
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:50 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/chr7_10675.phylip" (19 taxa, 718 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	-1886.5765	3867.0371	0.4919	0.4919
GTRI	44	-1886.9924	3867.8689	0.3245	0.8164
GTRIG	45	-1886.4280	3869.0168	0.1828	0.9992
HKYG	40	-1898.3121	3881.4691	0.0004	0.9996
HKYI	40	-1898.6125	3882.0700	0.0003	0.9998
HKYIG	41	-1898.0010	3883.0966	0.0002	1.0000
GTR	43	-1917.5595	3926.7332	0.0000	1.0000
HKY	39	-1929.4524	3941.5066	0.0000	1.0000
F81G	39	-1931.9117	3946.4251	0.0000	1.0000
F81I	39	-1932.0090	3946.6198	0.0000	1.0000
F81IG	40	-1931.8196	3948.4842	0.0000	1.0000
K2PG	37	-1956.6771	3991.4894	0.0000	1.0000
K2PI	37	-1956.9855	3992.1062	0.0000	1.0000
SYMG	41	-1952.5207	3992.1360	0.0000	1.0000
K2PIG	38	-1956.0991	3992.5634	0.0000	1.0000
SYMI	41	-1952.8233	3992.7412	0.0000	1.0000
SYMIG	42	-1952.0880	3993.5271	0.0000	1.0000
F81	38	-1965.1089	4010.5830	0.0000	1.0000
JC69G	36	-1983.4924	4042.8967	0.0000	1.0000
JC69IG	37	-1983.1181	4044.3715	0.0000	1.0000
JC69I	36	-1984.6927	4045.2972	0.0000	1.0000
SYM	40	-1985.5639	4055.9727	0.0000	1.0000
K2P	36	-1991.0384	4057.9886	0.0000	1.0000
JC69	35	-2017.6166	4108.9282	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1886.5765	3861.1530	0.4791	0.4791
GTRI	44	-1886.9924	3861.9848	0.3160	0.7951
GTRIG	45	-1886.4280	3862.8561	0.2044	0.9995
HKYG	40	-1898.3121	3876.6242	0.0002	0.9997
HKYI	40	-1898.6125	3877.2251	0.0002	0.9999
HKYIG	41	-1898.0010	3878.0020	0.0001	1.0000
GTR	43	-1917.5595	3921.1189	0.0000	1.0000
HKY	39	-1929.4524	3936.9048	0.0000	1.0000
F81G	39	-1931.9117	3941.8233	0.0000	1.0000
F81I	39	-1932.0090	3942.0181	0.0000	1.0000
F81IG	40	-1931.8196	3943.6393	0.0000	1.0000
SYMG	41	-1952.5207	3987.0413	0.0000	1.0000
K2PG	37	-1956.6771	3987.3541	0.0000	1.0000
SYMI	41	-1952.8233	3987.6465	0.0000	1.0000
K2PI	37	-1956.9855	3987.9709	0.0000	1.0000
SYMIG	42	-1952.0880	3988.1760	0.0000	1.0000
K2PIG	38	-1956.0991	3988.1981	0.0000	1.0000
F81	38	-1965.1089	4006.2177	0.0000	1.0000
JC69G	36	-1983.4924	4038.9848	0.0000	1.0000
JC69IG	37	-1983.1181	4040.2362	0.0000	1.0000
JC69I	36	-1984.6927	4041.3853	0.0000	1.0000
SYM	40	-1985.5639	4051.1278	0.0000	1.0000
K2P	36	-1991.0384	4054.0767	0.0000	1.0000
JC69	35	-2017.6166	4105.2332	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1898.3121	4059.6830	0.4537	0.4537
HKYI	40	-1898.6125	4060.2838	0.3360	0.7896
GTRG	44	-1886.5765	4062.5176	0.1100	0.8996
GTRI	44	-1886.9924	4063.3495	0.0725	0.9721
HKYIG	41	-1898.0010	4065.6372	0.0231	0.9952
GTRIG	45	-1886.4280	4068.7972	0.0048	1.0000
HKY	39	-1929.4524	4115.3871	0.0000	1.0000
GTR	43	-1917.5595	4117.9071	0.0000	1.0000
F81G	39	-1931.9117	4120.3056	0.0000	1.0000
F81I	39	-1932.0090	4120.5004	0.0000	1.0000
F81IG	40	-1931.8196	4126.6981	0.0000	1.0000
K2PG	37	-1956.6771	4156.6835	0.0000	1.0000
K2PI	37	-1956.9855	4157.3003	0.0000	1.0000
K2PIG	38	-1956.0991	4162.1040	0.0000	1.0000
SYMG	41	-1952.5207	4174.6766	0.0000	1.0000
SYMI	41	-1952.8233	4175.2818	0.0000	1.0000
F81	38	-1965.1089	4180.1236	0.0000	1.0000
SYMIG	42	-1952.0880	4180.3877	0.0000	1.0000
JC69G	36	-1983.4924	4203.7377	0.0000	1.0000
JC69I	36	-1984.6927	4206.1382	0.0000	1.0000
JC69IG	37	-1983.1181	4209.5655	0.0000	1.0000
K2P	36	-1991.0384	4218.8296	0.0000	1.0000
SYM	40	-1985.5639	4234.1866	0.0000	1.0000
JC69	35	-2017.6166	4265.4096	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/chr7_10675.phylip = 1 - 718;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10675.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/chr7_10675.phylip = 1 - 718;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10675.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/chr7_10675.phylip = 1 - 718;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10675.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

