
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:04 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_32208.phylip" (19 taxa, 509 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	-1717.7797	3532.0939	0.8308	0.8308
HKYG	40	-1724.3866	3535.7818	0.1314	0.9622
HKYIG	41	-1724.7735	3538.9217	0.0273	0.9895
GTRIG	45	-1721.2584	3541.4585	0.0077	0.9972
GTRI	44	-1723.9567	3544.4480	0.0017	0.9989
HKYI	40	-1729.2035	3545.4156	0.0011	1.0000
GTR	43	-1737.5599	3569.2574	0.0000	1.0000
HKY	39	-1743.8134	3572.2793	0.0000	1.0000
K2PG	37	-1747.2715	3574.5134	0.0000	1.0000
SYMG	41	-1744.3960	3578.1667	0.0000	1.0000
K2PIG	38	-1748.9534	3580.2131	0.0000	1.0000
SYMIG	42	-1745.9659	3583.6828	0.0000	1.0000
K2PI	37	-1754.3191	3588.6086	0.0000	1.0000
SYMI	41	-1750.8758	3591.1263	0.0000	1.0000
K2P	36	-1766.7547	3611.1535	0.0000	1.0000
SYM	40	-1763.4769	3613.9624	0.0000	1.0000
F81G	39	-1778.4291	3641.5107	0.0000	1.0000
F81IG	40	-1782.7878	3652.5841	0.0000	1.0000
F81I	39	-1784.6682	3653.9888	0.0000	1.0000
JC69G	36	-1795.0638	3667.7717	0.0000	1.0000
F81	38	-1795.6318	3673.5699	0.0000	1.0000
JC69IG	37	-1799.9308	3679.8319	0.0000	1.0000
JC69I	36	-1804.8227	3687.2894	0.0000	1.0000
JC69	35	-1814.6026	3704.5328	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1717.7797	3523.5594	0.9040	0.9040
HKYG	40	-1724.3866	3528.7733	0.0667	0.9707
HKYIG	41	-1724.7735	3531.5470	0.0167	0.9873
GTRIG	45	-1721.2584	3532.5168	0.0103	0.9976
GTRI	44	-1723.9567	3535.9135	0.0019	0.9995
HKYI	40	-1729.2035	3538.4070	0.0005	1.0000
GTR	43	-1737.5599	3561.1198	0.0000	1.0000
HKY	39	-1743.8134	3565.6269	0.0000	1.0000
K2PG	37	-1747.2715	3568.5431	0.0000	1.0000
SYMG	41	-1744.3960	3570.7919	0.0000	1.0000
K2PIG	38	-1748.9534	3573.9067	0.0000	1.0000
SYMIG	42	-1745.9659	3575.9317	0.0000	1.0000
K2PI	37	-1754.3191	3582.6383	0.0000	1.0000
SYMI	41	-1750.8758	3583.7516	0.0000	1.0000
K2P	36	-1766.7547	3605.5094	0.0000	1.0000
SYM	40	-1763.4769	3606.9538	0.0000	1.0000
F81G	39	-1778.4291	3634.8583	0.0000	1.0000
F81IG	40	-1782.7878	3645.5755	0.0000	1.0000
F81I	39	-1784.6682	3647.3364	0.0000	1.0000
JC69G	36	-1795.0638	3662.1276	0.0000	1.0000
F81	38	-1795.6318	3667.2636	0.0000	1.0000
JC69IG	37	-1799.9308	3673.8616	0.0000	1.0000
JC69I	36	-1804.8227	3681.6454	0.0000	1.0000
JC69	35	-1814.6026	3699.2051	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1724.3866	3698.0712	0.9606	0.9606
HKYIG	41	-1724.7735	3705.0774	0.0289	0.9895
HKYI	40	-1729.2035	3707.7049	0.0078	0.9972
GTRG	44	-1717.7797	3709.7871	0.0027	1.0000
GTRI	44	-1723.9567	3722.1412	0.0000	1.0000
GTRIG	45	-1721.2584	3722.9769	0.0000	1.0000
K2PG	37	-1747.2715	3725.1437	0.0000	1.0000
HKY	39	-1743.8134	3730.6923	0.0000	1.0000
K2PIG	38	-1748.9534	3734.7397	0.0000	1.0000
K2PI	37	-1754.3191	3739.2389	0.0000	1.0000
GTR	43	-1737.5599	3743.1150	0.0000	1.0000
SYMG	41	-1744.3960	3744.3223	0.0000	1.0000
SYMIG	42	-1745.9659	3753.6945	0.0000	1.0000
SYMI	41	-1750.8758	3757.2819	0.0000	1.0000
K2P	36	-1766.7547	3757.8775	0.0000	1.0000
SYM	40	-1763.4769	3776.2518	0.0000	1.0000
F81G	39	-1778.4291	3799.9237	0.0000	1.0000
F81I	39	-1784.6682	3812.4018	0.0000	1.0000
JC69G	36	-1795.0638	3814.4957	0.0000	1.0000
F81IG	40	-1782.7878	3814.8735	0.0000	1.0000
F81	38	-1795.6318	3828.0966	0.0000	1.0000
JC69IG	37	-1799.9308	3830.4622	0.0000	1.0000
JC69I	36	-1804.8227	3834.0135	0.0000	1.0000
JC69	35	-1814.6026	3847.3408	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_32208.phylip = 1 - 509;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_32208.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_32208.phylip = 1 - 509;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_32208.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_32208.phylip = 1 - 509;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_32208.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

