
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:21 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/chr1_14888.phylip" (19 taxa, 1369 characters)

Minimum AIC  model: GTRIG
Minimum AICc model: GTRIG
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
GTRIG	45	-4732.6816	9558.4925	0.4511	0.4511
GTRG	44	-4734.0185	9559.0279	0.3451	0.7962
HKYIG	41	-4738.2933	9561.1818	0.1176	0.9137
HKYG	40	-4739.6653	9561.8006	0.0863	1.0000
K2PIG	38	-4755.7423	9589.7132	0.0000	1.0000
K2PG	37	-4757.0997	9590.3121	0.0000	1.0000
SYMG	41	-4755.5239	9595.6431	0.0000	1.0000
SYMIG	42	-4754.6918	9596.1076	0.0000	1.0000
GTRI	44	-4753.3965	9597.7838	0.0000	1.0000
HKYI	40	-4758.1906	9598.8510	0.0000	1.0000
K2PI	37	-4774.8577	9625.8281	0.0000	1.0000
SYMI	41	-4773.1335	9630.8622	0.0000	1.0000
F81IG	40	-4821.4512	9725.3723	0.0000	1.0000
F81G	39	-4822.7293	9725.8063	0.0000	1.0000
JC69IG	37	-4834.7269	9745.5665	0.0000	1.0000
JC69G	36	-4836.1390	9746.2779	0.0000	1.0000
GTR	43	-4830.0302	9748.9162	0.0000	1.0000
HKY	39	-4837.5869	9755.5214	0.0000	1.0000
F81I	39	-4842.2300	9764.8075	0.0000	1.0000
JC69I	36	-4855.4816	9784.9631	0.0000	1.0000
K2P	36	-4857.0153	9788.0306	0.0000	1.0000
SYM	40	-4853.9013	9790.2725	0.0000	1.0000
F81	38	-4913.3118	9904.8522	0.0000	1.0000
JC69	35	-4928.2706	9928.4317	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRIG	45	-4732.6816	9555.3633	0.4875	0.4875
GTRG	44	-4734.0185	9556.0370	0.3481	0.8356
HKYIG	41	-4738.2933	9558.5865	0.0973	0.9329
HKYG	40	-4739.6653	9559.3307	0.0671	1.0000
K2PIG	38	-4755.7423	9587.4846	0.0000	1.0000
K2PG	37	-4757.0997	9588.1994	0.0000	1.0000
SYMG	41	-4755.5239	9593.0478	0.0000	1.0000
SYMIG	42	-4754.6918	9593.3836	0.0000	1.0000
GTRI	44	-4753.3965	9594.7929	0.0000	1.0000
HKYI	40	-4758.1906	9596.3812	0.0000	1.0000
K2PI	37	-4774.8577	9623.7154	0.0000	1.0000
SYMI	41	-4773.1335	9628.2669	0.0000	1.0000
F81IG	40	-4821.4512	9722.9024	0.0000	1.0000
F81G	39	-4822.7293	9723.4587	0.0000	1.0000
JC69IG	37	-4834.7269	9743.4538	0.0000	1.0000
JC69G	36	-4836.1390	9744.2779	0.0000	1.0000
GTR	43	-4830.0302	9746.0604	0.0000	1.0000
HKY	39	-4837.5869	9753.1738	0.0000	1.0000
F81I	39	-4842.2300	9762.4599	0.0000	1.0000
JC69I	36	-4855.4816	9782.9631	0.0000	1.0000
K2P	36	-4857.0153	9786.0306	0.0000	1.0000
SYM	40	-4853.9013	9787.8026	0.0000	1.0000
F81	38	-4913.3118	9902.6236	0.0000	1.0000
JC69	35	-4928.2706	9926.5412	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-4739.6653	9768.2041	0.9023	0.9023
HKYIG	41	-4738.2933	9772.6818	0.0962	0.9985
K2PG	37	-4757.0997	9781.4073	0.0012	0.9997
GTRG	44	-4734.0185	9785.7978	0.0001	0.9999
K2PIG	38	-4755.7423	9785.9144	0.0001	1.0000
GTRIG	45	-4732.6816	9790.3459	0.0000	1.0000
HKYI	40	-4758.1906	9805.2546	0.0000	1.0000
SYMG	41	-4755.5239	9807.1431	0.0000	1.0000
SYMIG	42	-4754.6918	9812.7007	0.0000	1.0000
K2PI	37	-4774.8577	9816.9233	0.0000	1.0000
GTRI	44	-4753.3965	9824.5537	0.0000	1.0000
SYMI	41	-4773.1335	9842.3622	0.0000	1.0000
F81G	39	-4822.7293	9927.1103	0.0000	1.0000
F81IG	40	-4821.4512	9931.7759	0.0000	1.0000
JC69G	36	-4836.1390	9932.2640	0.0000	1.0000
JC69IG	37	-4834.7269	9936.6617	0.0000	1.0000
HKY	39	-4837.5869	9956.8254	0.0000	1.0000
F81I	39	-4842.2300	9966.1115	0.0000	1.0000
GTR	43	-4830.0302	9970.5993	0.0000	1.0000
JC69I	36	-4855.4816	9970.9492	0.0000	1.0000
K2P	36	-4857.0153	9974.0166	0.0000	1.0000
SYM	40	-4853.9013	9996.6761	0.0000	1.0000
F81	38	-4913.3118	10101.0534	0.0000	1.0000
JC69	35	-4928.2706	10109.3055	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_14888.phylip = 1 - 1369;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_14888.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_14888.phylip = 1 - 1369;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_14888.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
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/chr1_14888.phylip = 1 - 1369;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_14888.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

