
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:16 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/chr1_28846.phylip" (19 taxa, 775 characters)

Minimum AIC  model: HKYIG
Minimum AICc model: HKYIG
Minimum BIC  model: K2PG


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
HKYIG	41	-2088.8573	4264.4131	0.4656	0.4656
HKYG	40	-2089.9793	4264.4272	0.4623	0.9278
GTRG	44	-2088.4451	4270.3148	0.0243	0.9522
GTRIG	45	-2087.3683	4270.4156	0.0232	0.9753
HKYI	40	-2093.0824	4270.6334	0.0208	0.9961
K2PG	37	-2099.1923	4276.2000	0.0013	0.9974
K2PIG	38	-2098.0984	4276.2239	0.0013	0.9986
GTRI	44	-2091.4183	4276.2613	0.0012	0.9999
K2PI	37	-2102.1397	4282.0949	0.0001	1.0000
SYMG	41	-2098.8508	4284.4002	0.0000	1.0000
SYMIG	42	-2097.7482	4284.4308	0.0000	1.0000
SYMI	41	-2101.8310	4290.3606	0.0000	1.0000
HKY	39	-2125.6184	4333.4817	0.0000	1.0000
GTR	43	-2124.4988	4340.1741	0.0000	1.0000
K2P	36	-2134.6902	4344.9902	0.0000	1.0000
F81G	39	-2131.9208	4346.0865	0.0000	1.0000
F81IG	40	-2131.0783	4346.6253	0.0000	1.0000
F81I	39	-2134.5720	4351.3889	0.0000	1.0000
SYM	40	-2134.4171	4353.3028	0.0000	1.0000
JC69G	36	-2140.3734	4356.3565	0.0000	1.0000
JC69IG	37	-2139.5096	4356.8348	0.0000	1.0000
JC69I	36	-2143.0690	4361.7477	0.0000	1.0000
F81	38	-2165.9788	4411.9848	0.0000	1.0000
JC69	35	-2174.4530	4422.3160	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYIG	41	-2088.8573	4259.7146	0.4787	0.4787
HKYG	40	-2089.9793	4259.9586	0.4237	0.9024
GTRIG	45	-2087.3683	4264.7366	0.0389	0.9413
GTRG	44	-2088.4451	4264.8902	0.0360	0.9773
HKYI	40	-2093.0824	4266.1648	0.0190	0.9963
GTRI	44	-2091.4183	4270.8367	0.0018	0.9981
K2PIG	38	-2098.0984	4272.1967	0.0009	0.9991
K2PG	37	-2099.1923	4272.3846	0.0008	0.9999
K2PI	37	-2102.1397	4278.2795	0.0000	1.0000
SYMIG	42	-2097.7482	4279.4964	0.0000	1.0000
SYMG	41	-2098.8508	4279.7017	0.0000	1.0000
SYMI	41	-2101.8310	4285.6621	0.0000	1.0000
HKY	39	-2125.6184	4329.2368	0.0000	1.0000
GTR	43	-2124.4988	4334.9976	0.0000	1.0000
K2P	36	-2134.6902	4341.3804	0.0000	1.0000
F81G	39	-2131.9208	4341.8416	0.0000	1.0000
F81IG	40	-2131.0783	4342.1567	0.0000	1.0000
F81I	39	-2134.5720	4347.1440	0.0000	1.0000
SYM	40	-2134.4171	4348.8342	0.0000	1.0000
JC69G	36	-2140.3734	4352.7467	0.0000	1.0000
JC69IG	37	-2139.5096	4353.0193	0.0000	1.0000
JC69I	36	-2143.0690	4358.1380	0.0000	1.0000
F81	38	-2165.9788	4407.9577	0.0000	1.0000
JC69	35	-2174.4530	4418.9060	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-2099.1923	4444.5405	0.5894	0.5894
HKYG	40	-2089.9793	4446.0731	0.2739	0.8633
K2PIG	38	-2098.0984	4449.0055	0.0632	0.9266
K2PI	37	-2102.1397	4450.4354	0.0309	0.9575
HKYIG	41	-2088.8573	4450.4820	0.0302	0.9877
HKYI	40	-2093.0824	4452.2793	0.0123	1.0000
GTRG	44	-2088.4451	4469.6161	0.0000	1.0000
SYMG	41	-2098.8508	4470.4691	0.0000	1.0000
GTRIG	45	-2087.3683	4474.1154	0.0000	1.0000
SYMIG	42	-2097.7482	4474.9166	0.0000	1.0000
GTRI	44	-2091.4183	4475.5626	0.0000	1.0000
SYMI	41	-2101.8310	4476.4295	0.0000	1.0000
K2P	36	-2134.6902	4508.8835	0.0000	1.0000
HKY	39	-2125.6184	4510.6985	0.0000	1.0000
JC69G	36	-2140.3734	4520.2498	0.0000	1.0000
F81G	39	-2131.9208	4523.3032	0.0000	1.0000
JC69IG	37	-2139.5096	4525.1752	0.0000	1.0000
JC69I	36	-2143.0690	4525.6410	0.0000	1.0000
F81IG	40	-2131.0783	4528.2712	0.0000	1.0000
F81I	39	-2134.5720	4528.6057	0.0000	1.0000
SYM	40	-2134.4171	4534.9487	0.0000	1.0000
GTR	43	-2124.4988	4535.0707	0.0000	1.0000
JC69	35	-2174.4530	4581.7562	0.0000	1.0000
F81	38	-2165.9788	4584.7665	0.0000	1.0000



To specify default values for best AIC, AICc, or BIC models in MrBayes:

[Mrbayes block for the best AIC model (HKYIG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_28846.phylip = 1 - 775;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_28846.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best AICc model (HKYIG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_28846.phylip = 1 - 775;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_28846.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best BIC model (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_28846.phylip = 1 - 775;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_28846.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=gamma;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


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End of Output

