
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:16 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/chr1_5442.phylip" (19 taxa, 806 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	-2243.4054	4582.2581	0.5872	0.5872
GTRG	44	-2245.0089	4583.2215	0.3627	0.9499
GTRI	44	-2247.0083	4587.2203	0.0491	0.9991
HKYIG	41	-2254.7968	4596.1014	0.0006	0.9996
HKYG	40	-2256.5532	4597.3940	0.0003	0.9999
HKYI	40	-2258.3000	4600.8875	0.0001	1.0000
F81IG	40	-2275.6795	4635.6465	0.0000	1.0000
F81G	39	-2277.2397	4636.5526	0.0000	1.0000
F81I	39	-2278.9147	4639.9024	0.0000	1.0000
GTR	43	-2285.1922	4661.3502	0.0000	1.0000
HKY	39	-2295.9859	4674.0448	0.0000	1.0000
K2PIG	38	-2298.8125	4677.4894	0.0000	1.0000
K2PG	37	-2300.8247	4679.3108	0.0000	1.0000
SYMIG	42	-2295.8531	4680.4400	0.0000	1.0000
SYMG	41	-2297.7992	4682.1063	0.0000	1.0000
K2PI	37	-2302.5470	4682.7554	0.0000	1.0000
SYMI	41	-2299.4032	4685.3143	0.0000	1.0000
JC69IG	37	-2315.2859	4708.2333	0.0000	1.0000
JC69G	36	-2317.0518	4709.5678	0.0000	1.0000
F81	38	-2315.5475	4710.9595	0.0000	1.0000
JC69I	36	-2318.7456	4712.9554	0.0000	1.0000
K2P	36	-2341.0792	4757.6226	0.0000	1.0000
SYM	40	-2337.9543	4760.1961	0.0000	1.0000
JC69	35	-2356.1851	4785.6429	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRIG	45	-2243.4054	4576.8108	0.6166	0.6166
GTRG	44	-2245.0089	4578.0178	0.3372	0.9537
GTRI	44	-2247.0083	4582.0166	0.0457	0.9994
HKYIG	41	-2254.7968	4591.5935	0.0004	0.9998
HKYG	40	-2256.5532	4593.1064	0.0002	1.0000
HKYI	40	-2258.3000	4596.5999	0.0000	1.0000
F81IG	40	-2275.6795	4631.3590	0.0000	1.0000
F81G	39	-2277.2397	4632.4795	0.0000	1.0000
F81I	39	-2278.9147	4635.8293	0.0000	1.0000
GTR	43	-2285.1922	4656.3843	0.0000	1.0000
HKY	39	-2295.9859	4669.9717	0.0000	1.0000
K2PIG	38	-2298.8125	4673.6250	0.0000	1.0000
K2PG	37	-2300.8247	4675.6494	0.0000	1.0000
SYMIG	42	-2295.8531	4675.7061	0.0000	1.0000
SYMG	41	-2297.7992	4677.5984	0.0000	1.0000
K2PI	37	-2302.5470	4679.0939	0.0000	1.0000
SYMI	41	-2299.4032	4680.8064	0.0000	1.0000
JC69IG	37	-2315.2859	4704.5719	0.0000	1.0000
JC69G	36	-2317.0518	4706.1036	0.0000	1.0000
F81	38	-2315.5475	4707.0951	0.0000	1.0000
JC69I	36	-2318.7456	4709.4912	0.0000	1.0000
K2P	36	-2341.0792	4754.1583	0.0000	1.0000
SYM	40	-2337.9543	4755.9085	0.0000	1.0000
JC69	35	-2356.1851	4782.3702	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2256.5532	4780.7898	0.6303	0.6303
HKYIG	41	-2254.7968	4783.9690	0.1286	0.7589
HKYI	40	-2258.3000	4784.2833	0.1099	0.8688
GTRG	44	-2245.0089	4784.4695	0.1001	0.9689
GTRIG	45	-2243.4054	4787.9545	0.0175	0.9864
GTRI	44	-2247.0083	4788.4683	0.0136	1.0000
F81G	39	-2277.2397	4815.4707	0.0000	1.0000
F81I	39	-2278.9147	4818.8206	0.0000	1.0000
F81IG	40	-2275.6795	4819.0423	0.0000	1.0000
K2PG	37	-2300.8247	4849.2565	0.0000	1.0000
K2PIG	38	-2298.8125	4851.9242	0.0000	1.0000
K2PI	37	-2302.5470	4852.7010	0.0000	1.0000
HKY	39	-2295.9859	4852.9630	0.0000	1.0000
GTR	43	-2285.1922	4858.1439	0.0000	1.0000
SYMG	41	-2297.7992	4869.9739	0.0000	1.0000
SYMIG	42	-2295.8531	4872.7736	0.0000	1.0000
SYMI	41	-2299.4032	4873.1818	0.0000	1.0000
JC69G	36	-2317.0518	4875.0186	0.0000	1.0000
JC69IG	37	-2315.2859	4878.1790	0.0000	1.0000
JC69I	36	-2318.7456	4878.4062	0.0000	1.0000
F81	38	-2315.5475	4885.3942	0.0000	1.0000
K2P	36	-2341.0792	4923.0734	0.0000	1.0000
SYM	40	-2337.9543	4943.5919	0.0000	1.0000
JC69	35	-2356.1851	4946.5932	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/chr1_5442.phylip = 1 - 806;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_5442.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/chr1_5442.phylip = 1 - 806;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_5442.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/chr1_5442.phylip = 1 - 806;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_5442.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

