
Output from mraic.pl version 1.4.4 by Johan Nylander
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13:00 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_10865.phylip" (19 taxa, 750 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	-3592.2890	7278.1949	0.7186	0.7186
GTRIG	45	-3592.1050	7280.0907	0.2785	0.9971
GTRI	44	-3598.0647	7289.7464	0.0022	0.9993
HKYG	40	-3604.0058	7292.6379	0.0005	0.9998
HKYIG	41	-3603.8947	7294.6539	0.0002	1.0000
HKYI	40	-3608.9521	7302.5304	0.0000	1.0000
GTR	43	-3647.9693	7387.2984	0.0000	1.0000
K2PG	37	-3661.1750	7400.2994	0.0000	1.0000
SYMG	41	-3657.3152	7401.4947	0.0000	1.0000
K2PIG	38	-3661.1881	7402.5450	0.0000	1.0000
SYMIG	42	-3657.3196	7403.7482	0.0000	1.0000
HKY	39	-3663.5621	7409.5186	0.0000	1.0000
K2PI	37	-3666.3233	7410.5960	0.0000	1.0000
SYMI	41	-3662.5183	7411.9011	0.0000	1.0000
F81G	39	-3704.9015	7492.1974	0.0000	1.0000
F81IG	40	-3704.8793	7494.3849	0.0000	1.0000
F81I	39	-3709.6692	7501.7327	0.0000	1.0000
SYM	40	-3724.8132	7534.2526	0.0000	1.0000
K2P	36	-3730.0757	7535.8877	0.0000	1.0000
JC69G	36	-3749.4602	7574.6568	0.0000	1.0000
JC69IG	37	-3749.4679	7576.8852	0.0000	1.0000
JC69I	36	-3754.8546	7585.4455	0.0000	1.0000
F81	38	-3765.7238	7611.6163	0.0000	1.0000
JC69	35	-3815.5147	7704.5588	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-3592.2890	7272.5779	0.6916	0.6916
GTRIG	45	-3592.1050	7274.2100	0.3058	0.9974
GTRI	44	-3598.0647	7284.1294	0.0021	0.9996
HKYG	40	-3604.0058	7288.0116	0.0003	0.9999
HKYIG	41	-3603.8947	7289.7895	0.0001	1.0000
HKYI	40	-3608.9521	7297.9042	0.0000	1.0000
GTR	43	-3647.9693	7381.9386	0.0000	1.0000
K2PG	37	-3661.1750	7396.3500	0.0000	1.0000
SYMG	41	-3657.3152	7396.6303	0.0000	1.0000
K2PIG	38	-3661.1881	7398.3763	0.0000	1.0000
SYMIG	42	-3657.3196	7398.6393	0.0000	1.0000
HKY	39	-3663.5621	7405.1243	0.0000	1.0000
K2PI	37	-3666.3233	7406.6465	0.0000	1.0000
SYMI	41	-3662.5183	7407.0367	0.0000	1.0000
F81G	39	-3704.9015	7487.8030	0.0000	1.0000
F81IG	40	-3704.8793	7489.7587	0.0000	1.0000
F81I	39	-3709.6692	7497.3384	0.0000	1.0000
SYM	40	-3724.8132	7529.6264	0.0000	1.0000
K2P	36	-3730.0757	7532.1514	0.0000	1.0000
JC69G	36	-3749.4602	7570.9205	0.0000	1.0000
JC69IG	37	-3749.4679	7572.9358	0.0000	1.0000
JC69I	36	-3754.8546	7581.7092	0.0000	1.0000
F81	38	-3765.7238	7607.4475	0.0000	1.0000
JC69	35	-3815.5147	7701.0294	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-3604.0058	7472.8145	0.7836	0.7836
GTRG	44	-3592.2890	7475.8611	0.1708	0.9544
HKYIG	41	-3603.8947	7479.2125	0.0320	0.9864
GTRIG	45	-3592.1050	7482.1133	0.0075	0.9939
HKYI	40	-3608.9521	7482.7071	0.0056	0.9995
GTRI	44	-3598.0647	7487.4126	0.0005	1.0000
K2PG	37	-3661.1750	7567.2927	0.0000	1.0000
K2PIG	38	-3661.1881	7573.9390	0.0000	1.0000
K2PI	37	-3666.3233	7577.5892	0.0000	1.0000
GTR	43	-3647.9693	7580.6018	0.0000	1.0000
HKY	39	-3663.5621	7585.3071	0.0000	1.0000
SYMG	41	-3657.3152	7586.0533	0.0000	1.0000
SYMIG	42	-3657.3196	7592.6824	0.0000	1.0000
SYMI	41	-3662.5183	7596.4597	0.0000	1.0000
F81G	39	-3704.9015	7667.9859	0.0000	1.0000
F81IG	40	-3704.8793	7674.5616	0.0000	1.0000
F81I	39	-3709.6692	7677.5212	0.0000	1.0000
K2P	36	-3730.0757	7698.4740	0.0000	1.0000
SYM	40	-3724.8132	7714.4293	0.0000	1.0000
JC69G	36	-3749.4602	7737.2431	0.0000	1.0000
JC69IG	37	-3749.4679	7743.8785	0.0000	1.0000
JC69I	36	-3754.8546	7748.0318	0.0000	1.0000
F81	38	-3765.7238	7783.0103	0.0000	1.0000
JC69	35	-3815.5147	7862.7319	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_10865.phylip = 1 - 750;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10865.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_10865.phylip = 1 - 750;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10865.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_10865.phylip = 1 - 750;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10865.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

