
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:17 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/chr3_5514.phylip" (19 taxa, 621 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
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
GTRG	44	-2481.5382	5057.9514	0.6885	0.6885
GTRIG	45	-2481.5453	5060.2906	0.2138	0.9023
GTRI	44	-2483.5377	5061.9503	0.0932	0.9955
HKYG	40	-2491.5792	5068.8135	0.0030	0.9986
HKYIG	41	-2491.5799	5071.1079	0.0010	0.9995
HKYI	40	-2493.5094	5072.6740	0.0004	1.0000
SYMG	41	-2495.4639	5078.8761	0.0000	1.0000
K2PG	37	-2500.9418	5080.7068	0.0000	1.0000
SYMIG	42	-2495.4652	5081.1795	0.0000	1.0000
SYMI	41	-2497.1372	5082.2226	0.0000	1.0000
K2PIG	38	-2500.9425	5082.9778	0.0000	1.0000
K2PI	37	-2502.8747	5084.5726	0.0000	1.0000
GTR	43	-2517.2867	5127.1314	0.0000	1.0000
HKY	39	-2526.4086	5136.1872	0.0000	1.0000
SYM	40	-2530.2313	5146.1178	0.0000	1.0000
K2P	36	-2535.9785	5148.5186	0.0000	1.0000
F81G	39	-2540.9608	5165.2917	0.0000	1.0000
F81IG	40	-2540.9619	5167.5790	0.0000	1.0000
F81I	39	-2542.8443	5169.0587	0.0000	1.0000
JC69G	36	-2547.5372	5171.6359	0.0000	1.0000
JC69IG	37	-2547.5448	5173.9130	0.0000	1.0000
JC69I	36	-2549.5311	5175.6239	0.0000	1.0000
F81	38	-2573.6840	5228.4608	0.0000	1.0000
JC69	35	-2580.5158	5235.3393	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2481.5382	5051.0764	0.6648	0.6648
GTRIG	45	-2481.5453	5053.0906	0.2428	0.9076
GTRI	44	-2483.5377	5055.0753	0.0900	0.9976
HKYG	40	-2491.5792	5063.1583	0.0016	0.9992
HKYIG	41	-2491.5799	5065.1598	0.0006	0.9997
HKYI	40	-2493.5094	5067.0188	0.0002	1.0000
SYMG	41	-2495.4639	5072.9279	0.0000	1.0000
SYMIG	42	-2495.4652	5074.9303	0.0000	1.0000
K2PG	37	-2500.9418	5075.8835	0.0000	1.0000
SYMI	41	-2497.1372	5076.2744	0.0000	1.0000
K2PIG	38	-2500.9425	5077.8851	0.0000	1.0000
K2PI	37	-2502.8747	5079.7493	0.0000	1.0000
GTR	43	-2517.2867	5120.5733	0.0000	1.0000
HKY	39	-2526.4086	5130.8171	0.0000	1.0000
SYM	40	-2530.2313	5140.4626	0.0000	1.0000
K2P	36	-2535.9785	5143.9570	0.0000	1.0000
F81G	39	-2540.9608	5159.9217	0.0000	1.0000
F81IG	40	-2540.9619	5161.9238	0.0000	1.0000
F81I	39	-2542.8443	5163.6886	0.0000	1.0000
JC69G	36	-2547.5372	5167.0743	0.0000	1.0000
JC69IG	37	-2547.5448	5169.0897	0.0000	1.0000
JC69I	36	-2549.5311	5171.0622	0.0000	1.0000
F81	38	-2573.6840	5223.3681	0.0000	1.0000
JC69	35	-2580.5158	5231.0316	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-2500.9418	5239.8428	0.4695	0.4695
HKYG	40	-2491.5792	5240.4116	0.3533	0.8227
K2PI	37	-2502.8747	5243.7086	0.0679	0.8907
HKYI	40	-2493.5094	5244.2720	0.0513	0.9419
GTRG	44	-2481.5382	5246.0549	0.0210	0.9630
K2PIG	38	-2500.9425	5246.2756	0.0188	0.9818
HKYIG	41	-2491.5799	5246.8443	0.0142	0.9960
GTRI	44	-2483.5377	5250.0539	0.0028	0.9988
GTRIG	45	-2481.5453	5252.5005	0.0008	0.9996
SYMG	41	-2495.4639	5254.6125	0.0003	0.9999
SYMI	41	-2497.1372	5257.9590	0.0001	1.0000
SYMIG	42	-2495.4652	5261.0462	0.0000	1.0000
K2P	36	-2535.9785	5303.4849	0.0000	1.0000
HKY	39	-2526.4086	5303.6390	0.0000	1.0000
GTR	43	-2517.2867	5311.1205	0.0000	1.0000
SYM	40	-2530.2313	5317.7158	0.0000	1.0000
JC69G	36	-2547.5372	5326.6022	0.0000	1.0000
JC69I	36	-2549.5311	5330.5902	0.0000	1.0000
F81G	39	-2540.9608	5332.7436	0.0000	1.0000
JC69IG	37	-2547.5448	5333.0489	0.0000	1.0000
F81I	39	-2542.8443	5336.5105	0.0000	1.0000
F81IG	40	-2540.9619	5339.1770	0.0000	1.0000
JC69	35	-2580.5158	5386.1281	0.0000	1.0000
F81	38	-2573.6840	5391.7586	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/chr3_5514.phylip = 1 - 621;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_5514.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/chr3_5514.phylip = 1 - 621;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_5514.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 (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_5514.phylip = 1 - 621;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_5514.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

