
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:10 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_454.phylip" (19 taxa, 741 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	-2546.0693	5185.8282	0.6884	0.6884
GTRIG	45	-2545.8979	5187.7526	0.2630	0.9514
GTRI	44	-2548.7834	5191.2566	0.0456	0.9970
HKYG	40	-2556.4856	5197.6569	0.0019	0.9989
HKYIG	41	-2556.2692	5199.4654	0.0008	0.9997
HKYI	40	-2558.1705	5201.0266	0.0003	1.0000
GTR	43	-2575.4609	5242.3508	0.0000	1.0000
HKY	39	-2583.3087	5249.0681	0.0000	1.0000
K2PG	37	-2599.8800	5277.7600	0.0000	1.0000
K2PIG	38	-2599.6029	5279.4279	0.0000	1.0000
SYMG	41	-2596.5650	5280.0571	0.0000	1.0000
K2PI	37	-2601.2476	5280.4952	0.0000	1.0000
SYMIG	42	-2596.2781	5281.7310	0.0000	1.0000
SYMI	41	-2597.9174	5282.7618	0.0000	1.0000
F81G	39	-2617.6522	5317.7553	0.0000	1.0000
F81IG	40	-2617.4494	5319.5844	0.0000	1.0000
F81I	39	-2618.8531	5320.1570	0.0000	1.0000
K2P	36	-2628.9841	5333.7524	0.0000	1.0000
SYM	40	-2625.3557	5335.3971	0.0000	1.0000
F81	38	-2644.7053	5369.6327	0.0000	1.0000
JC69G	36	-2650.6930	5377.1700	0.0000	1.0000
JC69I	36	-2651.5699	5378.9239	0.0000	1.0000
JC69IG	37	-2650.4736	5378.9471	0.0000	1.0000
JC69	35	-2678.1980	5429.9704	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2546.0693	5180.1385	0.6642	0.6642
GTRIG	45	-2545.8979	5181.7958	0.2900	0.9542
GTRI	44	-2548.7834	5185.5669	0.0440	0.9982
HKYG	40	-2556.4856	5192.9712	0.0011	0.9993
HKYIG	41	-2556.2692	5194.5384	0.0005	0.9998
HKYI	40	-2558.1705	5196.3409	0.0002	1.0000
GTR	43	-2575.4609	5236.9218	0.0000	1.0000
HKY	39	-2583.3087	5244.6173	0.0000	1.0000
K2PG	37	-2599.8800	5273.7600	0.0000	1.0000
SYMG	41	-2596.5650	5275.1300	0.0000	1.0000
K2PIG	38	-2599.6029	5275.2057	0.0000	1.0000
K2PI	37	-2601.2476	5276.4952	0.0000	1.0000
SYMIG	42	-2596.2781	5276.5562	0.0000	1.0000
SYMI	41	-2597.9174	5277.8347	0.0000	1.0000
F81G	39	-2617.6522	5313.3045	0.0000	1.0000
F81IG	40	-2617.4494	5314.8987	0.0000	1.0000
F81I	39	-2618.8531	5315.7062	0.0000	1.0000
K2P	36	-2628.9841	5329.9683	0.0000	1.0000
SYM	40	-2625.3557	5330.7113	0.0000	1.0000
F81	38	-2644.7053	5365.4105	0.0000	1.0000
JC69G	36	-2650.6930	5373.3859	0.0000	1.0000
JC69IG	37	-2650.4736	5374.9471	0.0000	1.0000
JC69I	36	-2651.5699	5375.1398	0.0000	1.0000
JC69	35	-2678.1980	5426.3959	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2556.4856	5377.2912	0.7701	0.7701
HKYI	40	-2558.1705	5380.6609	0.1428	0.9129
GTRG	44	-2546.0693	5382.8906	0.0468	0.9597
HKYIG	41	-2556.2692	5383.4664	0.0351	0.9949
GTRI	44	-2548.7834	5388.3189	0.0031	0.9980
GTRIG	45	-2545.8979	5389.1558	0.0020	1.0000
HKY	39	-2583.3087	5424.3294	0.0000	1.0000
GTR	43	-2575.4609	5435.0658	0.0000	1.0000
K2PG	37	-2599.8800	5444.2560	0.0000	1.0000
K2PI	37	-2601.2476	5446.9912	0.0000	1.0000
K2PIG	38	-2599.6029	5450.3097	0.0000	1.0000
SYMG	41	-2596.5650	5464.0581	0.0000	1.0000
SYMI	41	-2597.9174	5466.7627	0.0000	1.0000
SYMIG	42	-2596.2781	5470.0922	0.0000	1.0000
F81G	39	-2617.6522	5493.0165	0.0000	1.0000
F81I	39	-2618.8531	5495.4182	0.0000	1.0000
K2P	36	-2628.9841	5495.8563	0.0000	1.0000
F81IG	40	-2617.4494	5499.2187	0.0000	1.0000
SYM	40	-2625.3557	5515.0314	0.0000	1.0000
JC69G	36	-2650.6930	5539.2739	0.0000	1.0000
F81	38	-2644.7053	5540.5145	0.0000	1.0000
JC69I	36	-2651.5699	5541.0278	0.0000	1.0000
JC69IG	37	-2650.4736	5545.4431	0.0000	1.0000
JC69	35	-2678.1980	5587.6759	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/chr3_454.phylip = 1 - 741;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_454.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/chr3_454.phylip = 1 - 741;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_454.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/chr3_454.phylip = 1 - 741;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_454.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

