
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:48 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_6244.phylip" (19 taxa, 454 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	-1689.0018	3475.6858	0.7003	0.7003
GTRIG	45	-1688.9098	3477.9667	0.2239	0.9242
GTRI	44	-1691.2559	3480.1940	0.0735	0.9977
HKYG	40	-1700.0235	3487.9888	0.0015	0.9992
HKYIG	41	-1700.0206	3490.4004	0.0004	0.9996
HKYI	40	-1701.3493	3490.6406	0.0004	1.0000
K2PG	37	-1722.3890	3525.5377	0.0000	1.0000
K2PIG	38	-1722.2136	3527.5694	0.0000	1.0000
K2PI	37	-1724.2245	3529.2086	0.0000	1.0000
SYMG	41	-1719.4666	3529.2924	0.0000	1.0000
SYMIG	42	-1719.3350	3531.4584	0.0000	1.0000
SYMI	41	-1721.3922	3533.1436	0.0000	1.0000
F81G	39	-1736.4507	3558.4377	0.0000	1.0000
GTR	43	-1731.6473	3558.5239	0.0000	1.0000
F81IG	40	-1736.3754	3560.6927	0.0000	1.0000
F81I	39	-1743.5438	3572.6237	0.0000	1.0000
HKY	39	-1745.8802	3577.2966	0.0000	1.0000
JC69G	36	-1754.4202	3587.2288	0.0000	1.0000
JC69IG	37	-1754.2242	3589.2081	0.0000	1.0000
JC69I	36	-1756.0705	3590.5294	0.0000	1.0000
SYM	40	-1764.4631	3616.8680	0.0000	1.0000
K2P	36	-1770.3136	3619.0156	0.0000	1.0000
F81	38	-1779.8376	3642.8174	0.0000	1.0000
JC69	35	-1800.0208	3676.0704	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1689.0018	3466.0037	0.6624	0.6624
GTRIG	45	-1688.9098	3467.8196	0.2672	0.9295
GTRI	44	-1691.2559	3470.5118	0.0695	0.9990
HKYG	40	-1700.0235	3480.0469	0.0006	0.9996
HKYIG	41	-1700.0206	3482.0411	0.0002	0.9998
HKYI	40	-1701.3493	3482.6987	0.0002	1.0000
K2PG	37	-1722.3890	3518.7781	0.0000	1.0000
K2PIG	38	-1722.2136	3520.4272	0.0000	1.0000
SYMG	41	-1719.4666	3520.9332	0.0000	1.0000
K2PI	37	-1724.2245	3522.4490	0.0000	1.0000
SYMIG	42	-1719.3350	3522.6701	0.0000	1.0000
SYMI	41	-1721.3922	3524.7844	0.0000	1.0000
GTR	43	-1731.6473	3549.2947	0.0000	1.0000
F81G	39	-1736.4507	3550.9015	0.0000	1.0000
F81IG	40	-1736.3754	3552.7509	0.0000	1.0000
F81I	39	-1743.5438	3565.0875	0.0000	1.0000
HKY	39	-1745.8802	3569.7604	0.0000	1.0000
JC69G	36	-1754.4202	3580.8403	0.0000	1.0000
JC69IG	37	-1754.2242	3582.4485	0.0000	1.0000
JC69I	36	-1756.0705	3584.1409	0.0000	1.0000
SYM	40	-1764.4631	3608.9261	0.0000	1.0000
K2P	36	-1770.3136	3612.6271	0.0000	1.0000
F81	38	-1779.8376	3635.6752	0.0000	1.0000
JC69	35	-1800.0208	3670.0417	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1700.0235	3644.7708	0.6039	0.6039
GTRG	44	-1689.0018	3647.1999	0.1793	0.7832
HKYI	40	-1701.3493	3647.4226	0.1604	0.9435
HKYIG	41	-1700.0206	3650.8831	0.0284	0.9720
GTRI	44	-1691.2559	3651.7081	0.0188	0.9908
GTRIG	45	-1688.9098	3653.1340	0.0092	1.0000
K2PG	37	-1722.3890	3671.1477	0.0000	1.0000
K2PI	37	-1724.2245	3674.8186	0.0000	1.0000
K2PIG	38	-1722.2136	3676.9149	0.0000	1.0000
SYMG	41	-1719.4666	3689.7752	0.0000	1.0000
SYMI	41	-1721.3922	3693.6264	0.0000	1.0000
SYMIG	42	-1719.3350	3695.6302	0.0000	1.0000
F81G	39	-1736.4507	3711.5073	0.0000	1.0000
F81IG	40	-1736.3754	3717.4747	0.0000	1.0000
F81I	39	-1743.5438	3725.6933	0.0000	1.0000
GTR	43	-1731.6473	3726.3729	0.0000	1.0000
JC69G	36	-1754.4202	3729.0918	0.0000	1.0000
HKY	39	-1745.8802	3730.3662	0.0000	1.0000
JC69I	36	-1756.0705	3732.3924	0.0000	1.0000
JC69IG	37	-1754.2242	3734.8181	0.0000	1.0000
K2P	36	-1770.3136	3760.8786	0.0000	1.0000
SYM	40	-1764.4631	3773.6500	0.0000	1.0000
F81	38	-1779.8376	3792.1629	0.0000	1.0000
JC69	35	-1800.0208	3814.1751	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_6244.phylip = 1 - 454;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_6244.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_6244.phylip = 1 - 454;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_6244.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_6244.phylip = 1 - 454;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_6244.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

