
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:29 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/chr5_10047.phylip" (19 taxa, 773 characters)

Minimum AIC  model: GTRIG
Minimum AICc model: GTRIG
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
GTRIG	45	-2266.6877	4629.0701	0.7360	0.7360
GTRG	44	-2268.8890	4631.2176	0.2515	0.9875
HKYIG	41	-2275.7779	4638.2671	0.0074	0.9949
GTRI	44	-2273.3041	4640.0478	0.0030	0.9979
HKYG	40	-2278.1918	4640.8644	0.0020	1.0000
HKYI	40	-2282.0861	4648.6531	0.0000	1.0000
SYMG	41	-2286.0479	4658.8072	0.0000	1.0000
SYMIG	42	-2284.9427	4658.8333	0.0000	1.0000
K2PG	37	-2290.9869	4659.7996	0.0000	1.0000
K2PIG	38	-2289.9186	4659.8754	0.0000	1.0000
SYMI	41	-2289.8076	4666.3266	0.0000	1.0000
K2PI	37	-2294.6911	4667.2081	0.0000	1.0000
F81IG	40	-2318.1736	4720.8282	0.0000	1.0000
GTR	43	-2315.3829	4721.9564	0.0000	1.0000
F81G	39	-2320.2482	4722.7528	0.0000	1.0000
F81I	39	-2324.0412	4730.3388	0.0000	1.0000
HKY	39	-2324.5854	4731.4273	0.0000	1.0000
JC69IG	37	-2329.2519	4736.3296	0.0000	1.0000
JC69G	36	-2331.3564	4738.3323	0.0000	1.0000
JC69I	36	-2335.0757	4745.7709	0.0000	1.0000
SYM	40	-2331.8261	4748.1330	0.0000	1.0000
K2P	36	-2337.6669	4750.9534	0.0000	1.0000
F81	38	-2364.8061	4809.6504	0.0000	1.0000
JC69	35	-2376.2571	4825.9334	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRIG	45	-2266.6877	4623.3754	0.7621	0.7621
GTRG	44	-2268.8890	4625.7780	0.2292	0.9914
HKYIG	41	-2275.7779	4633.5557	0.0047	0.9961
GTRI	44	-2273.3041	4634.6083	0.0028	0.9988
HKYG	40	-2278.1918	4636.3836	0.0011	1.0000
HKYI	40	-2282.0861	4644.1722	0.0000	1.0000
SYMIG	42	-2284.9427	4653.8853	0.0000	1.0000
SYMG	41	-2286.0479	4654.0958	0.0000	1.0000
K2PIG	38	-2289.9186	4655.8373	0.0000	1.0000
K2PG	37	-2290.9869	4655.9737	0.0000	1.0000
SYMI	41	-2289.8076	4661.6153	0.0000	1.0000
K2PI	37	-2294.6911	4663.3823	0.0000	1.0000
F81IG	40	-2318.1736	4716.3473	0.0000	1.0000
GTR	43	-2315.3829	4716.7657	0.0000	1.0000
F81G	39	-2320.2482	4718.4964	0.0000	1.0000
F81I	39	-2324.0412	4726.0823	0.0000	1.0000
HKY	39	-2324.5854	4727.1708	0.0000	1.0000
JC69IG	37	-2329.2519	4732.5038	0.0000	1.0000
JC69G	36	-2331.3564	4734.7128	0.0000	1.0000
JC69I	36	-2335.0757	4742.1513	0.0000	1.0000
SYM	40	-2331.8261	4743.6521	0.0000	1.0000
K2P	36	-2337.6669	4747.3339	0.0000	1.0000
F81	38	-2364.8061	4805.6122	0.0000	1.0000
JC69	35	-2376.2571	4822.5141	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2278.1918	4822.3947	0.6604	0.6604
HKYIG	41	-2275.7779	4824.2172	0.2655	0.9259
K2PG	37	-2290.9869	4828.0340	0.0394	0.9652
HKYI	40	-2282.0861	4830.1834	0.0134	0.9787
GTRG	44	-2268.8890	4830.3903	0.0121	0.9908
K2PIG	38	-2289.9186	4832.5479	0.0041	0.9949
GTRIG	45	-2266.6877	4832.6380	0.0039	0.9989
K2PI	37	-2294.6911	4835.4426	0.0010	0.9998
GTRI	44	-2273.3041	4839.2205	0.0001	1.0000
SYMG	41	-2286.0479	4844.7573	0.0000	1.0000
SYMIG	42	-2284.9427	4849.1971	0.0000	1.0000
SYMI	41	-2289.8076	4852.2767	0.0000	1.0000
F81G	39	-2320.2482	4899.8572	0.0000	1.0000
JC69G	36	-2331.3564	4902.1228	0.0000	1.0000
F81IG	40	-2318.1736	4902.3584	0.0000	1.0000
JC69IG	37	-2329.2519	4904.5641	0.0000	1.0000
F81I	39	-2324.0412	4907.4432	0.0000	1.0000
HKY	39	-2324.5854	4908.5317	0.0000	1.0000
JC69I	36	-2335.0757	4909.5614	0.0000	1.0000
K2P	36	-2337.6669	4914.7439	0.0000	1.0000
GTR	43	-2315.3829	4916.7277	0.0000	1.0000
SYM	40	-2331.8261	4929.6633	0.0000	1.0000
F81	38	-2364.8061	4982.3228	0.0000	1.0000
JC69	35	-2376.2571	4985.2739	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/chr5_10047.phylip = 1 - 773;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_10047.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/chr5_10047.phylip = 1 - 773;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_10047.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 (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_10047.phylip = 1 - 773;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_10047.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

