
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:16 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/chr1_32337.phylip" (19 taxa, 896 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	-2665.1877	5425.2459	0.4100	0.4100
GTRG	44	-2666.8357	5426.3248	0.2390	0.6490
GTRI	44	-2666.9934	5426.6401	0.2042	0.8532
HKYIG	41	-2671.3340	5428.7009	0.0729	0.9260
HKYG	40	-2672.9950	5429.8262	0.0415	0.9676
HKYI	40	-2673.2414	5430.3191	0.0324	1.0000
GTR	43	-2685.6674	5461.7762	0.0000	1.0000
HKY	39	-2691.4464	5464.5376	0.0000	1.0000
K2PG	37	-2696.2146	5469.7066	0.0000	1.0000
K2PIG	38	-2695.3086	5470.0757	0.0000	1.0000
K2PI	37	-2696.7157	5470.7087	0.0000	1.0000
SYMG	41	-2694.3261	5474.6850	0.0000	1.0000
SYMI	41	-2694.7381	5475.5090	0.0000	1.0000
SYMIG	42	-2694.8532	5477.9409	0.0000	1.0000
K2P	36	-2714.5820	5504.2654	0.0000	1.0000
SYM	40	-2712.4503	5508.7369	0.0000	1.0000
F81G	39	-2743.3861	5568.4170	0.0000	1.0000
F81I	39	-2743.7900	5569.2248	0.0000	1.0000
F81IG	40	-2743.3935	5570.6232	0.0000	1.0000
JC69G	36	-2762.3587	5599.8186	0.0000	1.0000
F81	38	-2760.5887	5600.6361	0.0000	1.0000
JC69I	36	-2762.9425	5600.9862	0.0000	1.0000
JC69IG	37	-2762.1816	5601.6406	0.0000	1.0000
JC69	35	-2779.9795	5632.8892	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRIG	45	-2665.1877	5420.3753	0.4557	0.4557
GTRG	44	-2666.8357	5421.6715	0.2384	0.6941
GTRI	44	-2666.9934	5421.9867	0.2036	0.8977
HKYIG	41	-2671.3340	5424.6681	0.0533	0.9510
HKYG	40	-2672.9950	5425.9900	0.0275	0.9785
HKYI	40	-2673.2414	5426.4828	0.0215	1.0000
GTR	43	-2685.6674	5457.3349	0.0000	1.0000
HKY	39	-2691.4464	5460.8928	0.0000	1.0000
K2PG	37	-2696.2146	5466.4292	0.0000	1.0000
K2PIG	38	-2695.3086	5466.6172	0.0000	1.0000
K2PI	37	-2696.7157	5467.4313	0.0000	1.0000
SYMG	41	-2694.3261	5470.6522	0.0000	1.0000
SYMI	41	-2694.7381	5471.4762	0.0000	1.0000
SYMIG	42	-2694.8532	5473.7064	0.0000	1.0000
K2P	36	-2714.5820	5501.1641	0.0000	1.0000
SYM	40	-2712.4503	5504.9006	0.0000	1.0000
F81G	39	-2743.3861	5564.7721	0.0000	1.0000
F81I	39	-2743.7900	5565.5799	0.0000	1.0000
F81IG	40	-2743.3935	5566.7869	0.0000	1.0000
JC69G	36	-2762.3587	5596.7173	0.0000	1.0000
F81	38	-2760.5887	5597.1775	0.0000	1.0000
JC69I	36	-2762.9425	5597.8849	0.0000	1.0000
JC69IG	37	-2762.1816	5598.3632	0.0000	1.0000
JC69	35	-2779.9795	5629.9589	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2672.9950	5617.9076	0.5106	0.5106
HKYI	40	-2673.2414	5618.4005	0.3990	0.9096
HKYIG	41	-2671.3340	5621.3837	0.0898	0.9994
GTRG	44	-2666.8357	5632.7809	0.0003	0.9997
GTRI	44	-2666.9934	5633.0961	0.0003	0.9999
GTRIG	45	-2665.1877	5636.2827	0.0001	1.0000
K2PG	37	-2696.2146	5643.9530	0.0000	1.0000
K2PI	37	-2696.7157	5644.9551	0.0000	1.0000
HKY	39	-2691.4464	5648.0125	0.0000	1.0000
K2PIG	38	-2695.3086	5648.9389	0.0000	1.0000
GTR	43	-2685.6674	5663.6463	0.0000	1.0000
SYMG	41	-2694.3261	5667.3677	0.0000	1.0000
SYMI	41	-2694.7381	5668.1918	0.0000	1.0000
K2P	36	-2714.5820	5673.8900	0.0000	1.0000
SYMIG	42	-2694.8532	5675.2199	0.0000	1.0000
SYM	40	-2712.4503	5696.8182	0.0000	1.0000
F81G	39	-2743.3861	5751.8918	0.0000	1.0000
F81I	39	-2743.7900	5752.6996	0.0000	1.0000
F81IG	40	-2743.3935	5758.7045	0.0000	1.0000
JC69G	36	-2762.3587	5769.4432	0.0000	1.0000
JC69I	36	-2762.9425	5770.6108	0.0000	1.0000
JC69IG	37	-2762.1816	5775.8870	0.0000	1.0000
F81	38	-2760.5887	5779.4992	0.0000	1.0000
JC69	35	-2779.9795	5797.8869	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/chr1_32337.phylip = 1 - 896;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_32337.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/chr1_32337.phylip = 1 - 896;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_32337.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/chr1_32337.phylip = 1 - 896;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_32337.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;


-------------------------------------------------------------
End of Output

