
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:53 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_7915.phylip" (19 taxa, 535 characters)

Minimum AIC  model: GTRIG
Minimum AICc model: GTRIG
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
GTRIG	45	-2858.7118	5815.8898	0.3932	0.3932
HKYG	40	-2865.0783	5816.7963	0.2499	0.6431
GTRG	44	-2860.5748	5817.2313	0.2010	0.8441
HKYIG	41	-2864.7010	5818.3878	0.1128	0.9569
GTRI	44	-2862.3991	5820.8799	0.0324	0.9893
HKYI	40	-2868.2313	5823.1023	0.0107	1.0000
SYMG	41	-2881.2160	5851.4179	0.0000	1.0000
SYMIG	42	-2880.5314	5852.4043	0.0000	1.0000
SYMI	41	-2882.3946	5853.7751	0.0000	1.0000
K2PG	37	-2887.6878	5855.0336	0.0000	1.0000
K2PIG	38	-2887.6929	5857.3615	0.0000	1.0000
K2PI	37	-2890.3567	5860.3713	0.0000	1.0000
HKY	39	-2895.3479	5874.9989	0.0000	1.0000
GTR	43	-2892.3227	5878.3522	0.0000	1.0000
SYM	40	-2908.8994	5904.4384	0.0000	1.0000
K2P	36	-2915.5927	5908.5347	0.0000	1.0000
F81G	39	-2988.2538	6060.8107	0.0000	1.0000
F81I	39	-2988.5597	6061.4225	0.0000	1.0000
F81IG	40	-2987.3968	6061.4333	0.0000	1.0000
JC69I	36	-3002.5334	6082.4162	0.0000	1.0000
JC69IG	37	-3001.8268	6083.3115	0.0000	1.0000
JC69G	36	-3003.0307	6083.4108	0.0000	1.0000
F81	38	-3011.5428	6105.0614	0.0000	1.0000
JC69	35	-3024.0411	6123.1323	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRIG	45	-2858.7118	5807.4235	0.5284	0.5284
GTRG	44	-2860.5748	5809.1496	0.2229	0.7513
HKYG	40	-2865.0783	5810.1567	0.1347	0.8860
HKYIG	41	-2864.7010	5811.4020	0.0723	0.9583
GTRI	44	-2862.3991	5812.7983	0.0360	0.9942
HKYI	40	-2868.2313	5816.4626	0.0058	1.0000
SYMG	41	-2881.2160	5844.4321	0.0000	1.0000
SYMIG	42	-2880.5314	5845.0629	0.0000	1.0000
SYMI	41	-2882.3946	5846.7893	0.0000	1.0000
K2PG	37	-2887.6878	5849.3756	0.0000	1.0000
K2PIG	38	-2887.6929	5851.3857	0.0000	1.0000
K2PI	37	-2890.3567	5854.7134	0.0000	1.0000
HKY	39	-2895.3479	5868.6959	0.0000	1.0000
GTR	43	-2892.3227	5870.6455	0.0000	1.0000
SYM	40	-2908.8994	5897.7987	0.0000	1.0000
K2P	36	-2915.5927	5903.1853	0.0000	1.0000
F81G	39	-2988.2538	6054.5077	0.0000	1.0000
F81IG	40	-2987.3968	6054.7937	0.0000	1.0000
F81I	39	-2988.5597	6055.1195	0.0000	1.0000
JC69I	36	-3002.5334	6077.0668	0.0000	1.0000
JC69IG	37	-3001.8268	6077.6536	0.0000	1.0000
JC69G	36	-3003.0307	6078.0614	0.0000	1.0000
F81	38	-3011.5428	6099.0856	0.0000	1.0000
JC69	35	-3024.0411	6118.0822	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2865.0783	5981.4473	0.9040	0.9040
HKYIG	41	-2864.7010	5986.9749	0.0570	0.9610
HKYI	40	-2868.2313	5987.7533	0.0386	0.9996
GTRG	44	-2860.5748	5997.5694	0.0003	0.9999
GTRIG	45	-2858.7118	6000.1255	0.0001	1.0000
GTRI	44	-2862.3991	6001.2180	0.0000	1.0000
K2PG	37	-2887.6878	6007.8195	0.0000	1.0000
K2PI	37	-2890.3567	6013.1572	0.0000	1.0000
K2PIG	38	-2887.6929	6014.1119	0.0000	1.0000
SYMG	41	-2881.2160	6020.0050	0.0000	1.0000
SYMI	41	-2882.3946	6022.3622	0.0000	1.0000
SYMIG	42	-2880.5314	6024.9181	0.0000	1.0000
HKY	39	-2895.3479	6035.7043	0.0000	1.0000
GTR	43	-2892.3227	6054.7830	0.0000	1.0000
K2P	36	-2915.5927	6057.3469	0.0000	1.0000
SYM	40	-2908.8994	6069.0894	0.0000	1.0000
F81G	39	-2988.2538	6221.5161	0.0000	1.0000
F81I	39	-2988.5597	6222.1279	0.0000	1.0000
F81IG	40	-2987.3968	6226.0843	0.0000	1.0000
JC69I	36	-3002.5334	6231.2284	0.0000	1.0000
JC69G	36	-3003.0307	6232.2230	0.0000	1.0000
JC69IG	37	-3001.8268	6236.0975	0.0000	1.0000
F81	38	-3011.5428	6261.8117	0.0000	1.0000
JC69	35	-3024.0411	6267.9615	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_7915.phylip = 1 - 535;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_7915.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_7915.phylip = 1 - 535;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_7915.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 (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_7915.phylip = 1 - 535;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_7915.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

