIC, AICc, or BIC models in MrBayes:

[Mrbayes block for the best AIC model (GTRIG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_17769.phylip = 1 - 643;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_17769.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best AICc model (GTRIG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_17769.phylip = 1 - 643;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_17769.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best BIC model (HKYIG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_17769.phylip = 1 - 643;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_17769.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
END;


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End of Output

