
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:36 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/chr11_3256.phylip" (19 taxa, 1114 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
Minimum BIC  model: GTRG


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	-4264.8309	8621.3662	0.7404	0.7404
GTRIG	45	-4264.7930	8623.4624	0.2596	1.0000
HKYG	40	-4281.3111	8645.6791	0.0000	1.0000
HKYIG	41	-4281.2710	8647.7547	0.0000	1.0000
GTRI	44	-4281.0667	8653.8378	0.0000	1.0000
HKYI	40	-4295.0395	8673.1358	0.0000	1.0000
GTR	43	-4329.4890	8748.5145	0.0000	1.0000
HKY	39	-4339.8372	8760.5795	0.0000	1.0000
K2PG	37	-4356.6729	8789.9592	0.0000	1.0000
K2PIG	38	-4356.6350	8792.0271	0.0000	1.0000
SYMG	41	-4354.4721	8794.1569	0.0000	1.0000
SYMIG	42	-4354.7931	8796.9587	0.0000	1.0000
K2PI	37	-4368.7274	8814.0681	0.0000	1.0000
SYMI	41	-4367.3465	8819.9058	0.0000	1.0000
K2P	36	-4411.6388	8897.7511	0.0000	1.0000
F81G	39	-4410.4204	8901.7459	0.0000	1.0000
SYM	40	-4409.6811	8902.4190	0.0000	1.0000
F81IG	40	-4410.4121	8903.8810	0.0000	1.0000
F81I	39	-4421.6821	8924.2692	0.0000	1.0000
F81	38	-4461.4651	9001.6873	0.0000	1.0000
JC69G	36	-4464.3329	9003.1393	0.0000	1.0000
JC69IG	37	-4464.3268	9005.2669	0.0000	1.0000
JC69I	36	-4475.2532	9024.9800	0.0000	1.0000
JC69	35	-4514.5989	9101.5355	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-4264.8309	8617.6618	0.7235	0.7235
GTRIG	45	-4264.7930	8619.5860	0.2765	1.0000
HKYG	40	-4281.3111	8642.6222	0.0000	1.0000
HKYIG	41	-4281.2710	8644.5420	0.0000	1.0000
GTRI	44	-4281.0667	8650.1334	0.0000	1.0000
HKYI	40	-4295.0395	8670.0789	0.0000	1.0000
GTR	43	-4329.4890	8744.9780	0.0000	1.0000
HKY	39	-4339.8372	8757.6745	0.0000	1.0000
K2PG	37	-4356.6729	8787.3458	0.0000	1.0000
K2PIG	38	-4356.6350	8789.2699	0.0000	1.0000
SYMG	41	-4354.4721	8790.9442	0.0000	1.0000
SYMIG	42	-4354.7931	8793.5862	0.0000	1.0000
K2PI	37	-4368.7274	8811.4547	0.0000	1.0000
SYMI	41	-4367.3465	8816.6931	0.0000	1.0000
K2P	36	-4411.6388	8895.2776	0.0000	1.0000
F81G	39	-4410.4204	8898.8409	0.0000	1.0000
SYM	40	-4409.6811	8899.3622	0.0000	1.0000
F81IG	40	-4410.4121	8900.8241	0.0000	1.0000
F81I	39	-4421.6821	8921.3642	0.0000	1.0000
F81	38	-4461.4651	8998.9301	0.0000	1.0000
JC69G	36	-4464.3329	9000.6658	0.0000	1.0000
JC69IG	37	-4464.3268	9002.6535	0.0000	1.0000
JC69I	36	-4475.2532	9022.5064	0.0000	1.0000
JC69	35	-4514.5989	9099.1978	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
GTRG	44	-4264.8309	8838.3531	0.8927	0.8927
HKYG	40	-4281.3111	8843.2507	0.0771	0.9698
GTRIG	45	-4264.7930	8845.2930	0.0278	0.9976
HKYIG	41	-4281.2710	8850.1862	0.0024	1.0000
HKYI	40	-4295.0395	8870.7074	0.0000	1.0000
GTRI	44	-4281.0667	8870.8247	0.0000	1.0000
HKY	39	-4339.8372	8953.2872	0.0000	1.0000
GTR	43	-4329.4890	8960.6537	0.0000	1.0000
K2PG	37	-4356.6729	8972.9272	0.0000	1.0000
K2PIG	38	-4356.6350	8979.8670	0.0000	1.0000
SYMG	41	-4354.4721	8996.5884	0.0000	1.0000
K2PI	37	-4368.7274	8997.0361	0.0000	1.0000
SYMIG	42	-4354.7931	9004.2461	0.0000	1.0000
SYMI	41	-4367.3465	9022.3373	0.0000	1.0000
K2P	36	-4411.6388	9075.8432	0.0000	1.0000
F81G	39	-4410.4204	9094.4536	0.0000	1.0000
SYM	40	-4409.6811	9099.9907	0.0000	1.0000
F81IG	40	-4410.4121	9101.4526	0.0000	1.0000
F81I	39	-4421.6821	9116.9769	0.0000	1.0000
JC69G	36	-4464.3329	9181.2314	0.0000	1.0000
JC69IG	37	-4464.3268	9188.2349	0.0000	1.0000
F81	38	-4461.4651	9189.5272	0.0000	1.0000
JC69I	36	-4475.2532	9203.0721	0.0000	1.0000
JC69	35	-4514.5989	9274.7478	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/chr11_3256.phylip = 1 - 1114;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_3256.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/chr11_3256.phylip = 1 - 1114;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_3256.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 (GTRG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_3256.phylip = 1 - 1114;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_3256.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;


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End of Output

