
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:49 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_17438.phylip" (19 taxa, 928 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	-4297.8345	8688.1536	0.6943	0.6943
GTRIG	45	-4297.8327	8690.3593	0.2305	0.9248
HKYG	40	-4304.7411	8693.1801	0.0562	0.9811
HKYIG	41	-4304.7356	8695.3583	0.0189	1.0000
GTRI	44	-4308.8672	8710.2192	0.0000	1.0000
HKYI	40	-4316.5907	8716.8792	0.0000	1.0000
SYMG	41	-4342.6889	8771.2649	0.0000	1.0000
K2PG	37	-4347.2231	8771.6057	0.0000	1.0000
SYMIG	42	-4342.6668	8773.4149	0.0000	1.0000
K2PIG	38	-4347.1995	8773.7331	0.0000	1.0000
SYMI	41	-4354.5403	8794.9677	0.0000	1.0000
K2PI	37	-4359.6931	8796.5457	0.0000	1.0000
GTR	43	-4357.8631	8806.0067	0.0000	1.0000
HKY	39	-4365.2810	8812.0754	0.0000	1.0000
SYM	40	-4402.8947	8889.4873	0.0000	1.0000
K2P	36	-4408.2381	8891.4661	0.0000	1.0000
F81G	39	-4435.2971	8952.1077	0.0000	1.0000
F81IG	40	-4435.2967	8954.2913	0.0000	1.0000
F81I	39	-4446.2921	8974.0977	0.0000	1.0000
JC69G	36	-4464.6104	9004.2107	0.0000	1.0000
JC69IG	37	-4464.6013	9006.3621	0.0000	1.0000
JC69I	36	-4476.2099	9027.4097	0.0000	1.0000
F81	38	-4491.3941	9062.1223	0.0000	1.0000
JC69	35	-4521.7846	9116.3943	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-4297.8345	8683.6689	0.6928	0.6928
GTRIG	45	-4297.8327	8685.6654	0.2553	0.9481
HKYG	40	-4304.7411	8689.4823	0.0379	0.9860
HKYIG	41	-4304.7356	8691.4711	0.0140	1.0000
GTRI	44	-4308.8672	8705.7345	0.0000	1.0000
HKYI	40	-4316.5907	8713.1813	0.0000	1.0000
SYMG	41	-4342.6889	8767.3778	0.0000	1.0000
K2PG	37	-4347.2231	8768.4462	0.0000	1.0000
SYMIG	42	-4342.6668	8769.3336	0.0000	1.0000
K2PIG	38	-4347.1995	8770.3990	0.0000	1.0000
SYMI	41	-4354.5403	8791.0805	0.0000	1.0000
K2PI	37	-4359.6931	8793.3862	0.0000	1.0000
GTR	43	-4357.8631	8801.7261	0.0000	1.0000
HKY	39	-4365.2810	8808.5619	0.0000	1.0000
SYM	40	-4402.8947	8885.7895	0.0000	1.0000
K2P	36	-4408.2381	8888.4762	0.0000	1.0000
F81G	39	-4435.2971	8948.5942	0.0000	1.0000
F81IG	40	-4435.2967	8950.5934	0.0000	1.0000
F81I	39	-4446.2921	8970.5842	0.0000	1.0000
JC69G	36	-4464.6104	9001.2208	0.0000	1.0000
JC69IG	37	-4464.6013	9003.2026	0.0000	1.0000
JC69I	36	-4476.2099	9024.4198	0.0000	1.0000
F81	38	-4491.3941	9058.7883	0.0000	1.0000
JC69	35	-4521.7846	9113.5692	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-4304.7411	8882.8035	0.9669	0.9669
HKYIG	41	-4304.7356	8889.6254	0.0319	0.9988
GTRG	44	-4297.8345	8896.3223	0.0011	1.0000
GTRIG	45	-4297.8327	8903.1518	0.0000	1.0000
HKYI	40	-4316.5907	8906.5026	0.0000	1.0000
GTRI	44	-4308.8672	8918.3879	0.0000	1.0000
K2PG	37	-4347.2231	8947.2684	0.0000	1.0000
K2PIG	38	-4347.1995	8954.0542	0.0000	1.0000
SYMG	41	-4342.6889	8965.5321	0.0000	1.0000
K2PI	37	-4359.6931	8972.2084	0.0000	1.0000
SYMIG	42	-4342.6668	8972.3209	0.0000	1.0000
SYMI	41	-4354.5403	8989.2348	0.0000	1.0000
HKY	39	-4365.2810	8997.0501	0.0000	1.0000
GTR	43	-4357.8631	9009.5465	0.0000	1.0000
K2P	36	-4408.2381	9062.4653	0.0000	1.0000
SYM	40	-4402.8947	9079.1107	0.0000	1.0000
F81G	39	-4435.2971	9137.0825	0.0000	1.0000
F81IG	40	-4435.2967	9143.9147	0.0000	1.0000
F81I	39	-4446.2921	9159.0725	0.0000	1.0000
JC69G	36	-4464.6104	9175.2100	0.0000	1.0000
JC69IG	37	-4464.6013	9182.0247	0.0000	1.0000
JC69I	36	-4476.2099	9198.4090	0.0000	1.0000
F81	38	-4491.3941	9242.4435	0.0000	1.0000
JC69	35	-4521.7846	9282.7253	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_17438.phylip = 1 - 928;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_17438.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_17438.phylip = 1 - 928;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_17438.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_17438.phylip = 1 - 928;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_17438.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

