
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:01 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_27968.phylip" (19 taxa, 867 characters)

Minimum AIC  model: HKYG
Minimum AICc model: HKYG
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
HKYG	40	-2527.1030	5138.1769	0.4146	0.4146
HKYI	40	-2527.4985	5138.9679	0.2792	0.6938
HKYIG	41	-2526.8903	5139.9552	0.1704	0.8642
GTRG	44	-2524.5673	5141.9522	0.0628	0.9270
GTRI	44	-2524.8900	5142.5975	0.0455	0.9725
GTRIG	45	-2524.2806	5143.6039	0.0275	1.0000
K2PG	37	-2551.4526	5180.2972	0.0000	1.0000
K2PI	37	-2552.0357	5181.4634	0.0000	1.0000
K2PIG	38	-2551.3536	5182.2870	0.0000	1.0000
SYMG	41	-2550.3657	5186.9060	0.0000	1.0000
SYMI	41	-2551.1141	5188.4027	0.0000	1.0000
SYMIG	42	-2550.1900	5188.7636	0.0000	1.0000
HKY	39	-2571.1334	5224.0395	0.0000	1.0000
GTR	43	-2568.5372	5227.6723	0.0000	1.0000
F81G	39	-2581.7841	5245.3409	0.0000	1.0000
F81I	39	-2581.8430	5245.4587	0.0000	1.0000
F81IG	40	-2581.7840	5247.5389	0.0000	1.0000
K2P	36	-2594.7749	5264.7595	0.0000	1.0000
SYM	40	-2593.8169	5271.6047	0.0000	1.0000
JC69G	36	-2606.1474	5287.5045	0.0000	1.0000
JC69I	36	-2606.4199	5288.0493	0.0000	1.0000
JC69IG	37	-2606.1604	5289.7129	0.0000	1.0000
F81	38	-2623.7899	5327.1594	0.0000	1.0000
JC69	35	-2648.3155	5369.6635	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-2527.1030	5134.2060	0.3787	0.3787
HKYI	40	-2527.4985	5134.9970	0.2550	0.6337
HKYIG	41	-2526.8903	5135.7807	0.1723	0.8061
GTRG	44	-2524.5673	5137.1347	0.0876	0.8937
GTRI	44	-2524.8900	5137.7800	0.0634	0.9571
GTRIG	45	-2524.2806	5138.5612	0.0429	1.0000
K2PG	37	-2551.4526	5176.9051	0.0000	1.0000
K2PI	37	-2552.0357	5178.0714	0.0000	1.0000
K2PIG	38	-2551.3536	5178.7072	0.0000	1.0000
SYMG	41	-2550.3657	5182.7314	0.0000	1.0000
SYMI	41	-2551.1141	5184.2282	0.0000	1.0000
SYMIG	42	-2550.1900	5184.3801	0.0000	1.0000
HKY	39	-2571.1334	5220.2669	0.0000	1.0000
GTR	43	-2568.5372	5223.0745	0.0000	1.0000
F81G	39	-2581.7841	5241.5682	0.0000	1.0000
F81I	39	-2581.8430	5241.6860	0.0000	1.0000
F81IG	40	-2581.7840	5243.5680	0.0000	1.0000
K2P	36	-2594.7749	5261.5499	0.0000	1.0000
SYM	40	-2593.8169	5267.6338	0.0000	1.0000
JC69G	36	-2606.1474	5284.2948	0.0000	1.0000
JC69I	36	-2606.4199	5284.8397	0.0000	1.0000
JC69IG	37	-2606.1604	5286.3208	0.0000	1.0000
F81	38	-2623.7899	5323.5797	0.0000	1.0000
JC69	35	-2648.3155	5366.6310	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2527.1030	5324.8075	0.5830	0.5830
HKYI	40	-2527.4985	5325.5986	0.3925	0.9755
HKYIG	41	-2526.8903	5331.1473	0.0245	1.0000
GTRG	44	-2524.5673	5346.7964	0.0000	1.0000
GTRI	44	-2524.8900	5347.4417	0.0000	1.0000
GTRIG	45	-2524.2806	5352.9880	0.0000	1.0000
K2PG	37	-2551.4526	5353.2116	0.0000	1.0000
K2PI	37	-2552.0357	5354.3778	0.0000	1.0000
K2PIG	38	-2551.3536	5359.7787	0.0000	1.0000
SYMG	41	-2550.3657	5378.0980	0.0000	1.0000
SYMI	41	-2551.1141	5379.5948	0.0000	1.0000
SYMIG	42	-2550.1900	5384.5117	0.0000	1.0000
HKY	39	-2571.1334	5406.1034	0.0000	1.0000
F81G	39	-2581.7841	5427.4047	0.0000	1.0000
F81I	39	-2581.8430	5427.5225	0.0000	1.0000
GTR	43	-2568.5372	5427.9712	0.0000	1.0000
K2P	36	-2594.7749	5433.0913	0.0000	1.0000
F81IG	40	-2581.7840	5434.1695	0.0000	1.0000
JC69G	36	-2606.1474	5455.8362	0.0000	1.0000
JC69I	36	-2606.4199	5456.3811	0.0000	1.0000
SYM	40	-2593.8169	5458.2353	0.0000	1.0000
JC69IG	37	-2606.1604	5462.6273	0.0000	1.0000
F81	38	-2623.7899	5504.6512	0.0000	1.0000
JC69	35	-2648.3155	5533.4074	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_27968.phylip = 1 - 867;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_27968.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;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_27968.phylip = 1 - 867;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_27968.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;


[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_27968.phylip = 1 - 867;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_27968.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

