
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:23 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/chr6_3147.phylip" (19 taxa, 559 characters)

Minimum AIC  model: GTRIG
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	-1461.4411	3018.5866	0.3994	0.3994
GTRIG	45	-1460.2585	3018.5872	0.3992	0.7986
GTRI	44	-1462.2073	3020.1188	0.1856	0.9842
HKYIG	41	-1469.1101	3026.8816	0.0063	0.9905
HKYG	40	-1470.4047	3027.1414	0.0055	0.9961
HKYI	40	-1470.7523	3027.8366	0.0039	1.0000
GTR	43	-1494.1937	3081.7349	0.0000	1.0000
F81IG	40	-1498.0926	3082.5173	0.0000	1.0000
F81G	39	-1499.2905	3082.5925	0.0000	1.0000
F81I	39	-1499.5885	3083.1886	0.0000	1.0000
HKY	39	-1503.0992	3090.2100	0.0000	1.0000
K2PIG	38	-1505.1618	3092.0236	0.0000	1.0000
K2PG	37	-1506.5856	3092.5686	0.0000	1.0000
K2PI	37	-1506.7494	3092.8960	0.0000	1.0000
SYMIG	42	-1501.6519	3094.3039	0.0000	1.0000
SYMG	41	-1502.8865	3094.4345	0.0000	1.0000
SYMI	41	-1503.1444	3094.9502	0.0000	1.0000
JC69IG	37	-1530.0111	3139.4195	0.0000	1.0000
JC69G	36	-1531.2534	3139.6102	0.0000	1.0000
JC69I	36	-1531.4666	3140.0366	0.0000	1.0000
F81	38	-1532.5437	3146.7875	0.0000	1.0000
K2P	36	-1540.5724	3158.2482	0.0000	1.0000
SYM	40	-1536.3715	3159.0750	0.0000	1.0000
JC69	35	-1565.2116	3205.2415	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRIG	45	-1460.2585	3010.5170	0.4468	0.4468
GTRG	44	-1461.4411	3010.8823	0.3722	0.8191
GTRI	44	-1462.2073	3012.4146	0.1730	0.9921
HKYIG	41	-1469.1101	3020.2201	0.0035	0.9956
HKYG	40	-1470.4047	3020.8094	0.0026	0.9982
HKYI	40	-1470.7523	3021.5046	0.0018	1.0000
GTR	43	-1494.1937	3074.3874	0.0000	1.0000
F81IG	40	-1498.0926	3076.1852	0.0000	1.0000
F81G	39	-1499.2905	3076.5810	0.0000	1.0000
F81I	39	-1499.5885	3077.1770	0.0000	1.0000
HKY	39	-1503.0992	3084.1984	0.0000	1.0000
K2PIG	38	-1505.1618	3086.3236	0.0000	1.0000
K2PG	37	-1506.5856	3087.1713	0.0000	1.0000
SYMIG	42	-1501.6519	3087.3039	0.0000	1.0000
K2PI	37	-1506.7494	3087.4987	0.0000	1.0000
SYMG	41	-1502.8865	3087.7730	0.0000	1.0000
SYMI	41	-1503.1444	3088.2887	0.0000	1.0000
JC69IG	37	-1530.0111	3134.0222	0.0000	1.0000
JC69G	36	-1531.2534	3134.5067	0.0000	1.0000
JC69I	36	-1531.4666	3134.9331	0.0000	1.0000
F81	38	-1532.5437	3141.0875	0.0000	1.0000
SYM	40	-1536.3715	3152.7430	0.0000	1.0000
K2P	36	-1540.5724	3153.1447	0.0000	1.0000
JC69	35	-1565.2116	3200.4232	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1470.4047	3193.8554	0.5261	0.5261
HKYI	40	-1470.7523	3194.5505	0.3716	0.8977
HKYIG	41	-1469.1101	3197.5923	0.0812	0.9789
GTRG	44	-1461.4411	3201.2329	0.0132	0.9921
GTRI	44	-1462.2073	3202.7651	0.0061	0.9982
GTRIG	45	-1460.2585	3205.1938	0.0018	1.0000
F81G	39	-1499.2905	3245.3008	0.0000	1.0000
F81I	39	-1499.5885	3245.8968	0.0000	1.0000
K2PG	37	-1506.5856	3247.2388	0.0000	1.0000
K2PI	37	-1506.7494	3247.5663	0.0000	1.0000
F81IG	40	-1498.0926	3249.2312	0.0000	1.0000
K2PIG	38	-1505.1618	3250.7173	0.0000	1.0000
HKY	39	-1503.0992	3252.9183	0.0000	1.0000
GTR	43	-1494.1937	3260.4118	0.0000	1.0000
SYMG	41	-1502.8865	3265.1451	0.0000	1.0000
SYMI	41	-1503.1444	3265.6608	0.0000	1.0000
SYMIG	42	-1501.6519	3269.0022	0.0000	1.0000
JC69G	36	-1531.2534	3290.2481	0.0000	1.0000
JC69I	36	-1531.4666	3290.6745	0.0000	1.0000
JC69IG	37	-1530.0111	3294.0897	0.0000	1.0000
F81	38	-1532.5437	3305.4812	0.0000	1.0000
K2P	36	-1540.5724	3308.8861	0.0000	1.0000
SYM	40	-1536.3715	3325.7889	0.0000	1.0000
JC69	35	-1565.2116	3351.8384	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/chr6_3147.phylip = 1 - 559;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_3147.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 (GTRG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_3147.phylip = 1 - 559;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_3147.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/chr6_3147.phylip = 1 - 559;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_3147.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

