
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:16 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/chr3_6115.phylip" (19 taxa, 663 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	-2694.1388	5482.6853	0.9558	0.9558
HKYG	40	-2702.4245	5490.1223	0.0232	0.9790
HKYIG	41	-2702.3273	5492.2005	0.0082	0.9872
GTRI	44	-2699.1109	5492.6296	0.0066	0.9938
GTRIG	45	-2698.0515	5492.8128	0.0060	0.9999
HKYI	40	-2707.5111	5500.2954	0.0001	1.0000
K2PG	37	-2715.8770	5510.2532	0.0000	1.0000
SYMG	41	-2711.5552	5510.6564	0.0000	1.0000
K2PIG	38	-2715.7614	5512.2727	0.0000	1.0000
SYMIG	42	-2711.4857	5512.7972	0.0000	1.0000
SYMI	41	-2716.3206	5520.1871	0.0000	1.0000
K2PI	37	-2720.9582	5520.4155	0.0000	1.0000
GTR	43	-2738.6793	5569.4717	0.0000	1.0000
HKY	39	-2746.5372	5576.0824	0.0000	1.0000
SYM	40	-2754.9016	5595.0766	0.0000	1.0000
K2P	36	-2759.6842	5595.6241	0.0000	1.0000
F81G	39	-2764.2491	5611.5063	0.0000	1.0000
F81IG	40	-2764.1949	5613.6631	0.0000	1.0000
F81I	39	-2768.2719	5619.5518	0.0000	1.0000
JC69G	36	-2774.1395	5624.5347	0.0000	1.0000
JC69IG	37	-2774.0751	5626.6494	0.0000	1.0000
JC69I	36	-2778.2855	5632.8265	0.0000	1.0000
F81	38	-2804.3596	5689.4691	0.0000	1.0000
JC69	35	-2814.4910	5703.0011	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2694.1388	5476.2776	0.9674	0.9674
HKYG	40	-2702.4245	5484.8490	0.0133	0.9807
GTRIG	45	-2698.0515	5486.1029	0.0071	0.9878
GTRI	44	-2699.1109	5486.2218	0.0067	0.9945
HKYIG	41	-2702.3273	5486.6546	0.0054	0.9999
HKYI	40	-2707.5111	5495.0221	0.0001	1.0000
SYMG	41	-2711.5552	5505.1105	0.0000	1.0000
K2PG	37	-2715.8770	5505.7540	0.0000	1.0000
SYMIG	42	-2711.4857	5506.9714	0.0000	1.0000
K2PIG	38	-2715.7614	5507.5227	0.0000	1.0000
SYMI	41	-2716.3206	5514.6412	0.0000	1.0000
K2PI	37	-2720.9582	5515.9163	0.0000	1.0000
GTR	43	-2738.6793	5563.3586	0.0000	1.0000
HKY	39	-2746.5372	5571.0744	0.0000	1.0000
SYM	40	-2754.9016	5589.8033	0.0000	1.0000
K2P	36	-2759.6842	5591.3685	0.0000	1.0000
F81G	39	-2764.2491	5606.4983	0.0000	1.0000
F81IG	40	-2764.1949	5608.3898	0.0000	1.0000
F81I	39	-2768.2719	5614.5437	0.0000	1.0000
JC69G	36	-2774.1395	5620.2791	0.0000	1.0000
JC69IG	37	-2774.0751	5622.1502	0.0000	1.0000
JC69I	36	-2778.2855	5628.5709	0.0000	1.0000
F81	38	-2804.3596	5684.7191	0.0000	1.0000
JC69	35	-2814.4910	5698.9819	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2702.4245	5664.7200	0.9226	0.9226
HKYIG	41	-2702.3273	5671.0224	0.0395	0.9621
K2PG	37	-2715.8770	5672.1347	0.0226	0.9848
GTRG	44	-2694.1388	5674.1357	0.0083	0.9931
HKYI	40	-2707.5111	5674.8931	0.0057	0.9988
K2PIG	38	-2715.7614	5678.4002	0.0010	0.9998
K2PI	37	-2720.9582	5682.2970	0.0001	0.9999
GTRI	44	-2699.1109	5684.0799	0.0001	1.0000
GTRIG	45	-2698.0515	5688.4578	0.0000	1.0000
SYMG	41	-2711.5552	5689.4783	0.0000	1.0000
SYMIG	42	-2711.4857	5695.8359	0.0000	1.0000
SYMI	41	-2716.3206	5699.0090	0.0000	1.0000
HKY	39	-2746.5372	5746.4486	0.0000	1.0000
K2P	36	-2759.6842	5753.2524	0.0000	1.0000
GTR	43	-2738.6793	5756.7199	0.0000	1.0000
SYM	40	-2754.9016	5769.6743	0.0000	1.0000
F81G	39	-2764.2491	5781.8725	0.0000	1.0000
JC69G	36	-2774.1395	5782.1630	0.0000	1.0000
F81IG	40	-2764.1949	5788.2608	0.0000	1.0000
JC69IG	37	-2774.0751	5788.5309	0.0000	1.0000
F81I	39	-2768.2719	5789.9180	0.0000	1.0000
JC69I	36	-2778.2855	5790.4548	0.0000	1.0000
F81	38	-2804.3596	5855.5966	0.0000	1.0000
JC69	35	-2814.4910	5856.3690	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_6115.phylip = 1 - 663;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_6115.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_6115.phylip = 1 - 663;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_6115.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_6115.phylip = 1 - 663;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_6115.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

