
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:07 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/chr13_3033.phylip" (19 taxa, 683 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	-2649.2387	5392.6843	0.4081	0.4081
HKYG	40	-2653.7976	5392.7042	0.4041	0.8122
HKYIG	41	-2653.7822	5394.9373	0.1323	0.9445
GTRIG	45	-2650.5245	5397.5483	0.0359	0.9804
HKYI	40	-2657.0619	5399.2329	0.0154	0.9958
GTRI	44	-2653.8214	5401.8497	0.0042	1.0000
GTR	43	-2673.7283	5439.3783	0.0000	1.0000
HKY	39	-2678.5569	5439.9660	0.0000	1.0000
K2PG	37	-2711.3662	5501.0921	0.0000	1.0000
K2PIG	38	-2711.3448	5503.2921	0.0000	1.0000
SYMG	41	-2709.3090	5505.9909	0.0000	1.0000
K2PI	37	-2714.5424	5507.4444	0.0000	1.0000
SYMIG	42	-2710.4934	5510.6306	0.0000	1.0000
SYMI	41	-2713.7327	5514.8382	0.0000	1.0000
K2P	36	-2736.8212	5549.7662	0.0000	1.0000
F81G	39	-2733.8169	5550.4860	0.0000	1.0000
SYM	40	-2733.6425	5552.3940	0.0000	1.0000
F81IG	40	-2736.4010	5557.9111	0.0000	1.0000
F81I	39	-2739.3748	5561.6019	0.0000	1.0000
F81	38	-2755.7652	5592.1328	0.0000	1.0000
JC69G	36	-2776.4812	5629.0862	0.0000	1.0000
JC69IG	37	-2776.4607	5631.2810	0.0000	1.0000
JC69I	36	-2782.5988	5641.3214	0.0000	1.0000
JC69	35	-2799.1991	5672.2931	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2649.2387	5386.4774	0.5210	0.5210
HKYG	40	-2653.7976	5387.5952	0.2980	0.8190
HKYIG	41	-2653.7822	5389.5645	0.1113	0.9303
GTRIG	45	-2650.5245	5391.0490	0.0530	0.9833
HKYI	40	-2657.0619	5394.1239	0.0114	0.9947
GTRI	44	-2653.8214	5395.6428	0.0053	1.0000
GTR	43	-2673.7283	5433.4566	0.0000	1.0000
HKY	39	-2678.5569	5435.1138	0.0000	1.0000
K2PG	37	-2711.3662	5496.7325	0.0000	1.0000
K2PIG	38	-2711.3448	5498.6896	0.0000	1.0000
SYMG	41	-2709.3090	5500.6180	0.0000	1.0000
K2PI	37	-2714.5424	5503.0848	0.0000	1.0000
SYMIG	42	-2710.4934	5504.9868	0.0000	1.0000
SYMI	41	-2713.7327	5509.4653	0.0000	1.0000
F81G	39	-2733.8169	5545.6337	0.0000	1.0000
K2P	36	-2736.8212	5545.6423	0.0000	1.0000
SYM	40	-2733.6425	5547.2850	0.0000	1.0000
F81IG	40	-2736.4010	5552.8020	0.0000	1.0000
F81I	39	-2739.3748	5556.7496	0.0000	1.0000
F81	38	-2755.7652	5587.5304	0.0000	1.0000
JC69G	36	-2776.4812	5624.9623	0.0000	1.0000
JC69IG	37	-2776.4607	5626.9213	0.0000	1.0000
JC69I	36	-2782.5988	5637.1976	0.0000	1.0000
JC69	35	-2799.1991	5668.3982	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2653.7976	5568.6550	0.9283	0.9283
HKYIG	41	-2653.7822	5575.1508	0.0361	0.9643
HKYI	40	-2657.0619	5575.1837	0.0355	0.9998
GTRG	44	-2649.2387	5585.6432	0.0002	1.0000
GTRIG	45	-2650.5245	5594.7413	0.0000	1.0000
GTRI	44	-2653.8214	5594.8086	0.0000	1.0000
HKY	39	-2678.5569	5611.6471	0.0000	1.0000
GTR	43	-2673.7283	5628.0959	0.0000	1.0000
K2PG	37	-2711.3662	5664.2128	0.0000	1.0000
K2PI	37	-2714.5424	5670.5651	0.0000	1.0000
K2PIG	38	-2711.3448	5670.6964	0.0000	1.0000
SYMG	41	-2709.3090	5686.2043	0.0000	1.0000
SYMI	41	-2713.7327	5695.0516	0.0000	1.0000
SYMIG	42	-2710.4934	5695.0996	0.0000	1.0000
K2P	36	-2736.8212	5708.5961	0.0000	1.0000
F81G	39	-2733.8169	5722.1670	0.0000	1.0000
SYM	40	-2733.6425	5728.3448	0.0000	1.0000
F81I	39	-2739.3748	5733.2829	0.0000	1.0000
F81IG	40	-2736.4010	5733.8618	0.0000	1.0000
F81	38	-2755.7652	5759.5372	0.0000	1.0000
JC69G	36	-2776.4812	5787.9162	0.0000	1.0000
JC69IG	37	-2776.4607	5794.4016	0.0000	1.0000
JC69I	36	-2782.5988	5800.1514	0.0000	1.0000
JC69	35	-2799.1991	5826.8255	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/chr13_3033.phylip = 1 - 683;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr13_3033.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/chr13_3033.phylip = 1 - 683;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr13_3033.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/chr13_3033.phylip = 1 - 683;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr13_3033.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

