
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:26 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/chr12_5828.phylip" (19 taxa, 613 characters)

Minimum AIC  model: GTRIG
Minimum AICc model: GTRIG
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
GTRIG	45	-2745.6777	5588.6571	0.5245	0.5245
GTRG	44	-2746.9434	5588.8585	0.4742	0.9987
HKYIG	41	-2756.9694	5601.9703	0.0007	0.9994
HKYG	40	-2759.2568	5604.2478	0.0002	0.9996
SYMG	41	-2758.1728	5604.3770	0.0002	0.9998
K2PIG	38	-2762.3865	5605.9368	0.0001	0.9999
K2PG	37	-2763.8869	5606.6643	0.0001	0.9999
SYMIG	42	-2758.3329	5607.0027	0.0001	1.0000
GTRI	44	-2761.7838	5618.5395	0.0000	1.0000
HKYI	40	-2773.1813	5632.0969	0.0000	1.0000
SYMI	41	-2773.0111	5634.0537	0.0000	1.0000
K2PI	37	-2779.4129	5637.7163	0.0000	1.0000
F81IG	40	-2817.6266	5720.9875	0.0000	1.0000
F81G	39	-2819.6680	5722.7811	0.0000	1.0000
JC69IG	37	-2823.0645	5725.0194	0.0000	1.0000
JC69G	36	-2824.4163	5725.4576	0.0000	1.0000
F81I	39	-2834.5852	5752.6154	0.0000	1.0000
JC69I	36	-2840.3713	5757.3675	0.0000	1.0000
GTR	43	-2833.6487	5759.9476	0.0000	1.0000
HKY	39	-2848.6993	5780.8437	0.0000	1.0000
SYM	40	-2849.2176	5784.1695	0.0000	1.0000
K2P	36	-2858.0748	5792.7746	0.0000	1.0000
F81	38	-2907.8152	5896.7941	0.0000	1.0000
JC69	35	-2915.8305	5906.0285	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRIG	45	-2745.6777	5581.3555	0.5656	0.5656
GTRG	44	-2746.9434	5581.8867	0.4337	0.9993
HKYIG	41	-2756.9694	5595.9388	0.0004	0.9997
SYMG	41	-2758.1728	5598.3455	0.0001	0.9998
HKYG	40	-2759.2568	5598.5135	0.0001	0.9999
SYMIG	42	-2758.3329	5600.6659	0.0000	0.9999
K2PIG	38	-2762.3865	5600.7731	0.0000	1.0000
K2PG	37	-2763.8869	5601.7738	0.0000	1.0000
GTRI	44	-2761.7838	5611.5677	0.0000	1.0000
HKYI	40	-2773.1813	5626.3626	0.0000	1.0000
SYMI	41	-2773.0111	5628.0222	0.0000	1.0000
K2PI	37	-2779.4129	5632.8259	0.0000	1.0000
F81IG	40	-2817.6266	5715.2533	0.0000	1.0000
F81G	39	-2819.6680	5717.3361	0.0000	1.0000
JC69IG	37	-2823.0645	5720.1290	0.0000	1.0000
JC69G	36	-2824.4163	5720.8326	0.0000	1.0000
F81I	39	-2834.5852	5747.1704	0.0000	1.0000
JC69I	36	-2840.3713	5752.7425	0.0000	1.0000
GTR	43	-2833.6487	5753.2973	0.0000	1.0000
HKY	39	-2848.6993	5775.3987	0.0000	1.0000
SYM	40	-2849.2176	5778.4352	0.0000	1.0000
K2P	36	-2858.0748	5788.1496	0.0000	1.0000
F81	38	-2907.8152	5891.6304	0.0000	1.0000
JC69	35	-2915.8305	5901.6611	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-2763.8869	5765.2533	0.8362	0.8362
K2PIG	38	-2762.3865	5768.6709	0.1514	0.9876
HKYG	40	-2759.2568	5775.2481	0.0056	0.9932
GTRG	44	-2746.9434	5776.2948	0.0033	0.9966
HKYIG	41	-2756.9694	5777.0917	0.0022	0.9988
SYMG	41	-2758.1728	5779.4985	0.0007	0.9995
GTRIG	45	-2745.6777	5780.1819	0.0005	1.0000
SYMIG	42	-2758.3329	5786.2372	0.0000	1.0000
K2PI	37	-2779.4129	5796.3054	0.0000	1.0000
HKYI	40	-2773.1813	5803.0972	0.0000	1.0000
GTRI	44	-2761.7838	5805.9758	0.0000	1.0000
SYMI	41	-2773.0111	5809.1752	0.0000	1.0000
JC69G	36	-2824.4163	5879.8938	0.0000	1.0000
JC69IG	37	-2823.0645	5883.6085	0.0000	1.0000
F81G	39	-2819.6680	5889.6523	0.0000	1.0000
F81IG	40	-2817.6266	5891.9879	0.0000	1.0000
JC69I	36	-2840.3713	5911.8037	0.0000	1.0000
F81I	39	-2834.5852	5919.4866	0.0000	1.0000
GTR	43	-2833.6487	5943.2870	0.0000	1.0000
K2P	36	-2858.0748	5947.2107	0.0000	1.0000
HKY	39	-2848.6993	5947.7149	0.0000	1.0000
SYM	40	-2849.2176	5955.1698	0.0000	1.0000
JC69	35	-2915.8305	6056.3038	0.0000	1.0000
F81	38	-2907.8152	6059.5282	0.0000	1.0000



To specify default values for best AIC, AICc, or BIC models in MrBayes:

[Mrbayes block for the best AIC model (GTRIG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr12_5828.phylip = 1 - 613;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr12_5828.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best AICc model (GTRIG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr12_5828.phylip = 1 - 613;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr12_5828.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
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/chr12_5828.phylip = 1 - 613;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr12_5828.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

