
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:24 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_5474.phylip" (19 taxa, 822 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	-3288.7683	6670.6331	0.5089	0.5089
HKYG	40	-3293.8140	6671.8277	0.2801	0.7890
HKYIG	41	-3293.6465	6673.7083	0.1094	0.8984
GTRIG	45	-3289.2815	6673.8981	0.0995	0.9979
GTRI	44	-3294.8492	6682.7949	0.0012	0.9990
HKYI	40	-3299.4687	6683.1372	0.0010	1.0000
K2PG	37	-3352.3223	6782.2313	0.0000	1.0000
SYMG	41	-3348.9004	6784.2162	0.0000	1.0000
K2PIG	38	-3352.2814	6784.3483	0.0000	1.0000
SYMIG	42	-3348.9025	6786.4418	0.0000	1.0000
SYMI	41	-3352.4533	6791.3221	0.0000	1.0000
K2PI	37	-3357.2129	6792.0125	0.0000	1.0000
F81G	39	-3379.3413	6840.6723	0.0000	1.0000
F81IG	40	-3379.2980	6842.7958	0.0000	1.0000
HKY	39	-3382.2720	6846.5337	0.0000	1.0000
GTR	43	-3378.4551	6847.7739	0.0000	1.0000
F81I	39	-3383.1791	6848.3479	0.0000	1.0000
JC69IG	37	-3421.7161	6921.0190	0.0000	1.0000
JC69G	36	-3423.4571	6922.3078	0.0000	1.0000
JC69I	36	-3425.6762	6926.7460	0.0000	1.0000
K2P	36	-3437.5753	6950.5443	0.0000	1.0000
SYM	40	-3434.1047	6952.4092	0.0000	1.0000
F81	38	-3461.0987	7001.9829	0.0000	1.0000
JC69	35	-3505.2598	7083.7257	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-3288.7683	6665.5366	0.5787	0.5787
HKYG	40	-3293.8140	6667.6280	0.2034	0.7821
GTRIG	45	-3289.2815	6668.5630	0.1274	0.9095
HKYIG	41	-3293.6465	6669.2929	0.0885	0.9980
GTRI	44	-3294.8492	6677.6984	0.0013	0.9993
HKYI	40	-3299.4687	6678.9374	0.0007	1.0000
K2PG	37	-3352.3223	6778.6445	0.0000	1.0000
SYMG	41	-3348.9004	6779.8009	0.0000	1.0000
K2PIG	38	-3352.2814	6780.5629	0.0000	1.0000
SYMIG	42	-3348.9025	6781.8051	0.0000	1.0000
SYMI	41	-3352.4533	6786.9067	0.0000	1.0000
K2PI	37	-3357.2129	6788.4258	0.0000	1.0000
F81G	39	-3379.3413	6836.6826	0.0000	1.0000
F81IG	40	-3379.2980	6838.5961	0.0000	1.0000
HKY	39	-3382.2720	6842.5440	0.0000	1.0000
GTR	43	-3378.4551	6842.9102	0.0000	1.0000
F81I	39	-3383.1791	6844.3581	0.0000	1.0000
JC69IG	37	-3421.7161	6917.4322	0.0000	1.0000
JC69G	36	-3423.4571	6918.9141	0.0000	1.0000
JC69I	36	-3425.6762	6923.3524	0.0000	1.0000
K2P	36	-3437.5753	6947.1506	0.0000	1.0000
SYM	40	-3434.1047	6948.2094	0.0000	1.0000
F81	38	-3461.0987	6998.1975	0.0000	1.0000
JC69	35	-3505.2598	7080.5196	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-3293.8140	6856.0976	0.9570	0.9570
HKYIG	41	-3293.6465	6862.4743	0.0395	0.9964
HKYI	40	-3299.4687	6867.4071	0.0034	0.9998
GTRG	44	-3288.7683	6872.8531	0.0002	1.0000
GTRIG	45	-3289.2815	6880.5913	0.0000	1.0000
GTRI	44	-3294.8492	6885.0149	0.0000	1.0000
K2PG	37	-3352.3223	6952.9789	0.0000	1.0000
K2PIG	38	-3352.2814	6959.6090	0.0000	1.0000
K2PI	37	-3357.2129	6962.7602	0.0000	1.0000
SYMG	41	-3348.9004	6972.9822	0.0000	1.0000
SYMIG	42	-3348.9025	6979.6982	0.0000	1.0000
SYMI	41	-3352.4533	6980.0880	0.0000	1.0000
F81G	39	-3379.3413	7020.4405	0.0000	1.0000
HKY	39	-3382.2720	7026.3018	0.0000	1.0000
F81IG	40	-3379.2980	7027.0657	0.0000	1.0000
F81I	39	-3383.1791	7028.1160	0.0000	1.0000
GTR	43	-3378.4551	7045.5150	0.0000	1.0000
JC69G	36	-3423.4571	7088.5368	0.0000	1.0000
JC69IG	37	-3421.7161	7091.7666	0.0000	1.0000
JC69I	36	-3425.6762	7092.9750	0.0000	1.0000
K2P	36	-3437.5753	7116.7733	0.0000	1.0000
SYM	40	-3434.1047	7136.6791	0.0000	1.0000
F81	38	-3461.0987	7177.2436	0.0000	1.0000
JC69	35	-3505.2598	7245.4305	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/chr1_5474.phylip = 1 - 822;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_5474.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/chr1_5474.phylip = 1 - 822;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_5474.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/chr1_5474.phylip = 1 - 822;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_5474.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

