
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:47 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/chr5_3401.phylip" (19 taxa, 1075 characters)

Minimum AIC  model: HKYG
Minimum AICc model: HKYG
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
HKYG	40	-3609.1639	7301.5000	0.4366	0.4366
GTRG	44	-3605.3808	7302.6063	0.2511	0.6878
HKYIG	41	-3608.9906	7303.3152	0.1762	0.8639
GTRIG	45	-3605.2201	7304.4634	0.0992	0.9632
HKYI	40	-3612.0606	7307.2934	0.0241	0.9873
GTRI	44	-3608.3634	7308.5715	0.0127	1.0000
K2PG	37	-3636.6428	7349.9972	0.0000	1.0000
K2PI	37	-3639.1159	7354.9435	0.0000	1.0000
SYMG	41	-3635.0602	7355.4545	0.0000	1.0000
K2PIG	38	-3640.0630	7358.9870	0.0000	1.0000
SYMI	41	-3637.4500	7360.2340	0.0000	1.0000
SYMIG	42	-3638.5974	7364.6947	0.0000	1.0000
HKY	39	-3671.6055	7424.2255	0.0000	1.0000
F81G	39	-3671.8322	7424.6789	0.0000	1.0000
F81IG	40	-3671.7292	7426.6306	0.0000	1.0000
GTR	43	-3668.7904	7427.2511	0.0000	1.0000
F81I	39	-3674.0942	7429.2029	0.0000	1.0000
K2P	36	-3696.9927	7468.5519	0.0000	1.0000
JC69G	36	-3697.7722	7470.1109	0.0000	1.0000
JC69IG	37	-3697.6663	7472.0443	0.0000	1.0000
SYM	40	-3695.3942	7473.9605	0.0000	1.0000
JC69I	36	-3699.9498	7474.4661	0.0000	1.0000
F81	38	-3730.5478	7539.9566	0.0000	1.0000
JC69	35	-3755.8483	7584.1220	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-3609.1639	7298.3279	0.3723	0.3723
GTRG	44	-3605.3808	7298.7616	0.2997	0.6719
HKYIG	41	-3608.9906	7299.9812	0.1629	0.8348
GTRIG	45	-3605.2201	7300.4401	0.1295	0.9643
HKYI	40	-3612.0606	7304.1213	0.0206	0.9848
GTRI	44	-3608.3634	7304.7268	0.0152	1.0000
K2PG	37	-3636.6428	7347.2855	0.0000	1.0000
SYMG	41	-3635.0602	7352.1205	0.0000	1.0000
K2PI	37	-3639.1159	7352.2318	0.0000	1.0000
K2PIG	38	-3640.0630	7356.1260	0.0000	1.0000
SYMI	41	-3637.4500	7356.9000	0.0000	1.0000
SYMIG	42	-3638.5974	7361.1947	0.0000	1.0000
HKY	39	-3671.6055	7421.2110	0.0000	1.0000
F81G	39	-3671.8322	7421.6644	0.0000	1.0000
F81IG	40	-3671.7292	7423.4584	0.0000	1.0000
GTR	43	-3668.7904	7423.5809	0.0000	1.0000
F81I	39	-3674.0942	7426.1884	0.0000	1.0000
K2P	36	-3696.9927	7465.9854	0.0000	1.0000
JC69G	36	-3697.7722	7467.5444	0.0000	1.0000
JC69IG	37	-3697.6663	7469.3327	0.0000	1.0000
SYM	40	-3695.3942	7470.7884	0.0000	1.0000
JC69I	36	-3699.9498	7471.8996	0.0000	1.0000
F81	38	-3730.5478	7537.0956	0.0000	1.0000
JC69	35	-3755.8483	7581.6966	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-3609.1639	7497.5309	0.9162	0.9162
HKYI	40	-3612.0606	7503.3243	0.0506	0.9667
HKYIG	41	-3608.9906	7504.1644	0.0332	1.0000
GTRG	44	-3605.3808	7517.8849	0.0000	1.0000
GTRI	44	-3608.3634	7523.8502	0.0000	1.0000
GTRIG	45	-3605.2201	7524.5435	0.0000	1.0000
K2PG	37	-3636.6428	7531.5483	0.0000	1.0000
K2PI	37	-3639.1159	7536.4946	0.0000	1.0000
K2PIG	38	-3640.0630	7545.3689	0.0000	1.0000
SYMG	41	-3635.0602	7556.3036	0.0000	1.0000
SYMI	41	-3637.4500	7561.0831	0.0000	1.0000
SYMIG	42	-3638.5974	7570.3579	0.0000	1.0000
HKY	39	-3671.6055	7615.4339	0.0000	1.0000
F81G	39	-3671.8322	7615.8874	0.0000	1.0000
F81I	39	-3674.0942	7620.4114	0.0000	1.0000
F81IG	40	-3671.7292	7622.6615	0.0000	1.0000
GTR	43	-3668.7904	7637.7241	0.0000	1.0000
K2P	36	-3696.9927	7645.2682	0.0000	1.0000
JC69G	36	-3697.7722	7646.8272	0.0000	1.0000
JC69I	36	-3699.9498	7651.1824	0.0000	1.0000
JC69IG	37	-3697.6663	7653.5955	0.0000	1.0000
SYM	40	-3695.3942	7669.9914	0.0000	1.0000
F81	38	-3730.5478	7726.3385	0.0000	1.0000
JC69	35	-3755.8483	7755.9993	0.0000	1.0000



To specify default values for best AIC, AICc, or BIC models in MrBayes:

[Mrbayes block for the best AIC model (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_3401.phylip = 1 - 1075;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_3401.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;


[Mrbayes block for the best AICc model (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_3401.phylip = 1 - 1075;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_3401.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;


[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/chr5_3401.phylip = 1 - 1075;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_3401.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

