
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:43 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/chr7_10268.phylip" (19 taxa, 692 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	-2251.4425	4597.0056	0.6730	0.6730
GTRIG	45	-2251.4423	4599.2932	0.2144	0.8874
GTRI	44	-2253.2760	4600.6725	0.1076	0.9950
HKYG	40	-2261.5627	4608.1638	0.0025	0.9975
GTR	43	-2258.8942	4609.6280	0.0012	0.9988
HKYIG	41	-2261.5624	4610.4233	0.0008	0.9996
HKYI	40	-2263.3686	4611.7756	0.0004	1.0000
HKY	39	-2268.6677	4620.1208	0.0000	1.0000
K2PG	37	-2294.4335	4667.1667	0.0000	1.0000
SYMG	41	-2291.0136	4669.3256	0.0000	1.0000
K2PIG	38	-2294.4331	4669.4053	0.0000	1.0000
K2PI	37	-2296.3642	4671.0281	0.0000	1.0000
SYMIG	42	-2291.0168	4671.5991	0.0000	1.0000
SYMI	41	-2292.8795	4673.0574	0.0000	1.0000
K2P	36	-2302.7437	4681.5545	0.0000	1.0000
SYM	40	-2299.2100	4683.4584	0.0000	1.0000
F81G	39	-2312.1656	4707.1164	0.0000	1.0000
F81IG	40	-2312.1653	4709.3689	0.0000	1.0000
F81I	39	-2313.7361	4710.2574	0.0000	1.0000
F81	38	-2318.7430	4718.0251	0.0000	1.0000
JC69G	36	-2338.6460	4753.3592	0.0000	1.0000
JC69IG	37	-2338.6456	4755.5910	0.0000	1.0000
JC69I	36	-2340.3511	4756.7693	0.0000	1.0000
JC69	35	-2346.0331	4765.9076	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2251.4425	4590.8850	0.6524	0.6524
GTRIG	45	-2251.4423	4592.8846	0.2401	0.8925
GTRI	44	-2253.2760	4594.5519	0.1043	0.9968
HKYG	40	-2261.5627	4603.1254	0.0014	0.9982
GTR	43	-2258.8942	4603.7885	0.0010	0.9992
HKYIG	41	-2261.5624	4605.1248	0.0005	0.9998
HKYI	40	-2263.3686	4606.7372	0.0002	1.0000
HKY	39	-2268.6677	4615.3355	0.0000	1.0000
K2PG	37	-2294.4335	4662.8670	0.0000	1.0000
SYMG	41	-2291.0136	4664.0272	0.0000	1.0000
K2PIG	38	-2294.4331	4664.8662	0.0000	1.0000
SYMIG	42	-2291.0168	4666.0337	0.0000	1.0000
K2PI	37	-2296.3642	4666.7284	0.0000	1.0000
SYMI	41	-2292.8795	4667.7589	0.0000	1.0000
K2P	36	-2302.7437	4677.4874	0.0000	1.0000
SYM	40	-2299.2100	4678.4200	0.0000	1.0000
F81G	39	-2312.1656	4702.3311	0.0000	1.0000
F81IG	40	-2312.1653	4704.3305	0.0000	1.0000
F81I	39	-2313.7361	4705.4721	0.0000	1.0000
F81	38	-2318.7430	4713.4860	0.0000	1.0000
JC69G	36	-2338.6460	4749.2920	0.0000	1.0000
JC69IG	37	-2338.6456	4751.2913	0.0000	1.0000
JC69I	36	-2340.3511	4752.7021	0.0000	1.0000
JC69	35	-2346.0331	4762.0662	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2261.5627	4784.7088	0.7771	0.7771
HKYI	40	-2263.3686	4788.3206	0.1277	0.9048
GTRG	44	-2251.4425	4790.6268	0.0403	0.9451
HKYIG	41	-2261.5624	4791.2478	0.0295	0.9746
HKY	39	-2268.6677	4792.3793	0.0168	0.9914
GTRI	44	-2253.2760	4794.2937	0.0064	0.9979
GTRIG	45	-2251.4423	4797.1659	0.0015	0.9994
GTR	43	-2258.8942	4798.9907	0.0006	1.0000
K2PG	37	-2294.4335	4830.8317	0.0000	1.0000
K2PI	37	-2296.3642	4834.6931	0.0000	1.0000
K2PIG	38	-2294.4331	4837.3705	0.0000	1.0000
K2P	36	-2302.7437	4840.9125	0.0000	1.0000
SYMG	41	-2291.0136	4850.1502	0.0000	1.0000
SYMI	41	-2292.8795	4853.8819	0.0000	1.0000
SYMIG	42	-2291.0168	4856.6963	0.0000	1.0000
SYM	40	-2299.2100	4860.0035	0.0000	1.0000
F81G	39	-2312.1656	4879.3750	0.0000	1.0000
F81I	39	-2313.7361	4882.5160	0.0000	1.0000
F81IG	40	-2312.1653	4885.9139	0.0000	1.0000
F81	38	-2318.7430	4885.9903	0.0000	1.0000
JC69G	36	-2338.6460	4912.7171	0.0000	1.0000
JC69I	36	-2340.3511	4916.1272	0.0000	1.0000
JC69IG	37	-2338.6456	4919.2560	0.0000	1.0000
JC69	35	-2346.0331	4920.9517	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/chr7_10268.phylip = 1 - 692;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10268.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/chr7_10268.phylip = 1 - 692;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10268.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/chr7_10268.phylip = 1 - 692;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10268.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

