
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:47 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_6205.phylip" (19 taxa, 788 characters)

Minimum AIC  model: GTRIG
Minimum AICc model: GTRG
Minimum BIC  model: K2PG


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	-2547.7094	5188.7484	0.4960	0.4960
GTRIG	45	-2546.6732	5188.9259	0.4539	0.9498
GTRI	44	-2550.8725	5195.0748	0.0210	0.9708
HKYG	40	-2555.7578	5195.9064	0.0138	0.9847
HKYIG	41	-2554.7830	5196.1826	0.0121	0.9967
SYMG	41	-2557.2833	5201.1833	0.0010	0.9977
SYMIG	42	-2556.4670	5201.7823	0.0007	0.9984
HKYI	40	-2558.8243	5202.0395	0.0006	0.9991
K2PG	37	-2562.4638	5202.6770	0.0005	0.9995
K2PIG	38	-2561.5852	5203.1277	0.0004	0.9999
SYMI	41	-2560.1245	5206.8657	0.0001	1.0000
K2PI	37	-2565.5279	5208.8051	0.0000	1.0000
GTR	43	-2591.0166	5273.1192	0.0000	1.0000
F81G	39	-2598.4890	5279.1491	0.0000	1.0000
SYM	40	-2597.5025	5279.3959	0.0000	1.0000
F81IG	40	-2597.6646	5279.7202	0.0000	1.0000
HKY	39	-2599.0700	5280.3111	0.0000	1.0000
JC69G	36	-2602.8444	5281.2360	0.0000	1.0000
JC69IG	37	-2602.0608	5281.8708	0.0000	1.0000
K2P	36	-2604.1759	5283.8990	0.0000	1.0000
F81I	39	-2601.4435	5285.0582	0.0000	1.0000
JC69I	36	-2605.7892	5287.1257	0.0000	1.0000
F81	38	-2639.5829	5359.1231	0.0000	1.0000
JC69	35	-2643.2118	5359.7747	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRIG	45	-2546.6732	5183.3463	0.4896	0.4896
GTRG	44	-2547.7094	5183.4187	0.4722	0.9617
GTRI	44	-2550.8725	5189.7451	0.0200	0.9817
HKYG	40	-2555.7578	5191.5155	0.0082	0.9899
HKYIG	41	-2554.7830	5191.5660	0.0080	0.9980
SYMG	41	-2557.2833	5196.5666	0.0007	0.9986
SYMIG	42	-2556.4670	5196.9340	0.0005	0.9992
HKYI	40	-2558.8243	5197.6486	0.0004	0.9996
K2PG	37	-2562.4638	5198.9277	0.0002	0.9998
K2PIG	38	-2561.5852	5199.1704	0.0002	1.0000
SYMI	41	-2560.1245	5202.2490	0.0000	1.0000
K2PI	37	-2565.5279	5205.0557	0.0000	1.0000
GTR	43	-2591.0166	5268.0332	0.0000	1.0000
F81G	39	-2598.4890	5274.9780	0.0000	1.0000
SYM	40	-2597.5025	5275.0050	0.0000	1.0000
F81IG	40	-2597.6646	5275.3293	0.0000	1.0000
HKY	39	-2599.0700	5276.1400	0.0000	1.0000
JC69G	36	-2602.8444	5277.6887	0.0000	1.0000
JC69IG	37	-2602.0608	5278.1215	0.0000	1.0000
K2P	36	-2604.1759	5280.3517	0.0000	1.0000
F81I	39	-2601.4435	5280.8871	0.0000	1.0000
JC69I	36	-2605.7892	5283.5784	0.0000	1.0000
F81	38	-2639.5829	5355.1659	0.0000	1.0000
JC69	35	-2643.2118	5356.4237	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-2562.4638	5371.6991	0.8509	0.8509
K2PIG	38	-2561.5852	5376.6114	0.0730	0.9239
K2PI	37	-2565.5279	5377.8272	0.0397	0.9637
HKYG	40	-2555.7578	5378.2954	0.0314	0.9951
HKYIG	41	-2554.7830	5383.0154	0.0030	0.9981
HKYI	40	-2558.8243	5384.4285	0.0015	0.9995
SYMG	41	-2557.2833	5388.0161	0.0002	0.9998
GTRG	44	-2547.7094	5388.8766	0.0002	0.9999
SYMIG	42	-2556.4670	5393.0529	0.0000	1.0000
GTRIG	45	-2546.6732	5393.4738	0.0000	1.0000
SYMI	41	-2560.1245	5393.6985	0.0000	1.0000
GTRI	44	-2550.8725	5395.2030	0.0000	1.0000
JC69G	36	-2602.8444	5445.7907	0.0000	1.0000
K2P	36	-2604.1759	5448.4536	0.0000	1.0000
JC69IG	37	-2602.0608	5450.8929	0.0000	1.0000
JC69I	36	-2605.7892	5451.6804	0.0000	1.0000
F81G	39	-2598.4890	5457.0884	0.0000	1.0000
HKY	39	-2599.0700	5458.2504	0.0000	1.0000
SYM	40	-2597.5025	5461.7849	0.0000	1.0000
F81IG	40	-2597.6646	5462.1092	0.0000	1.0000
F81I	39	-2601.4435	5462.9975	0.0000	1.0000
GTR	43	-2591.0166	5468.8216	0.0000	1.0000
JC69	35	-2643.2118	5519.8561	0.0000	1.0000
F81	38	-2639.5829	5532.6068	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/chr7_6205.phylip = 1 - 788;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_6205.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 (GTRG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_6205.phylip = 1 - 788;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_6205.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 (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_6205.phylip = 1 - 788;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_6205.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=gamma;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


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End of Output

