
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:31 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/chr3_7396.phylip" (19 taxa, 478 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	-1719.7432	3536.6318	0.5312	0.5312
GTRI	44	-1720.6325	3538.4105	0.2183	0.7495
GTRIG	45	-1719.5047	3538.5928	0.1993	0.9488
HKYG	40	-1727.6208	3542.7472	0.0250	0.9738
HKYI	40	-1728.0263	3543.5584	0.0166	0.9904
HKYIG	41	-1727.3815	3544.6621	0.0096	1.0000
GTR	43	-1735.2786	3565.2762	0.0000	1.0000
HKY	39	-1743.2021	3571.5274	0.0000	1.0000
F81G	39	-1777.5024	3640.1281	0.0000	1.0000
F81I	39	-1777.6118	3640.3470	0.0000	1.0000
K2PG	37	-1780.6039	3641.5988	0.0000	1.0000
F81IG	40	-1777.3062	3642.1180	0.0000	1.0000
K2PI	37	-1781.2718	3642.9345	0.0000	1.0000
K2PIG	38	-1781.0594	3644.8705	0.0000	1.0000
SYMG	41	-1778.3789	3646.6569	0.0000	1.0000
SYMI	41	-1778.9871	3647.8733	0.0000	1.0000
SYMIG	42	-1778.3249	3648.9533	0.0000	1.0000
F81	38	-1792.6740	3668.0997	0.0000	1.0000
K2P	36	-1798.5428	3675.1264	0.0000	1.0000
SYM	40	-1796.2334	3679.9724	0.0000	1.0000
JC69G	36	-1820.3635	3718.7678	0.0000	1.0000
JC69I	36	-1820.8349	3719.7106	0.0000	1.0000
JC69IG	37	-1820.2677	3720.9262	0.0000	1.0000
JC69	35	-1837.4055	3750.5124	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1719.7432	3527.4863	0.5203	0.5203
GTRIG	45	-1719.5047	3529.0095	0.2429	0.7632
GTRI	44	-1720.6325	3529.2650	0.2138	0.9770
HKYG	40	-1727.6208	3535.2415	0.0108	0.9878
HKYI	40	-1728.0263	3536.0527	0.0072	0.9950
HKYIG	41	-1727.3815	3536.7630	0.0050	1.0000
GTR	43	-1735.2786	3556.5573	0.0000	1.0000
HKY	39	-1743.2021	3564.4041	0.0000	1.0000
F81G	39	-1777.5024	3633.0048	0.0000	1.0000
F81I	39	-1777.6118	3633.2237	0.0000	1.0000
F81IG	40	-1777.3062	3634.6123	0.0000	1.0000
K2PG	37	-1780.6039	3635.2079	0.0000	1.0000
K2PI	37	-1781.2718	3636.5436	0.0000	1.0000
K2PIG	38	-1781.0594	3638.1188	0.0000	1.0000
SYMG	41	-1778.3789	3638.7578	0.0000	1.0000
SYMI	41	-1778.9871	3639.9742	0.0000	1.0000
SYMIG	42	-1778.3249	3640.6499	0.0000	1.0000
F81	38	-1792.6740	3661.3480	0.0000	1.0000
K2P	36	-1798.5428	3669.0855	0.0000	1.0000
SYM	40	-1796.2334	3672.4667	0.0000	1.0000
JC69G	36	-1820.3635	3712.7270	0.0000	1.0000
JC69I	36	-1820.8349	3713.6697	0.0000	1.0000
JC69IG	37	-1820.2677	3714.5353	0.0000	1.0000
JC69	35	-1837.4055	3744.8111	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1727.6208	3702.0259	0.5742	0.5742
HKYI	40	-1728.0263	3702.8371	0.3827	0.9569
HKYIG	41	-1727.3815	3707.7171	0.0334	0.9903
GTRG	44	-1719.7432	3710.9492	0.0066	0.9969
GTRI	44	-1720.6325	3712.7279	0.0027	0.9996
GTRIG	45	-1719.5047	3716.6420	0.0004	1.0000
HKY	39	-1743.2021	3727.0190	0.0000	1.0000
GTR	43	-1735.2786	3735.8506	0.0000	1.0000
K2PG	37	-1780.6039	3789.4835	0.0000	1.0000
K2PI	37	-1781.2718	3790.8192	0.0000	1.0000
F81G	39	-1777.5024	3795.6196	0.0000	1.0000
F81I	39	-1777.6118	3795.8385	0.0000	1.0000
K2PIG	38	-1781.0594	3796.5640	0.0000	1.0000
F81IG	40	-1777.3062	3801.3967	0.0000	1.0000
SYMG	41	-1778.3789	3809.7118	0.0000	1.0000
SYMI	41	-1778.9871	3810.9283	0.0000	1.0000
SYMIG	42	-1778.3249	3815.7735	0.0000	1.0000
K2P	36	-1798.5428	3819.1915	0.0000	1.0000
F81	38	-1792.6740	3819.7932	0.0000	1.0000
SYM	40	-1796.2334	3839.2511	0.0000	1.0000
JC69G	36	-1820.3635	3862.8330	0.0000	1.0000
JC69I	36	-1820.8349	3863.7757	0.0000	1.0000
JC69IG	37	-1820.2677	3868.8109	0.0000	1.0000
JC69	35	-1837.4055	3890.7474	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/chr3_7396.phylip = 1 - 478;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_7396.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/chr3_7396.phylip = 1 - 478;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_7396.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/chr3_7396.phylip = 1 - 478;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_7396.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

