
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:40 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_10497.phylip" (19 taxa, 787 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	-2218.2984	4529.9336	0.6137	0.6137
HKYG	40	-2223.2340	4530.8647	0.3853	0.9990
GTRIG	45	-2224.2205	4544.0280	0.0005	0.9995
HKYIG	41	-2228.7643	4544.1515	0.0005	1.0000
HKYI	40	-2233.9742	4552.3452	0.0000	1.0000
GTRI	44	-2231.1992	4555.7354	0.0000	1.0000
SYMG	41	-2240.8486	4568.3200	0.0000	1.0000
K2PG	37	-2248.9441	4575.6426	0.0000	1.0000
SYMIG	42	-2245.5523	4579.9595	0.0000	1.0000
K2PIG	38	-2252.8451	4585.6527	0.0000	1.0000
GTR	43	-2248.9327	4588.9582	0.0000	1.0000
SYMI	41	-2251.6389	4589.9007	0.0000	1.0000
HKY	39	-2254.1469	4590.4704	0.0000	1.0000
K2PI	37	-2258.4991	4594.7525	0.0000	1.0000
SYM	40	-2270.5521	4625.5010	0.0000	1.0000
K2P	36	-2280.1362	4635.8244	0.0000	1.0000
F81G	39	-2295.1521	4672.4809	0.0000	1.0000
F81IG	40	-2297.6525	4679.7017	0.0000	1.0000
F81I	39	-2301.8805	4685.9377	0.0000	1.0000
F81	38	-2319.6476	4719.2577	0.0000	1.0000
JC69G	36	-2324.6084	4724.7689	0.0000	1.0000
JC69IG	37	-2327.7682	4733.2907	0.0000	1.0000
JC69I	36	-2331.8975	4739.3470	0.0000	1.0000
JC69	35	-2347.3558	4768.0672	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2218.2984	4524.5967	0.7174	0.7174
HKYG	40	-2223.2340	4526.4679	0.2815	0.9989
GTRIG	45	-2224.2205	4538.4409	0.0007	0.9996
HKYIG	41	-2228.7643	4539.5287	0.0004	1.0000
HKYI	40	-2233.9742	4547.9484	0.0000	1.0000
GTRI	44	-2231.1992	4550.3984	0.0000	1.0000
SYMG	41	-2240.8486	4563.6972	0.0000	1.0000
K2PG	37	-2248.9441	4571.8883	0.0000	1.0000
SYMIG	42	-2245.5523	4575.1047	0.0000	1.0000
K2PIG	38	-2252.8451	4581.6901	0.0000	1.0000
GTR	43	-2248.9327	4583.8653	0.0000	1.0000
SYMI	41	-2251.6389	4585.2779	0.0000	1.0000
HKY	39	-2254.1469	4586.2937	0.0000	1.0000
K2PI	37	-2258.4991	4590.9982	0.0000	1.0000
SYM	40	-2270.5521	4621.1042	0.0000	1.0000
K2P	36	-2280.1362	4632.2724	0.0000	1.0000
F81G	39	-2295.1521	4668.3042	0.0000	1.0000
F81IG	40	-2297.6525	4675.3049	0.0000	1.0000
F81I	39	-2301.8805	4681.7610	0.0000	1.0000
F81	38	-2319.6476	4715.2951	0.0000	1.0000
JC69G	36	-2324.6084	4721.2169	0.0000	1.0000
JC69IG	37	-2327.7682	4729.5364	0.0000	1.0000
JC69I	36	-2331.8975	4735.7950	0.0000	1.0000
JC69	35	-2347.3558	4764.7117	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2223.2340	4713.1971	0.9996	0.9996
GTRG	44	-2218.2984	4729.9988	0.0002	0.9998
HKYIG	41	-2228.7643	4730.9260	0.0001	1.0000
HKYI	40	-2233.9742	4734.6776	0.0000	1.0000
K2PG	37	-2248.9441	4744.6127	0.0000	1.0000
GTRIG	45	-2224.2205	4748.5112	0.0000	1.0000
SYMG	41	-2240.8486	4755.0946	0.0000	1.0000
GTRI	44	-2231.1992	4755.8005	0.0000	1.0000
K2PIG	38	-2252.8451	4759.0828	0.0000	1.0000
K2PI	37	-2258.4991	4763.7226	0.0000	1.0000
HKY	39	-2254.1469	4768.3546	0.0000	1.0000
SYMIG	42	-2245.5523	4771.1703	0.0000	1.0000
SYMI	41	-2251.6389	4776.6752	0.0000	1.0000
GTR	43	-2248.9327	4784.5991	0.0000	1.0000
K2P	36	-2280.1362	4800.3287	0.0000	1.0000
SYM	40	-2270.5521	4807.8333	0.0000	1.0000
F81G	39	-2295.1521	4850.3651	0.0000	1.0000
F81IG	40	-2297.6525	4862.0341	0.0000	1.0000
F81I	39	-2301.8805	4863.8219	0.0000	1.0000
JC69G	36	-2324.6084	4889.2731	0.0000	1.0000
F81	38	-2319.6476	4892.6878	0.0000	1.0000
JC69IG	37	-2327.7682	4902.2608	0.0000	1.0000
JC69I	36	-2331.8975	4903.8512	0.0000	1.0000
JC69	35	-2347.3558	4928.0997	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_10497.phylip = 1 - 787;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10497.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_10497.phylip = 1 - 787;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10497.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_10497.phylip = 1 - 787;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10497.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

