
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:09 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_6444.phylip" (19 taxa, 719 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	-2448.6714	4991.2182	0.6332	0.6332
GTRIG	45	-2448.6712	4993.4940	0.2029	0.8361
HKYG	40	-2454.9844	4994.8066	0.1053	0.9414
HKYIG	41	-2454.9844	4997.0559	0.0342	0.9756
GTRI	44	-2452.0679	4998.0112	0.0212	0.9968
HKYI	40	-2458.4901	5001.8180	0.0032	0.9999
K2PG	37	-2466.6279	5011.3851	0.0000	1.0000
GTR	43	-2460.7737	5013.1533	0.0000	1.0000
K2PIG	38	-2466.6279	5013.6146	0.0000	1.0000
SYMG	41	-2463.4313	5013.9497	0.0000	1.0000
SYMIG	42	-2463.4312	5016.2056	0.0000	1.0000
HKY	39	-2467.5482	5017.6915	0.0000	1.0000
K2PI	37	-2470.1978	5018.5249	0.0000	1.0000
SYMI	41	-2466.9444	5020.9760	0.0000	1.0000
SYM	40	-2474.3209	5033.4796	0.0000	1.0000
K2P	36	-2478.8071	5033.5204	0.0000	1.0000
F81G	39	-2504.2317	5091.0584	0.0000	1.0000
F81IG	40	-2504.2315	5093.3008	0.0000	1.0000
F81I	39	-2507.2567	5097.1084	0.0000	1.0000
JC69G	36	-2512.8918	5101.6899	0.0000	1.0000
JC69IG	37	-2512.8917	5103.9126	0.0000	1.0000
JC69I	36	-2515.9354	5107.7770	0.0000	1.0000
F81	38	-2514.1411	5108.6410	0.0000	1.0000
JC69	35	-2522.6115	5118.9127	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2448.6714	4985.3428	0.6494	0.6494
GTRIG	45	-2448.6712	4987.3424	0.2390	0.8884
HKYG	40	-2454.9844	4989.9688	0.0643	0.9526
HKYIG	41	-2454.9844	4991.9687	0.0236	0.9763
GTRI	44	-2452.0679	4992.1359	0.0217	0.9980
HKYI	40	-2458.4901	4996.9803	0.0019	1.0000
K2PG	37	-2466.6279	5007.2559	0.0000	1.0000
GTR	43	-2460.7737	5007.5474	0.0000	1.0000
SYMG	41	-2463.4313	5008.8625	0.0000	1.0000
K2PIG	38	-2466.6279	5009.2558	0.0000	1.0000
SYMIG	42	-2463.4312	5010.8624	0.0000	1.0000
HKY	39	-2467.5482	5013.0965	0.0000	1.0000
K2PI	37	-2470.1978	5014.3957	0.0000	1.0000
SYMI	41	-2466.9444	5015.8889	0.0000	1.0000
SYM	40	-2474.3209	5028.6419	0.0000	1.0000
K2P	36	-2478.8071	5029.6142	0.0000	1.0000
F81G	39	-2504.2317	5086.4634	0.0000	1.0000
F81IG	40	-2504.2315	5088.4631	0.0000	1.0000
F81I	39	-2507.2567	5092.5134	0.0000	1.0000
JC69G	36	-2512.8918	5097.7837	0.0000	1.0000
JC69IG	37	-2512.8917	5099.7834	0.0000	1.0000
JC69I	36	-2515.9354	5103.8708	0.0000	1.0000
F81	38	-2514.1411	5104.2822	0.0000	1.0000
JC69	35	-2522.6115	5115.2231	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2454.9844	5173.0833	0.8007	0.8007
K2PG	37	-2466.6279	5176.6367	0.1355	0.9362
HKYIG	41	-2454.9844	5179.6610	0.0299	0.9661
HKYI	40	-2458.4901	5180.0947	0.0240	0.9901
K2PIG	38	-2466.6279	5183.2146	0.0051	0.9952
K2PI	37	-2470.1978	5183.7766	0.0038	0.9990
GTRG	44	-2448.6714	5186.7687	0.0009	0.9998
HKY	39	-2467.5482	5191.6331	0.0001	0.9999
GTRIG	45	-2448.6712	5193.3462	0.0000	0.9999
GTRI	44	-2452.0679	5193.5618	0.0000	1.0000
K2P	36	-2478.8071	5194.4172	0.0000	1.0000
SYMG	41	-2463.4313	5196.5548	0.0000	1.0000
SYMIG	42	-2463.4312	5203.1326	0.0000	1.0000
SYMI	41	-2466.9444	5203.5812	0.0000	1.0000
GTR	43	-2460.7737	5204.3954	0.0000	1.0000
SYM	40	-2474.3209	5211.7563	0.0000	1.0000
JC69G	36	-2512.8918	5262.5867	0.0000	1.0000
F81G	39	-2504.2317	5265.0000	0.0000	1.0000
JC69I	36	-2515.9354	5268.6738	0.0000	1.0000
JC69IG	37	-2512.8917	5269.1642	0.0000	1.0000
F81I	39	-2507.2567	5271.0500	0.0000	1.0000
F81IG	40	-2504.2315	5271.5775	0.0000	1.0000
JC69	35	-2522.6115	5275.4482	0.0000	1.0000
F81	38	-2514.1411	5278.2410	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/chr2_6444.phylip = 1 - 719;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_6444.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/chr2_6444.phylip = 1 - 719;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_6444.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/chr2_6444.phylip = 1 - 719;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_6444.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

