
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:11 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/chr2_24799.phylip" (19 taxa, 815 characters)

Minimum AIC  model: GTRIG
Minimum AICc model: GTRIG
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
GTRIG	45	-2582.9024	5261.1884	0.3969	0.3969
GTRG	44	-2584.6049	5262.3527	0.2217	0.6186
HKYIG	41	-2588.9167	5264.2888	0.0842	0.7028
HKYG	40	-2590.1794	5264.5965	0.0722	0.7750
K2PG	37	-2593.8902	5265.3995	0.0483	0.8233
K2PIG	38	-2592.7982	5265.4159	0.0479	0.8713
SYMIG	42	-2588.5516	5265.7820	0.0399	0.9112
GTRI	44	-2586.5863	5266.3154	0.0306	0.9418
SYMG	41	-2590.0808	5266.6169	0.0263	0.9680
HKYI	40	-2591.7504	5267.7386	0.0150	0.9831
K2PI	37	-2595.2968	5268.2126	0.0118	0.9949
SYMI	41	-2591.7198	5269.8949	0.0051	1.0000
GTR	43	-2644.7882	5380.4844	0.0000	1.0000
SYM	40	-2649.6969	5383.6315	0.0000	1.0000
HKY	39	-2652.9027	5387.8312	0.0000	1.0000
K2P	36	-2656.3514	5388.1269	0.0000	1.0000
JC69G	36	-2681.5074	5438.4390	0.0000	1.0000
JC69IG	37	-2680.6787	5438.9764	0.0000	1.0000
F81G	39	-2678.8244	5439.6745	0.0000	1.0000
F81IG	40	-2677.9168	5440.0713	0.0000	1.0000
JC69I	36	-2682.7140	5440.8521	0.0000	1.0000
F81I	39	-2680.1042	5442.2342	0.0000	1.0000
JC69	35	-2740.7515	5554.7378	0.0000	1.0000
F81	38	-2738.0269	5555.8735	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRIG	45	-2582.9024	5255.8048	0.4856	0.4856
GTRG	44	-2584.6049	5257.2098	0.2405	0.7261
HKYIG	41	-2588.9167	5259.8334	0.0648	0.7909
HKYG	40	-2590.1794	5260.3588	0.0498	0.8407
SYMIG	42	-2588.5516	5261.1033	0.0343	0.8750
GTRI	44	-2586.5863	5261.1726	0.0332	0.9082
K2PIG	38	-2592.7982	5261.5963	0.0268	0.9350
K2PG	37	-2593.8902	5261.7805	0.0245	0.9595
SYMG	41	-2590.0808	5262.1615	0.0202	0.9797
HKYI	40	-2591.7504	5263.5009	0.0104	0.9901
K2PI	37	-2595.2968	5264.5936	0.0060	0.9961
SYMI	41	-2591.7198	5265.4395	0.0039	1.0000
GTR	43	-2644.7882	5375.5764	0.0000	1.0000
SYM	40	-2649.6969	5379.3938	0.0000	1.0000
HKY	39	-2652.9027	5383.8054	0.0000	1.0000
K2P	36	-2656.3514	5384.7028	0.0000	1.0000
JC69G	36	-2681.5074	5435.0149	0.0000	1.0000
JC69IG	37	-2680.6787	5435.3574	0.0000	1.0000
F81G	39	-2678.8244	5435.6487	0.0000	1.0000
F81IG	40	-2677.9168	5435.8336	0.0000	1.0000
JC69I	36	-2682.7140	5437.4280	0.0000	1.0000
F81I	39	-2680.1042	5438.2084	0.0000	1.0000
JC69	35	-2740.7515	5551.5029	0.0000	1.0000
F81	38	-2738.0269	5552.0539	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-2593.8902	5435.7984	0.7397	0.7397
K2PI	37	-2595.2968	5438.6115	0.1812	0.9210
K2PIG	38	-2592.7982	5440.3174	0.0772	0.9982
HKYG	40	-2590.1794	5448.4863	0.0013	0.9995
HKYI	40	-2591.7504	5451.6284	0.0003	0.9998
HKYIG	41	-2588.9167	5452.6641	0.0002	0.9999
SYMG	41	-2590.0808	5454.9922	0.0001	1.0000
SYMI	41	-2591.7198	5458.2702	0.0000	1.0000
SYMIG	42	-2588.5516	5458.6372	0.0000	1.0000
GTRG	44	-2584.6049	5464.1501	0.0000	1.0000
GTRIG	45	-2582.9024	5467.4482	0.0000	1.0000
GTRI	44	-2586.5863	5468.1128	0.0000	1.0000
K2P	36	-2656.3514	5554.0176	0.0000	1.0000
HKY	39	-2652.9027	5567.2297	0.0000	1.0000
SYM	40	-2649.6969	5567.5213	0.0000	1.0000
GTR	43	-2644.7882	5577.8135	0.0000	1.0000
JC69G	36	-2681.5074	5604.3297	0.0000	1.0000
JC69I	36	-2682.7140	5606.7428	0.0000	1.0000
JC69IG	37	-2680.6787	5609.3753	0.0000	1.0000
F81G	39	-2678.8244	5619.0731	0.0000	1.0000
F81I	39	-2680.1042	5621.6328	0.0000	1.0000
F81IG	40	-2677.9168	5623.9611	0.0000	1.0000
JC69	35	-2740.7515	5716.1145	0.0000	1.0000
F81	38	-2738.0269	5730.7750	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_24799.phylip = 1 - 815;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_24799.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_24799.phylip = 1 - 815;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_24799.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=invgamma;
 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) 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/chr2_24799.phylip = 1 - 815;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_24799.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

