
Output from mraic.pl version 1.4.4 by Johan Nylander
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13:17 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/chr8_8806.phylip" (19 taxa, 633 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	-2184.9242	4464.5831	0.4834	0.4834
HKYG	40	-2189.8975	4465.3356	0.3318	0.8152
GTRIG	45	-2185.0399	4467.1325	0.1351	0.9503
HKYIG	41	-2190.6793	4469.1860	0.0484	0.9987
GTRI	44	-2190.9434	4476.6216	0.0012	0.9998
HKYI	40	-2197.4725	4480.4856	0.0002	1.0000
SYMG	41	-2206.0681	4499.9636	0.0000	1.0000
SYMIG	42	-2206.0463	4502.2147	0.0000	1.0000
SYMI	41	-2211.9246	4511.6767	0.0000	1.0000
K2PG	37	-2219.6500	4518.0260	0.0000	1.0000
K2PIG	38	-2219.2209	4519.4317	0.0000	1.0000
K2PI	37	-2226.8089	4532.3438	0.0000	1.0000
GTR	43	-2224.9237	4542.2718	0.0000	1.0000
HKY	39	-2229.7506	4542.7626	0.0000	1.0000
SYM	40	-2243.8641	4573.2687	0.0000	1.0000
K2P	36	-2258.2499	4592.9696	0.0000	1.0000
F81G	39	-2261.6023	4606.4660	0.0000	1.0000
F81IG	40	-2261.0810	4607.7026	0.0000	1.0000
F81I	39	-2267.2825	4617.8265	0.0000	1.0000
JC69G	36	-2297.0595	4670.5887	0.0000	1.0000
JC69IG	37	-2296.7683	4672.2626	0.0000	1.0000
JC69I	36	-2302.9500	4682.3698	0.0000	1.0000
F81	38	-2300.7098	4682.4095	0.0000	1.0000
JC69	35	-2331.8730	4737.9670	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2184.9242	4457.8484	0.5644	0.5644
HKYG	40	-2189.8975	4459.7950	0.2133	0.7777
GTRIG	45	-2185.0399	4460.0797	0.1850	0.9626
HKYIG	41	-2190.6793	4463.3586	0.0359	0.9985
GTRI	44	-2190.9434	4469.8869	0.0014	0.9999
HKYI	40	-2197.4725	4474.9451	0.0001	1.0000
SYMG	41	-2206.0681	4494.1362	0.0000	1.0000
SYMIG	42	-2206.0463	4496.0927	0.0000	1.0000
SYMI	41	-2211.9246	4505.8493	0.0000	1.0000
K2PG	37	-2219.6500	4513.2999	0.0000	1.0000
K2PIG	38	-2219.2209	4514.4418	0.0000	1.0000
K2PI	37	-2226.8089	4527.6178	0.0000	1.0000
GTR	43	-2224.9237	4535.8473	0.0000	1.0000
HKY	39	-2229.7506	4537.5012	0.0000	1.0000
SYM	40	-2243.8641	4567.7282	0.0000	1.0000
K2P	36	-2258.2499	4588.4998	0.0000	1.0000
F81G	39	-2261.6023	4601.2047	0.0000	1.0000
F81IG	40	-2261.0810	4602.1621	0.0000	1.0000
F81I	39	-2267.2825	4612.5651	0.0000	1.0000
JC69G	36	-2297.0595	4666.1189	0.0000	1.0000
JC69IG	37	-2296.7683	4667.5366	0.0000	1.0000
F81	38	-2300.7098	4677.4196	0.0000	1.0000
JC69I	36	-2302.9500	4677.9000	0.0000	1.0000
JC69	35	-2331.8730	4733.7459	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2189.8975	4637.8138	0.9813	0.9813
HKYIG	41	-2190.6793	4645.8278	0.0178	0.9991
HKYI	40	-2197.4725	4652.9639	0.0005	0.9996
GTRG	44	-2184.9242	4653.6691	0.0004	1.0000
GTRIG	45	-2185.0399	4660.3509	0.0000	1.0000
GTRI	44	-2190.9434	4665.7076	0.0000	1.0000
SYMG	41	-2206.0681	4676.6055	0.0000	1.0000
K2PG	37	-2219.6500	4677.9673	0.0000	1.0000
SYMIG	42	-2206.0463	4683.0124	0.0000	1.0000
K2PIG	38	-2219.2209	4683.5597	0.0000	1.0000
SYMI	41	-2211.9246	4688.3186	0.0000	1.0000
K2PI	37	-2226.8089	4692.2852	0.0000	1.0000
HKY	39	-2229.7506	4711.0695	0.0000	1.0000
GTR	43	-2224.9237	4727.2176	0.0000	1.0000
SYM	40	-2243.8641	4745.7470	0.0000	1.0000
K2P	36	-2258.2499	4748.7168	0.0000	1.0000
F81G	39	-2261.6023	4774.7730	0.0000	1.0000
F81IG	40	-2261.0810	4780.1809	0.0000	1.0000
F81I	39	-2267.2825	4786.1334	0.0000	1.0000
JC69G	36	-2297.0595	4826.3358	0.0000	1.0000
JC69IG	37	-2296.7683	4832.2040	0.0000	1.0000
JC69I	36	-2302.9500	4838.1170	0.0000	1.0000
F81	38	-2300.7098	4846.5375	0.0000	1.0000
JC69	35	-2331.8730	4889.5124	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/chr8_8806.phylip = 1 - 633;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_8806.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/chr8_8806.phylip = 1 - 633;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_8806.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/chr8_8806.phylip = 1 - 633;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_8806.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

