
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:18 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_5447.phylip" (19 taxa, 923 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
Minimum BIC  model: K2PG


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	-3680.3110	7453.1322	0.5753	0.5753
GTRIG	45	-3680.0476	7454.8159	0.2479	0.8232
HKYG	40	-3686.2544	7456.2277	0.1224	0.9456
HKYIG	41	-3685.9879	7457.8849	0.0534	0.9990
K2PG	37	-3695.3008	7467.7789	0.0004	0.9994
SYMG	41	-3691.7713	7469.4518	0.0002	0.9996
K2PIG	38	-3695.0614	7469.4757	0.0002	0.9997
GTRI	44	-3688.5553	7469.6209	0.0002	0.9999
SYMIG	42	-3691.5400	7471.1845	0.0001	0.9999
HKYI	40	-3694.0205	7471.7598	0.0001	1.0000
K2PI	37	-3703.0444	7483.2661	0.0000	1.0000
SYMI	41	-3699.2467	7484.4027	0.0000	1.0000
GTR	43	-3753.0602	7596.4254	0.0000	1.0000
HKY	39	-3757.7787	7597.0908	0.0000	1.0000
K2P	36	-3766.5404	7608.0876	0.0000	1.0000
SYM	40	-3762.8732	7609.4651	0.0000	1.0000
F81G	39	-3771.1879	7623.9091	0.0000	1.0000
F81IG	40	-3771.0111	7625.7410	0.0000	1.0000
JC69G	36	-3777.9182	7630.8432	0.0000	1.0000
JC69IG	37	-3777.7435	7632.6644	0.0000	1.0000
F81I	39	-3777.9111	7637.3556	0.0000	1.0000
JC69I	36	-3784.5068	7644.0203	0.0000	1.0000
F81	38	-3838.2755	7755.9040	0.0000	1.0000
JC69	35	-3844.7237	7762.2885	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-3680.3110	7448.6219	0.5911	0.5911
GTRIG	45	-3680.0476	7450.0953	0.2830	0.8740
HKYG	40	-3686.2544	7452.5089	0.0846	0.9587
HKYIG	41	-3685.9879	7453.9757	0.0407	0.9993
K2PG	37	-3695.3008	7464.6015	0.0002	0.9995
GTRI	44	-3688.5553	7465.1106	0.0002	0.9997
SYMG	41	-3691.7713	7465.5426	0.0001	0.9998
K2PIG	38	-3695.0614	7466.1228	0.0001	0.9999
SYMIG	42	-3691.5400	7467.0800	0.0001	1.0000
HKYI	40	-3694.0205	7468.0410	0.0000	1.0000
K2PI	37	-3703.0444	7480.0887	0.0000	1.0000
SYMI	41	-3699.2467	7480.4935	0.0000	1.0000
GTR	43	-3753.0602	7592.1205	0.0000	1.0000
HKY	39	-3757.7787	7593.5574	0.0000	1.0000
K2P	36	-3766.5404	7605.0809	0.0000	1.0000
SYM	40	-3762.8732	7605.7463	0.0000	1.0000
F81G	39	-3771.1879	7620.3757	0.0000	1.0000
F81IG	40	-3771.0111	7622.0222	0.0000	1.0000
JC69G	36	-3777.9182	7627.8364	0.0000	1.0000
JC69IG	37	-3777.7435	7629.4870	0.0000	1.0000
F81I	39	-3777.9111	7633.8222	0.0000	1.0000
JC69I	36	-3784.5068	7641.0135	0.0000	1.0000
F81	38	-3838.2755	7752.5510	0.0000	1.0000
JC69	35	-3844.7237	7759.4474	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-3695.3008	7643.2238	0.7362	0.7362
HKYG	40	-3686.2544	7645.6140	0.2228	0.9591
K2PIG	38	-3695.0614	7649.5727	0.0308	0.9899
HKYIG	41	-3685.9879	7651.9085	0.0096	0.9995
K2PI	37	-3703.0444	7658.7110	0.0003	0.9998
GTRG	44	-3680.3110	7661.0376	0.0001	0.9999
HKYI	40	-3694.0205	7661.1462	0.0001	1.0000
SYMG	41	-3691.7713	7663.4754	0.0000	1.0000
GTRIG	45	-3680.0476	7667.3386	0.0000	1.0000
SYMIG	42	-3691.5400	7669.8404	0.0000	1.0000
GTRI	44	-3688.5553	7677.5263	0.0000	1.0000
SYMI	41	-3699.2467	7678.4263	0.0000	1.0000
K2P	36	-3766.5404	7778.8755	0.0000	1.0000
HKY	39	-3757.7787	7781.8349	0.0000	1.0000
SYM	40	-3762.8732	7798.8515	0.0000	1.0000
GTR	43	-3753.0602	7799.7085	0.0000	1.0000
JC69G	36	-3777.9182	7801.6310	0.0000	1.0000
JC69IG	37	-3777.7435	7808.1093	0.0000	1.0000
F81G	39	-3771.1879	7808.6533	0.0000	1.0000
JC69I	36	-3784.5068	7814.8082	0.0000	1.0000
F81IG	40	-3771.0111	7815.1273	0.0000	1.0000
F81I	39	-3777.9111	7822.0998	0.0000	1.0000
JC69	35	-3844.7237	7928.4144	0.0000	1.0000
F81	38	-3838.2755	7936.0010	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_5447.phylip = 1 - 923;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_5447.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_5447.phylip = 1 - 923;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_5447.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 (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_5447.phylip = 1 - 923;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_5447.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=gamma;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


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End of Output

