
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:22 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/chr4_9320.phylip" (19 taxa, 1001 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	-3670.2216	7432.5854	0.4882	0.4882
GTRIG	45	-3670.1204	7434.5759	0.1805	0.6687
SYMG	41	-3674.6674	7434.9259	0.1515	0.8202
SYMIG	42	-3674.5637	7436.8978	0.0565	0.8767
K2PG	37	-3680.0165	7436.9530	0.0550	0.9317
HKYG	40	-3677.4498	7438.3163	0.0278	0.9595
K2PIG	38	-3679.9354	7438.9518	0.0202	0.9798
HKYIG	41	-3677.3589	7440.3090	0.0103	0.9900
GTRI	44	-3674.8102	7441.7627	0.0050	0.9950
SYMI	41	-3678.6923	7442.9759	0.0027	0.9977
K2PI	37	-3683.5292	7443.9784	0.0016	0.9994
HKYI	40	-3681.2147	7445.8460	0.0006	1.0000
GTR	43	-3727.0691	7544.0923	0.0000	1.0000
SYM	40	-3730.8434	7545.1035	0.0000	1.0000
K2P	36	-3735.6351	7546.0337	0.0000	1.0000
HKY	39	-3733.0536	7547.3538	0.0000	1.0000
JC69G	36	-3767.6208	7610.0050	0.0000	1.0000
JC69IG	37	-3767.5435	7612.0071	0.0000	1.0000
F81G	39	-3765.9528	7613.1522	0.0000	1.0000
F81IG	40	-3765.8782	7615.1731	0.0000	1.0000
JC69I	36	-3770.4584	7615.6802	0.0000	1.0000
F81I	39	-3768.8801	7619.0067	0.0000	1.0000
JC69	35	-3823.4368	7719.4849	0.0000	1.0000
F81	38	-3821.6952	7722.4714	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-3670.2216	7428.4432	0.5272	0.5272
GTRIG	45	-3670.1204	7430.2408	0.2146	0.7417
SYMG	41	-3674.6674	7431.3347	0.1242	0.8659
SYMIG	42	-3674.5637	7433.1275	0.0507	0.9166
K2PG	37	-3680.0165	7434.0330	0.0322	0.9488
HKYG	40	-3677.4498	7434.8996	0.0209	0.9697
K2PIG	38	-3679.9354	7435.8707	0.0129	0.9826
HKYIG	41	-3677.3589	7436.7178	0.0084	0.9910
GTRI	44	-3674.8102	7437.6204	0.0054	0.9963
SYMI	41	-3678.6923	7439.3847	0.0022	0.9986
K2PI	37	-3683.5292	7441.0583	0.0010	0.9995
HKYI	40	-3681.2147	7442.4294	0.0005	1.0000
GTR	43	-3727.0691	7540.1383	0.0000	1.0000
SYM	40	-3730.8434	7541.6868	0.0000	1.0000
K2P	36	-3735.6351	7543.2702	0.0000	1.0000
HKY	39	-3733.0536	7544.1072	0.0000	1.0000
JC69G	36	-3767.6208	7607.2415	0.0000	1.0000
JC69IG	37	-3767.5435	7609.0871	0.0000	1.0000
F81G	39	-3765.9528	7609.9056	0.0000	1.0000
F81IG	40	-3765.8782	7611.7564	0.0000	1.0000
JC69I	36	-3770.4584	7612.9167	0.0000	1.0000
F81I	39	-3768.8801	7615.7601	0.0000	1.0000
JC69	35	-3823.4368	7716.8735	0.0000	1.0000
F81	38	-3821.6952	7719.3903	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-3680.0165	7615.6569	0.9392	0.9392
K2PIG	38	-3679.9354	7622.4034	0.0322	0.9714
K2PI	37	-3683.5292	7622.6822	0.0280	0.9994
HKYG	40	-3677.4498	7631.2498	0.0004	0.9998
SYMG	41	-3674.6674	7632.5936	0.0002	1.0000
HKYIG	41	-3677.3589	7637.9767	0.0000	1.0000
HKYI	40	-3681.2147	7638.7796	0.0000	1.0000
SYMIG	42	-3674.5637	7639.2952	0.0000	1.0000
SYMI	41	-3678.6923	7640.6436	0.0000	1.0000
GTRG	44	-3670.2216	7644.4284	0.0000	1.0000
GTRIG	45	-3670.1204	7651.1347	0.0000	1.0000
GTRI	44	-3674.8102	7653.6057	0.0000	1.0000
K2P	36	-3735.6351	7719.9854	0.0000	1.0000
HKY	39	-3733.0536	7735.5486	0.0000	1.0000
SYM	40	-3730.8434	7738.0370	0.0000	1.0000
GTR	43	-3727.0691	7751.2147	0.0000	1.0000
JC69G	36	-3767.6208	7783.9567	0.0000	1.0000
JC69I	36	-3770.4584	7789.6319	0.0000	1.0000
JC69IG	37	-3767.5435	7790.7110	0.0000	1.0000
F81G	39	-3765.9528	7801.3470	0.0000	1.0000
F81I	39	-3768.8801	7807.2015	0.0000	1.0000
F81IG	40	-3765.8782	7808.1066	0.0000	1.0000
JC69	35	-3823.4368	7888.6799	0.0000	1.0000
F81	38	-3821.6952	7905.9230	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/chr4_9320.phylip = 1 - 1001;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_9320.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/chr4_9320.phylip = 1 - 1001;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_9320.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/chr4_9320.phylip = 1 - 1001;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_9320.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

