
Output from mraic.pl version 1.4.4 by Johan Nylander
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13:38 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/chrZ_6588.phylip" (19 taxa, 1220 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	-5425.8431	10945.2125	0.5700	0.5700
GTRG	44	-5427.2935	10945.9573	0.3928	0.9627
HKYIG	41	-5433.5037	10951.9311	0.0198	0.9826
HKYG	40	-5434.9658	10952.7135	0.0134	0.9960
GTRI	44	-5431.9208	10955.2118	0.0038	0.9998
HKYI	40	-5439.1425	10961.0670	0.0002	1.0000
SYMIG	42	-5469.7725	11026.6137	0.0000	1.0000
SYMG	41	-5472.0260	11028.9757	0.0000	1.0000
SYMI	41	-5473.4459	11031.8153	0.0000	1.0000
K2PIG	38	-5477.0552	11032.6202	0.0000	1.0000
K2PG	37	-5478.9616	11034.3022	0.0000	1.0000
K2PI	37	-5481.1783	11038.7356	0.0000	1.0000
F81IG	40	-5547.6987	11178.1794	0.0000	1.0000
F81G	39	-5549.3605	11179.3651	0.0000	1.0000
F81I	39	-5551.2821	11183.2083	0.0000	1.0000
JC69IG	37	-5578.0805	11232.5401	0.0000	1.0000
JC69G	36	-5579.8463	11233.9444	0.0000	1.0000
JC69I	36	-5581.1781	11236.6080	0.0000	1.0000
GTR	43	-5595.3418	11279.9012	0.0000	1.0000
HKY	39	-5601.8014	11284.2469	0.0000	1.0000
SYM	40	-5630.0914	11342.9648	0.0000	1.0000
K2P	36	-5638.8546	11351.9611	0.0000	1.0000
F81	38	-5701.3547	11481.2191	0.0000	1.0000
JC69	35	-5729.4435	11531.0153	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRIG	45	-5425.8431	10941.6861	0.5932	0.5932
GTRG	44	-5427.2935	10942.5870	0.3781	0.9713
HKYIG	41	-5433.5037	10949.0075	0.0153	0.9865
HKYG	40	-5434.9658	10949.9315	0.0096	0.9962
GTRI	44	-5431.9208	10951.8416	0.0037	0.9999
HKYI	40	-5439.1425	10958.2850	0.0001	1.0000
SYMIG	42	-5469.7725	11023.5449	0.0000	1.0000
SYMG	41	-5472.0260	11026.0521	0.0000	1.0000
SYMI	41	-5473.4459	11028.8917	0.0000	1.0000
K2PIG	38	-5477.0552	11030.1104	0.0000	1.0000
K2PG	37	-5478.9616	11031.9232	0.0000	1.0000
K2PI	37	-5481.1783	11036.3566	0.0000	1.0000
F81IG	40	-5547.6987	11175.3974	0.0000	1.0000
F81G	39	-5549.3605	11176.7210	0.0000	1.0000
F81I	39	-5551.2821	11180.5643	0.0000	1.0000
JC69IG	37	-5578.0805	11230.1610	0.0000	1.0000
JC69G	36	-5579.8463	11231.6925	0.0000	1.0000
JC69I	36	-5581.1781	11234.3561	0.0000	1.0000
GTR	43	-5595.3418	11276.6836	0.0000	1.0000
HKY	39	-5601.8014	11281.6028	0.0000	1.0000
SYM	40	-5630.0914	11340.1827	0.0000	1.0000
K2P	36	-5638.8546	11349.7092	0.0000	1.0000
F81	38	-5701.3547	11478.7094	0.0000	1.0000
JC69	35	-5729.4435	11528.8870	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-5434.9658	11154.1958	0.8768	0.8768
HKYIG	41	-5433.5037	11158.3784	0.1083	0.9851
HKYI	40	-5439.1425	11162.5492	0.0135	0.9986
GTRG	44	-5427.2935	11167.2777	0.0013	0.9998
GTRIG	45	-5425.8431	11171.4834	0.0002	1.0000
GTRI	44	-5431.9208	11176.5322	0.0000	1.0000
K2PG	37	-5478.9616	11220.8676	0.0000	1.0000
K2PIG	38	-5477.0552	11224.1615	0.0000	1.0000
K2PI	37	-5481.1783	11225.3010	0.0000	1.0000
SYMG	41	-5472.0260	11235.4229	0.0000	1.0000
SYMIG	42	-5469.7725	11238.0224	0.0000	1.0000
SYMI	41	-5473.4459	11238.2626	0.0000	1.0000
F81G	39	-5549.3605	11375.8787	0.0000	1.0000
F81IG	40	-5547.6987	11379.6617	0.0000	1.0000
F81I	39	-5551.2821	11379.7219	0.0000	1.0000
JC69G	36	-5579.8463	11415.5303	0.0000	1.0000
JC69I	36	-5581.1781	11418.1939	0.0000	1.0000
JC69IG	37	-5578.0805	11419.1055	0.0000	1.0000
HKY	39	-5601.8014	11480.7605	0.0000	1.0000
GTR	43	-5595.3418	11496.2676	0.0000	1.0000
K2P	36	-5638.8546	11533.5471	0.0000	1.0000
SYM	40	-5630.0914	11544.4470	0.0000	1.0000
F81	38	-5701.3547	11672.7604	0.0000	1.0000
JC69	35	-5729.4435	11707.6182	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/chrZ_6588.phylip = 1 - 1220;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_6588.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/chrZ_6588.phylip = 1 - 1220;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_6588.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/chrZ_6588.phylip = 1 - 1220;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_6588.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

