
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:55 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/chr3_292.phylip" (19 taxa, 1027 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	-4197.1508	8486.3342	0.7837	0.7837
GTRIG	45	-4197.3626	8488.9454	0.2124	0.9961
HKYG	40	-4207.0450	8497.4165	0.0031	0.9992
HKYIG	41	-4207.3012	8500.0988	0.0008	1.0000
GTRI	44	-4209.6352	8511.3031	0.0000	1.0000
HKYI	40	-4219.1111	8521.5488	0.0000	1.0000
GTR	43	-4250.0271	8589.9036	0.0000	1.0000
K2PG	37	-4260.8642	8598.5717	0.0000	1.0000
K2PIG	38	-4260.8066	8600.6132	0.0000	1.0000
SYMG	41	-4258.6448	8602.7860	0.0000	1.0000
HKY	39	-4261.2319	8603.6250	0.0000	1.0000
SYMIG	42	-4258.5978	8604.8663	0.0000	1.0000
K2PI	37	-4273.0664	8622.9760	0.0000	1.0000
SYMI	41	-4270.7090	8626.9145	0.0000	1.0000
F81G	39	-4303.1753	8687.5117	0.0000	1.0000
F81IG	40	-4305.1542	8693.6349	0.0000	1.0000
K2P	36	-4318.0729	8710.8367	0.0000	1.0000
F81I	39	-4316.1701	8713.5012	0.0000	1.0000
SYM	40	-4317.1417	8717.6100	0.0000	1.0000
JC69G	36	-4344.4333	8763.5574	0.0000	1.0000
JC69IG	37	-4344.4120	8765.6672	0.0000	1.0000
JC69I	36	-4355.4805	8785.6519	0.0000	1.0000
F81	38	-4355.5893	8790.1786	0.0000	1.0000
JC69	35	-4398.3791	8869.3011	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-4197.1508	8482.3016	0.7685	0.7685
GTRIG	45	-4197.3626	8484.7253	0.2288	0.9973
HKYG	40	-4207.0450	8494.0899	0.0021	0.9994
HKYIG	41	-4207.3012	8496.6024	0.0006	1.0000
GTRI	44	-4209.6352	8507.2705	0.0000	1.0000
HKYI	40	-4219.1111	8518.2222	0.0000	1.0000
GTR	43	-4250.0271	8586.0542	0.0000	1.0000
K2PG	37	-4260.8642	8595.7284	0.0000	1.0000
K2PIG	38	-4260.8066	8597.6132	0.0000	1.0000
SYMG	41	-4258.6448	8599.2896	0.0000	1.0000
HKY	39	-4261.2319	8600.4639	0.0000	1.0000
SYMIG	42	-4258.5978	8601.1955	0.0000	1.0000
K2PI	37	-4273.0664	8620.1327	0.0000	1.0000
SYMI	41	-4270.7090	8623.4180	0.0000	1.0000
F81G	39	-4303.1753	8684.3506	0.0000	1.0000
F81IG	40	-4305.1542	8690.3084	0.0000	1.0000
K2P	36	-4318.0729	8708.1458	0.0000	1.0000
F81I	39	-4316.1701	8710.3401	0.0000	1.0000
SYM	40	-4317.1417	8714.2834	0.0000	1.0000
JC69G	36	-4344.4333	8760.8665	0.0000	1.0000
JC69IG	37	-4344.4120	8762.8240	0.0000	1.0000
JC69I	36	-4355.4805	8782.9610	0.0000	1.0000
F81	38	-4355.5893	8787.1786	0.0000	1.0000
JC69	35	-4398.3791	8866.7582	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-4207.0450	8691.4658	0.9584	0.9584
HKYIG	41	-4207.3012	8698.9127	0.0231	0.9815
GTRG	44	-4197.1508	8699.4151	0.0180	0.9995
GTRIG	45	-4197.3626	8706.7731	0.0005	1.0000
HKYI	40	-4219.1111	8715.5981	0.0000	1.0000
GTRI	44	-4209.6352	8724.3840	0.0000	1.0000
K2PG	37	-4260.8642	8778.3011	0.0000	1.0000
K2PIG	38	-4260.8066	8785.1203	0.0000	1.0000
HKY	39	-4261.2319	8792.9054	0.0000	1.0000
GTR	43	-4250.0271	8798.2333	0.0000	1.0000
SYMG	41	-4258.6448	8801.5998	0.0000	1.0000
K2PI	37	-4273.0664	8802.7054	0.0000	1.0000
SYMIG	42	-4258.5978	8808.4402	0.0000	1.0000
SYMI	41	-4270.7090	8825.7283	0.0000	1.0000
F81G	39	-4303.1753	8876.7921	0.0000	1.0000
K2P	36	-4318.0729	8885.7841	0.0000	1.0000
F81IG	40	-4305.1542	8887.6842	0.0000	1.0000
F81I	39	-4316.1701	8902.7816	0.0000	1.0000
SYM	40	-4317.1417	8911.6593	0.0000	1.0000
JC69G	36	-4344.4333	8938.5048	0.0000	1.0000
JC69IG	37	-4344.4120	8945.3967	0.0000	1.0000
JC69I	36	-4355.4805	8960.5993	0.0000	1.0000
F81	38	-4355.5893	8974.6857	0.0000	1.0000
JC69	35	-4398.3791	9039.4621	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/chr3_292.phylip = 1 - 1027;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_292.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/chr3_292.phylip = 1 - 1027;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_292.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/chr3_292.phylip = 1 - 1027;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_292.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

