
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:37 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/chr6_3284.phylip" (19 taxa, 504 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	-1656.3319	3409.2912	0.5961	0.5961
GTRIG	45	-1656.2415	3411.5224	0.1954	0.7915
GTRI	44	-1658.1257	3412.8789	0.0991	0.8906
HKYG	40	-1663.2319	3413.5480	0.0710	0.9616
HKYIG	41	-1663.0272	3415.5089	0.0266	0.9882
HKYI	40	-1665.0273	3417.1388	0.0118	1.0000
SYMG	41	-1674.0438	3437.5422	0.0000	1.0000
SYMIG	42	-1675.8740	3443.5832	0.0000	1.0000
K2PG	37	-1683.6392	3447.3127	0.0000	1.0000
SYMI	41	-1679.6041	3448.6628	0.0000	1.0000
K2PIG	38	-1686.9442	3456.2626	0.0000	1.0000
K2PI	37	-1689.5144	3459.0632	0.0000	1.0000
GTR	43	-1692.7689	3479.7638	0.0000	1.0000
HKY	39	-1700.0942	3484.9126	0.0000	1.0000
F81G	39	-1706.6569	3498.0378	0.0000	1.0000
F81IG	40	-1706.2056	3499.4954	0.0000	1.0000
F81I	39	-1708.9783	3502.6807	0.0000	1.0000
SYM	40	-1711.6960	3510.4763	0.0000	1.0000
K2P	36	-1722.5499	3522.8043	0.0000	1.0000
JC69G	36	-1732.6117	3542.9278	0.0000	1.0000
JC69IG	37	-1732.0524	3544.1391	0.0000	1.0000
JC69I	36	-1735.6609	3549.0263	0.0000	1.0000
F81	38	-1745.8677	3574.1096	0.0000	1.0000
JC69	35	-1771.1982	3617.7810	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1656.3319	3400.6638	0.6031	0.6031
GTRIG	45	-1656.2415	3402.4831	0.2429	0.8460
GTRI	44	-1658.1257	3404.2514	0.1003	0.9463
HKYG	40	-1663.2319	3406.4638	0.0332	0.9795
HKYIG	41	-1663.0272	3408.0544	0.0150	0.9945
HKYI	40	-1665.0273	3410.0546	0.0055	1.0000
SYMG	41	-1674.0438	3430.0877	0.0000	1.0000
SYMIG	42	-1675.8740	3435.7481	0.0000	1.0000
SYMI	41	-1679.6041	3441.2083	0.0000	1.0000
K2PG	37	-1683.6392	3441.2784	0.0000	1.0000
K2PIG	38	-1686.9442	3449.8884	0.0000	1.0000
K2PI	37	-1689.5144	3453.0289	0.0000	1.0000
GTR	43	-1692.7689	3471.5378	0.0000	1.0000
HKY	39	-1700.0942	3478.1885	0.0000	1.0000
F81G	39	-1706.6569	3491.3137	0.0000	1.0000
F81IG	40	-1706.2056	3492.4112	0.0000	1.0000
F81I	39	-1708.9783	3495.9565	0.0000	1.0000
SYM	40	-1711.6960	3503.3920	0.0000	1.0000
K2P	36	-1722.5499	3517.0998	0.0000	1.0000
JC69G	36	-1732.6117	3537.2233	0.0000	1.0000
JC69IG	37	-1732.0524	3538.1047	0.0000	1.0000
JC69I	36	-1735.6609	3543.3218	0.0000	1.0000
F81	38	-1745.8677	3567.7354	0.0000	1.0000
JC69	35	-1771.1982	3612.3964	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1663.2319	3575.3669	0.8160	0.8160
HKYI	40	-1665.0273	3578.9576	0.1355	0.9515
HKYIG	41	-1663.0272	3581.1800	0.0446	0.9961
GTRG	44	-1656.3319	3586.4571	0.0032	0.9993
GTRI	44	-1658.1257	3590.0448	0.0005	0.9998
GTRIG	45	-1656.2415	3592.4990	0.0002	1.0000
K2PG	37	-1683.6392	3597.5137	0.0000	1.0000
SYMG	41	-1674.0438	3603.2133	0.0000	1.0000
K2PI	37	-1689.5144	3609.2642	0.0000	1.0000
K2PIG	38	-1686.9442	3610.3463	0.0000	1.0000
SYMIG	42	-1675.8740	3613.0963	0.0000	1.0000
SYMI	41	-1679.6041	3614.3339	0.0000	1.0000
HKY	39	-1700.0942	3642.8690	0.0000	1.0000
GTR	43	-1692.7689	3653.1085	0.0000	1.0000
F81G	39	-1706.6569	3655.9942	0.0000	1.0000
F81I	39	-1708.9783	3660.6370	0.0000	1.0000
F81IG	40	-1706.2056	3661.3142	0.0000	1.0000
K2P	36	-1722.5499	3669.1125	0.0000	1.0000
SYM	40	-1711.6960	3672.2951	0.0000	1.0000
JC69G	36	-1732.6117	3689.2361	0.0000	1.0000
JC69IG	37	-1732.0524	3694.3401	0.0000	1.0000
JC69I	36	-1735.6609	3695.3345	0.0000	1.0000
F81	38	-1745.8677	3728.1933	0.0000	1.0000
JC69	35	-1771.1982	3760.1865	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/chr6_3284.phylip = 1 - 504;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_3284.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/chr6_3284.phylip = 1 - 504;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_3284.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/chr6_3284.phylip = 1 - 504;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_3284.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

