
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
13:20 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_5228.phylip" (19 taxa, 897 characters)

Minimum AIC  model: GTRG
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	-2630.3786	5344.5890	0.3458	0.3458
GTRG	44	-2626.1257	5344.8992	0.2961	0.6419
HKYIG	41	-2630.1613	5346.3506	0.1433	0.7852
GTRIG	45	-2625.9488	5346.7624	0.1166	0.9019
HKYI	40	-2632.3175	5348.4667	0.0498	0.9516
GTRI	44	-2627.9372	5348.5223	0.0484	1.0000
GTR	43	-2645.8853	5382.2068	0.0000	1.0000
HKY	39	-2651.0317	5383.7040	0.0000	1.0000
SYMG	41	-2656.3480	5398.7240	0.0000	1.0000
SYMIG	42	-2656.1578	5400.5452	0.0000	1.0000
K2PG	37	-2661.9877	5401.2490	0.0000	1.0000
SYMI	41	-2658.1937	5402.4155	0.0000	1.0000
K2PIG	38	-2661.7566	5402.9677	0.0000	1.0000
K2PI	37	-2663.8931	5405.0597	0.0000	1.0000
SYM	40	-2676.0264	5435.8845	0.0000	1.0000
K2P	36	-2682.6190	5440.3356	0.0000	1.0000
F81G	39	-2679.3847	5440.4100	0.0000	1.0000
F81I	39	-2681.1980	5444.0367	0.0000	1.0000
F81IG	40	-2685.6951	5455.2219	0.0000	1.0000
F81	38	-2698.8669	5477.1883	0.0000	1.0000
JC69G	36	-2706.6645	5488.4268	0.0000	1.0000
JC69IG	37	-2706.4686	5490.2108	0.0000	1.0000
JC69I	36	-2708.4953	5492.0883	0.0000	1.0000
JC69	35	-2726.4813	5525.8894	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2626.1257	5340.2514	0.3514	0.3514
HKYG	40	-2630.3786	5340.7573	0.2729	0.6243
GTRIG	45	-2625.9488	5341.8975	0.1543	0.7786
HKYIG	41	-2630.1613	5342.3226	0.1248	0.9033
GTRI	44	-2627.9372	5343.8744	0.0574	0.9607
HKYI	40	-2632.3175	5344.6349	0.0393	1.0000
GTR	43	-2645.8853	5377.7707	0.0000	1.0000
HKY	39	-2651.0317	5380.0634	0.0000	1.0000
SYMG	41	-2656.3480	5394.6960	0.0000	1.0000
SYMIG	42	-2656.1578	5396.3157	0.0000	1.0000
K2PG	37	-2661.9877	5397.9754	0.0000	1.0000
SYMI	41	-2658.1937	5398.3874	0.0000	1.0000
K2PIG	38	-2661.7566	5399.5132	0.0000	1.0000
K2PI	37	-2663.8931	5401.7861	0.0000	1.0000
SYM	40	-2676.0264	5432.0527	0.0000	1.0000
F81G	39	-2679.3847	5436.7694	0.0000	1.0000
K2P	36	-2682.6190	5437.2380	0.0000	1.0000
F81I	39	-2681.1980	5440.3961	0.0000	1.0000
F81IG	40	-2685.6951	5451.3902	0.0000	1.0000
F81	38	-2698.8669	5473.7337	0.0000	1.0000
JC69G	36	-2706.6645	5485.3291	0.0000	1.0000
JC69IG	37	-2706.4686	5486.9372	0.0000	1.0000
JC69I	36	-2708.4953	5488.9906	0.0000	1.0000
JC69	35	-2726.4813	5522.9626	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2630.3786	5532.7195	0.8435	0.8435
HKYI	40	-2632.3175	5536.5971	0.1214	0.9649
HKYIG	41	-2630.1613	5539.0839	0.0350	0.9999
GTRG	44	-2626.1257	5551.4098	0.0001	1.0000
GTRI	44	-2627.9372	5555.0329	0.0000	1.0000
GTRIG	45	-2625.9488	5557.8550	0.0000	1.0000
HKY	39	-2651.0317	5567.2266	0.0000	1.0000
K2PG	37	-2661.9877	5575.5404	0.0000	1.0000
K2PI	37	-2663.8931	5579.3512	0.0000	1.0000
K2PIG	38	-2661.7566	5581.8773	0.0000	1.0000
GTR	43	-2645.8853	5584.1301	0.0000	1.0000
SYMG	41	-2656.3480	5591.4573	0.0000	1.0000
SYMI	41	-2658.1937	5595.1487	0.0000	1.0000
SYMIG	42	-2656.1578	5597.8760	0.0000	1.0000
K2P	36	-2682.6190	5610.0040	0.0000	1.0000
F81G	39	-2679.3847	5623.9326	0.0000	1.0000
SYM	40	-2676.0264	5624.0150	0.0000	1.0000
F81I	39	-2681.1980	5627.5592	0.0000	1.0000
F81IG	40	-2685.6951	5643.3524	0.0000	1.0000
F81	38	-2698.8669	5656.0979	0.0000	1.0000
JC69G	36	-2706.6645	5658.0951	0.0000	1.0000
JC69I	36	-2708.4953	5661.7567	0.0000	1.0000
JC69IG	37	-2706.4686	5664.5023	0.0000	1.0000
JC69	35	-2726.4813	5690.9295	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_5228.phylip = 1 - 897;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_5228.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 (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_5228.phylip = 1 - 897;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_5228.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/chr7_5228.phylip = 1 - 897;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_5228.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

