
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:37 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/chr24_2248.phylip" (19 taxa, 559 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	-1743.3418	3582.3879	0.4997	0.4997
GTRIG	45	-1742.9637	3583.9976	0.2234	0.7231
HKYG	40	-1749.4169	3585.1658	0.1246	0.8477
GTRI	44	-1745.0025	3585.7093	0.0949	0.9426
HKYIG	41	-1749.3817	3587.4250	0.0403	0.9829
HKYI	40	-1751.4023	3589.1366	0.0171	1.0000
GTR	43	-1761.5314	3616.4104	0.0000	1.0000
HKY	39	-1768.7004	3621.4123	0.0000	1.0000
SYMG	41	-1772.8390	3634.3395	0.0000	1.0000
SYMIG	42	-1772.1935	3635.3870	0.0000	1.0000
SYMI	41	-1773.8004	3636.2623	0.0000	1.0000
F81G	39	-1779.7152	3643.4419	0.0000	1.0000
K2PG	37	-1782.1164	3643.6301	0.0000	1.0000
K2PIG	38	-1781.9463	3645.5927	0.0000	1.0000
K2PI	37	-1783.7938	3646.9848	0.0000	1.0000
F81IG	40	-1780.7437	3647.8194	0.0000	1.0000
F81I	39	-1782.6303	3649.2722	0.0000	1.0000
SYM	40	-1790.9464	3668.2249	0.0000	1.0000
K2P	36	-1800.6438	3678.3911	0.0000	1.0000
F81	38	-1798.9354	3679.5708	0.0000	1.0000
JC69G	36	-1810.4820	3698.0675	0.0000	1.0000
JC69IG	37	-1811.5667	3702.5307	0.0000	1.0000
JC69I	36	-1813.3262	3703.7559	0.0000	1.0000
JC69	35	-1830.5008	3735.8199	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1743.3418	3574.6836	0.5215	0.5215
GTRIG	45	-1742.9637	3575.9274	0.2800	0.8015
GTRI	44	-1745.0025	3578.0050	0.0991	0.9006
HKYG	40	-1749.4169	3578.8338	0.0655	0.9661
HKYIG	41	-1749.3817	3580.7635	0.0249	0.9910
HKYI	40	-1751.4023	3582.8045	0.0090	1.0000
GTR	43	-1761.5314	3609.0628	0.0000	1.0000
HKY	39	-1768.7004	3615.4008	0.0000	1.0000
SYMG	41	-1772.8390	3627.6780	0.0000	1.0000
SYMIG	42	-1772.1935	3628.3870	0.0000	1.0000
SYMI	41	-1773.8004	3629.6008	0.0000	1.0000
F81G	39	-1779.7152	3637.4304	0.0000	1.0000
K2PG	37	-1782.1164	3638.2327	0.0000	1.0000
K2PIG	38	-1781.9463	3639.8927	0.0000	1.0000
F81IG	40	-1780.7437	3641.4873	0.0000	1.0000
K2PI	37	-1783.7938	3641.5875	0.0000	1.0000
F81I	39	-1782.6303	3643.2606	0.0000	1.0000
SYM	40	-1790.9464	3661.8929	0.0000	1.0000
K2P	36	-1800.6438	3673.2876	0.0000	1.0000
F81	38	-1798.9354	3673.8708	0.0000	1.0000
JC69G	36	-1810.4820	3692.9640	0.0000	1.0000
JC69IG	37	-1811.5667	3697.1334	0.0000	1.0000
JC69I	36	-1813.3262	3698.6524	0.0000	1.0000
JC69	35	-1830.5008	3731.0016	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1749.4169	3751.8798	0.8454	0.8454
HKYI	40	-1751.4023	3755.8505	0.1161	0.9615
HKYIG	41	-1749.3817	3758.1356	0.0370	0.9985
GTRG	44	-1743.3418	3765.0342	0.0012	0.9997
GTRI	44	-1745.0025	3768.3556	0.0002	0.9999
GTRIG	45	-1742.9637	3770.6041	0.0001	1.0000
HKY	39	-1768.7004	3784.1206	0.0000	1.0000
GTR	43	-1761.5314	3795.0873	0.0000	1.0000
K2PG	37	-1782.1164	3798.3003	0.0000	1.0000
K2PI	37	-1783.7938	3801.6551	0.0000	1.0000
K2PIG	38	-1781.9463	3804.2864	0.0000	1.0000
SYMG	41	-1772.8390	3805.0501	0.0000	1.0000
F81G	39	-1779.7152	3806.1502	0.0000	1.0000
SYMI	41	-1773.8004	3806.9730	0.0000	1.0000
SYMIG	42	-1772.1935	3810.0853	0.0000	1.0000
F81I	39	-1782.6303	3811.9804	0.0000	1.0000
F81IG	40	-1780.7437	3814.5333	0.0000	1.0000
K2P	36	-1800.6438	3829.0290	0.0000	1.0000
SYM	40	-1790.9464	3834.9388	0.0000	1.0000
F81	38	-1798.9354	3838.2645	0.0000	1.0000
JC69G	36	-1810.4820	3848.7054	0.0000	1.0000
JC69I	36	-1813.3262	3854.3938	0.0000	1.0000
JC69IG	37	-1811.5667	3857.2009	0.0000	1.0000
JC69	35	-1830.5008	3882.4168	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/chr24_2248.phylip = 1 - 559;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr24_2248.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/chr24_2248.phylip = 1 - 559;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr24_2248.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/chr24_2248.phylip = 1 - 559;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr24_2248.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

