
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:11 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/chr2_22017.phylip" (19 taxa, 884 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	-5060.2491	10213.2180	0.4380	0.4380
HKYG	40	-5064.9984	10213.8877	0.3134	0.7514
GTRIG	45	-5060.2494	10215.4392	0.1443	0.8957
HKYIG	41	-5064.9987	10216.0876	0.1043	1.0000
K2PG	37	-5079.0743	10235.4724	0.0000	1.0000
K2PIG	38	-5079.0745	10237.6567	0.0000	1.0000
SYMG	41	-5078.5081	10243.1066	0.0000	1.0000
SYMIG	42	-5078.5084	10245.3117	0.0000	1.0000
HKYI	40	-5085.1141	10254.1190	0.0000	1.0000
GTRI	44	-5081.7725	10256.2648	0.0000	1.0000
K2PI	37	-5097.9854	10273.2947	0.0000	1.0000
SYMI	41	-5097.0984	10280.2871	0.0000	1.0000
HKY	39	-5155.0907	10391.8780	0.0000	1.0000
GTR	43	-5151.0330	10392.5708	0.0000	1.0000
K2P	36	-5169.7497	10414.6447	0.0000	1.0000
SYM	40	-5168.6624	10421.2157	0.0000	1.0000
F81G	39	-5205.8030	10493.3026	0.0000	1.0000
F81IG	40	-5205.8032	10495.4973	0.0000	1.0000
JC69G	36	-5214.2767	10503.6987	0.0000	1.0000
JC69IG	37	-5214.2771	10505.8781	0.0000	1.0000
F81I	39	-5223.0295	10527.7557	0.0000	1.0000
JC69I	36	-5231.4271	10537.9993	0.0000	1.0000
F81	38	-5288.5492	10656.6061	0.0000	1.0000
JC69	35	-5297.7059	10668.3835	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-5060.2491	10208.4981	0.4965	0.4965
HKYG	40	-5064.9984	10209.9968	0.2347	0.7311
GTRIG	45	-5060.2494	10210.4988	0.1826	0.9137
HKYIG	41	-5064.9987	10211.9973	0.0863	1.0000
K2PG	37	-5079.0743	10232.1486	0.0000	1.0000
K2PIG	38	-5079.0745	10234.1490	0.0000	1.0000
SYMG	41	-5078.5081	10239.0163	0.0000	1.0000
SYMIG	42	-5078.5084	10241.0168	0.0000	1.0000
HKYI	40	-5085.1141	10250.2282	0.0000	1.0000
GTRI	44	-5081.7725	10251.5449	0.0000	1.0000
K2PI	37	-5097.9854	10269.9709	0.0000	1.0000
SYMI	41	-5097.0984	10276.1968	0.0000	1.0000
GTR	43	-5151.0330	10388.0661	0.0000	1.0000
HKY	39	-5155.0907	10388.1813	0.0000	1.0000
K2P	36	-5169.7497	10411.4994	0.0000	1.0000
SYM	40	-5168.6624	10417.3248	0.0000	1.0000
F81G	39	-5205.8030	10489.6059	0.0000	1.0000
F81IG	40	-5205.8032	10491.6065	0.0000	1.0000
JC69G	36	-5214.2767	10500.5534	0.0000	1.0000
JC69IG	37	-5214.2771	10502.5542	0.0000	1.0000
F81I	39	-5223.0295	10524.0591	0.0000	1.0000
JC69I	36	-5231.4271	10534.8541	0.0000	1.0000
F81	38	-5288.5492	10653.0984	0.0000	1.0000
JC69	35	-5297.7059	10665.4118	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-5064.9984	10401.3751	0.9481	0.9481
HKYIG	41	-5064.9987	10408.1601	0.0319	0.9800
K2PG	37	-5079.0743	10409.1735	0.0192	0.9992
K2PIG	38	-5079.0745	10415.9584	0.0006	0.9999
GTRG	44	-5060.2491	10419.0142	0.0001	1.0000
GTRIG	45	-5060.2494	10425.7994	0.0000	1.0000
SYMG	41	-5078.5081	10435.1790	0.0000	1.0000
HKYI	40	-5085.1141	10441.6065	0.0000	1.0000
SYMIG	42	-5078.5084	10441.9640	0.0000	1.0000
K2PI	37	-5097.9854	10446.9958	0.0000	1.0000
GTRI	44	-5081.7725	10462.0610	0.0000	1.0000
SYMI	41	-5097.0984	10472.3595	0.0000	1.0000
HKY	39	-5155.0907	10574.7751	0.0000	1.0000
K2P	36	-5169.7497	10583.7399	0.0000	1.0000
GTR	43	-5151.0330	10593.7977	0.0000	1.0000
SYM	40	-5168.6624	10608.7031	0.0000	1.0000
JC69G	36	-5214.2767	10672.7939	0.0000	1.0000
F81G	39	-5205.8030	10676.1997	0.0000	1.0000
JC69IG	37	-5214.2771	10679.5791	0.0000	1.0000
F81IG	40	-5205.8032	10682.9847	0.0000	1.0000
JC69I	36	-5231.4271	10707.0946	0.0000	1.0000
F81I	39	-5223.0295	10710.6529	0.0000	1.0000
JC69	35	-5297.7059	10832.8678	0.0000	1.0000
F81	38	-5288.5492	10834.9078	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/chr2_22017.phylip = 1 - 884;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_22017.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/chr2_22017.phylip = 1 - 884;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_22017.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/chr2_22017.phylip = 1 - 884;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_22017.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

