
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:36 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/chr5_2308.phylip" (19 taxa, 764 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	-2614.3480	5322.2037	0.5874	0.5874
GTRI	44	-2615.3832	5324.2741	0.2086	0.7960
GTRIG	45	-2614.2784	5324.3228	0.2036	0.9996
HKYG	40	-2626.8055	5338.1477	0.0002	0.9998
HKYI	40	-2627.6654	5339.8675	0.0001	0.9999
HKYIG	41	-2626.7431	5340.2562	0.0001	1.0000
SYMG	41	-2636.8232	5360.4166	0.0000	1.0000
SYMI	41	-2637.4002	5361.5704	0.0000	1.0000
SYMIG	42	-2636.7508	5362.5113	0.0000	1.0000
K2PG	37	-2644.6237	5367.1206	0.0000	1.0000
K2PI	37	-2645.4698	5368.8128	0.0000	1.0000
K2PIG	38	-2644.5934	5369.2751	0.0000	1.0000
GTR	43	-2641.5128	5374.2812	0.0000	1.0000
HKY	39	-2652.7407	5387.7907	0.0000	1.0000
SYM	40	-2661.4021	5407.3408	0.0000	1.0000
K2P	36	-2669.5843	5414.8330	0.0000	1.0000
F81G	39	-2703.5070	5489.3234	0.0000	1.0000
F81IG	40	-2703.4805	5491.4976	0.0000	1.0000
F81I	39	-2704.8343	5491.9781	0.0000	1.0000
JC69G	36	-2717.5532	5510.7708	0.0000	1.0000
JC69IG	37	-2717.5331	5512.9396	0.0000	1.0000
JC69I	36	-2718.7407	5513.1457	0.0000	1.0000
F81	38	-2730.1030	5540.2944	0.0000	1.0000
JC69	35	-2741.8765	5557.2146	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2614.3480	5316.6961	0.5714	0.5714
GTRIG	45	-2614.2784	5318.5567	0.2254	0.7968
GTRI	44	-2615.3832	5318.7664	0.2030	0.9998
HKYG	40	-2626.8055	5333.6110	0.0001	0.9999
HKYI	40	-2627.6654	5335.3308	0.0001	1.0000
HKYIG	41	-2626.7431	5335.4861	0.0000	1.0000
SYMG	41	-2636.8232	5355.6465	0.0000	1.0000
SYMI	41	-2637.4002	5356.8004	0.0000	1.0000
SYMIG	42	-2636.7508	5357.5016	0.0000	1.0000
K2PG	37	-2644.6237	5363.2473	0.0000	1.0000
K2PI	37	-2645.4698	5364.9395	0.0000	1.0000
K2PIG	38	-2644.5934	5365.1868	0.0000	1.0000
GTR	43	-2641.5128	5369.0256	0.0000	1.0000
HKY	39	-2652.7407	5383.4813	0.0000	1.0000
SYM	40	-2661.4021	5402.8042	0.0000	1.0000
K2P	36	-2669.5843	5411.1686	0.0000	1.0000
F81G	39	-2703.5070	5485.0140	0.0000	1.0000
F81IG	40	-2703.4805	5486.9609	0.0000	1.0000
F81I	39	-2704.8343	5487.6687	0.0000	1.0000
JC69G	36	-2717.5532	5507.1064	0.0000	1.0000
JC69IG	37	-2717.5331	5509.0663	0.0000	1.0000
JC69I	36	-2718.7407	5509.4813	0.0000	1.0000
F81	38	-2730.1030	5536.2061	0.0000	1.0000
JC69	35	-2741.8765	5553.7531	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2626.8055	5519.1537	0.4816	0.4816
GTRG	44	-2614.3480	5520.7930	0.2122	0.6938
HKYI	40	-2627.6654	5520.8736	0.2038	0.8976
GTRI	44	-2615.3832	5522.8634	0.0754	0.9729
HKYIG	41	-2626.7431	5525.6674	0.0185	0.9915
GTRIG	45	-2614.2784	5527.2923	0.0082	0.9997
K2PG	37	-2644.6237	5534.8743	0.0002	0.9999
K2PI	37	-2645.4698	5536.5665	0.0001	1.0000
K2PIG	38	-2644.5934	5541.4524	0.0000	1.0000
SYMG	41	-2636.8232	5545.8278	0.0000	1.0000
SYMI	41	-2637.4002	5546.9816	0.0000	1.0000
SYMIG	42	-2636.7508	5552.3214	0.0000	1.0000
HKY	39	-2652.7407	5564.3855	0.0000	1.0000
GTR	43	-2641.5128	5568.4840	0.0000	1.0000
K2P	36	-2669.5843	5578.1571	0.0000	1.0000
SYM	40	-2661.4021	5588.3469	0.0000	1.0000
F81G	39	-2703.5070	5665.9182	0.0000	1.0000
F81I	39	-2704.8343	5668.5728	0.0000	1.0000
F81IG	40	-2703.4805	5672.5037	0.0000	1.0000
JC69G	36	-2717.5532	5674.0948	0.0000	1.0000
JC69I	36	-2718.7407	5676.4698	0.0000	1.0000
JC69IG	37	-2717.5331	5680.6933	0.0000	1.0000
F81	38	-2730.1030	5712.4717	0.0000	1.0000
JC69	35	-2741.8765	5716.1030	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/chr5_2308.phylip = 1 - 764;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_2308.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/chr5_2308.phylip = 1 - 764;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_2308.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/chr5_2308.phylip = 1 - 764;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_2308.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

