
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
13:15 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/chr8_4123.phylip" (19 taxa, 888 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	-4320.4844	8733.6663	0.8074	0.8074
GTRIG	45	-4320.8083	8736.5335	0.1925	0.9999
HKYG	40	-4333.9876	8751.8476	0.0001	1.0000
HKYIG	41	-4333.9876	8754.0460	0.0000	1.0000
GTRI	44	-4335.8872	8764.4719	0.0000	1.0000
SYMG	41	-4346.2460	8778.5628	0.0000	1.0000
SYMIG	42	-4346.2460	8780.7665	0.0000	1.0000
K2PG	37	-4351.8912	8781.0905	0.0000	1.0000
HKYI	40	-4348.7095	8781.2915	0.0000	1.0000
K2PIG	38	-4351.8912	8783.2735	0.0000	1.0000
SYMI	41	-4358.4551	8802.9810	0.0000	1.0000
K2PI	37	-4365.9871	8809.2825	0.0000	1.0000
GTR	43	-4402.3886	8895.2605	0.0000	1.0000
HKY	39	-4413.1441	8907.9675	0.0000	1.0000
SYM	40	-4421.9467	8927.7660	0.0000	1.0000
K2P	36	-4428.8364	8932.8033	0.0000	1.0000
F81G	39	-4473.5682	9028.8157	0.0000	1.0000
F81IG	40	-4473.0687	9030.0099	0.0000	1.0000
JC69G	36	-4483.0000	9041.1305	0.0000	1.0000
JC69IG	37	-4483.0001	9043.3084	0.0000	1.0000
F81I	39	-4483.6296	9048.9384	0.0000	1.0000
JC69I	36	-4494.0919	9063.3143	0.0000	1.0000
F81	38	-4541.5798	9162.6508	0.0000	1.0000
JC69	35	-4552.0735	9177.1047	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-4320.4844	8728.9688	0.7898	0.7898
GTRIG	45	-4320.8083	8731.6167	0.2101	0.9999
HKYG	40	-4333.9876	8747.9751	0.0001	1.0000
HKYIG	41	-4333.9876	8749.9751	0.0000	1.0000
GTRI	44	-4335.8872	8759.7744	0.0000	1.0000
SYMG	41	-4346.2460	8774.4919	0.0000	1.0000
SYMIG	42	-4346.2460	8776.4920	0.0000	1.0000
HKYI	40	-4348.7095	8777.4190	0.0000	1.0000
K2PG	37	-4351.8912	8777.7823	0.0000	1.0000
K2PIG	38	-4351.8912	8779.7823	0.0000	1.0000
SYMI	41	-4358.4551	8798.9101	0.0000	1.0000
K2PI	37	-4365.9871	8805.9742	0.0000	1.0000
GTR	43	-4402.3886	8890.7771	0.0000	1.0000
HKY	39	-4413.1441	8904.2882	0.0000	1.0000
SYM	40	-4421.9467	8923.8935	0.0000	1.0000
K2P	36	-4428.8364	8929.6729	0.0000	1.0000
F81G	39	-4473.5682	9025.1365	0.0000	1.0000
F81IG	40	-4473.0687	9026.1374	0.0000	1.0000
JC69G	36	-4483.0000	9038.0000	0.0000	1.0000
JC69IG	37	-4483.0001	9040.0002	0.0000	1.0000
F81I	39	-4483.6296	9045.2591	0.0000	1.0000
JC69I	36	-4494.0919	9060.1838	0.0000	1.0000
F81	38	-4541.5798	9159.1597	0.0000	1.0000
JC69	35	-4552.0735	9174.1469	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-4333.9876	8939.5340	0.5039	0.5039
GTRG	44	-4320.4844	8939.6835	0.4676	0.9715
HKYIG	41	-4333.9876	8946.3230	0.0169	0.9884
GTRIG	45	-4320.8083	8947.1204	0.0113	0.9998
K2PG	37	-4351.8912	8954.9743	0.0002	1.0000
K2PIG	38	-4351.8912	8961.7632	0.0000	1.0000
HKYI	40	-4348.7095	8968.9779	0.0000	1.0000
GTRI	44	-4335.8872	8970.4892	0.0000	1.0000
SYMG	41	-4346.2460	8970.8398	0.0000	1.0000
SYMIG	42	-4346.2460	8977.6288	0.0000	1.0000
K2PI	37	-4365.9871	8983.1662	0.0000	1.0000
SYMI	41	-4358.4551	8995.2580	0.0000	1.0000
HKY	39	-4413.1441	9091.0581	0.0000	1.0000
GTR	43	-4402.3886	9096.7029	0.0000	1.0000
K2P	36	-4428.8364	9102.0759	0.0000	1.0000
SYM	40	-4421.9467	9115.4523	0.0000	1.0000
JC69G	36	-4483.0000	9210.4030	0.0000	1.0000
F81G	39	-4473.5682	9211.9064	0.0000	1.0000
JC69IG	37	-4483.0001	9217.1921	0.0000	1.0000
F81IG	40	-4473.0687	9217.6963	0.0000	1.0000
F81I	39	-4483.6296	9232.0290	0.0000	1.0000
JC69I	36	-4494.0919	9232.5868	0.0000	1.0000
F81	38	-4541.5798	9341.1406	0.0000	1.0000
JC69	35	-4552.0735	9341.7609	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/chr8_4123.phylip = 1 - 888;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_4123.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/chr8_4123.phylip = 1 - 888;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_4123.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/chr8_4123.phylip = 1 - 888;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_4123.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

