
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/chr11_3350.phylip" (19 taxa, 498 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	-1699.7894	3496.3206	0.5242	0.5242
GTRI	44	-1700.5062	3497.7542	0.2560	0.7802
GTRIG	45	-1699.4526	3498.0646	0.2192	0.9994
HKYG	40	-1711.9670	3511.1112	0.0003	0.9997
HKYI	40	-1712.5404	3512.2580	0.0002	0.9999
HKYIG	41	-1711.8751	3513.3028	0.0001	1.0000
SYMG	41	-1713.6922	3516.9371	0.0000	1.0000
SYMI	41	-1715.0249	3519.6024	0.0000	1.0000
SYMIG	42	-1714.0159	3519.9702	0.0000	1.0000
K2PG	37	-1721.0880	3522.2890	0.0000	1.0000
K2PIG	38	-1720.0422	3522.5419	0.0000	1.0000
K2PI	37	-1722.0611	3524.2353	0.0000	1.0000
GTR	43	-1738.2862	3570.9071	0.0000	1.0000
F81G	39	-1746.4726	3577.7575	0.0000	1.0000
F81I	39	-1747.1826	3579.1774	0.0000	1.0000
F81IG	40	-1746.5425	3580.2622	0.0000	1.0000
JC69G	36	-1753.2095	3584.1978	0.0000	1.0000
HKY	39	-1750.1626	3585.1374	0.0000	1.0000
JC69I	36	-1754.4934	3586.7656	0.0000	1.0000
JC69IG	37	-1753.4760	3587.0650	0.0000	1.0000
SYM	40	-1752.3394	3591.8560	0.0000	1.0000
K2P	36	-1759.7051	3597.1889	0.0000	1.0000
F81	38	-1782.8889	3648.2353	0.0000	1.0000
JC69	35	-1790.5906	3656.6358	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1699.7894	3487.5789	0.4990	0.4990
GTRIG	45	-1699.4526	3488.9053	0.2571	0.7561
GTRI	44	-1700.5062	3489.0125	0.2437	0.9997
HKYG	40	-1711.9670	3503.9340	0.0001	0.9998
HKYI	40	-1712.5404	3505.0807	0.0001	0.9999
HKYIG	41	-1711.8751	3505.7502	0.0001	1.0000
SYMG	41	-1713.6922	3509.3845	0.0000	1.0000
SYMIG	42	-1714.0159	3512.0317	0.0000	1.0000
SYMI	41	-1715.0249	3512.0498	0.0000	1.0000
K2PIG	38	-1720.0422	3516.0844	0.0000	1.0000
K2PG	37	-1721.0880	3516.1760	0.0000	1.0000
K2PI	37	-1722.0611	3518.1223	0.0000	1.0000
GTR	43	-1738.2862	3562.5723	0.0000	1.0000
F81G	39	-1746.4726	3570.9453	0.0000	1.0000
F81I	39	-1747.1826	3572.3652	0.0000	1.0000
F81IG	40	-1746.5425	3573.0850	0.0000	1.0000
HKY	39	-1750.1626	3578.3252	0.0000	1.0000
JC69G	36	-1753.2095	3578.4191	0.0000	1.0000
JC69IG	37	-1753.4760	3580.9519	0.0000	1.0000
JC69I	36	-1754.4934	3580.9869	0.0000	1.0000
SYM	40	-1752.3394	3584.6788	0.0000	1.0000
K2P	36	-1759.7051	3591.4102	0.0000	1.0000
F81	38	-1782.8889	3641.7778	0.0000	1.0000
JC69	35	-1790.5906	3651.1812	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-1721.0880	3671.9682	0.2603	0.2603
HKYG	40	-1711.9670	3672.3580	0.2142	0.4745
GTRG	44	-1699.7894	3672.8453	0.1679	0.6424
HKYI	40	-1712.5404	3673.5047	0.1207	0.7632
K2PI	37	-1722.0611	3673.9145	0.0984	0.8615
GTRI	44	-1700.5062	3674.2789	0.0820	0.9435
K2PIG	38	-1720.0422	3676.0872	0.0332	0.9767
GTRIG	45	-1699.4526	3678.3823	0.0105	0.9873
HKYIG	41	-1711.8751	3678.3848	0.0105	0.9978
SYMG	41	-1713.6922	3682.0191	0.0017	0.9995
SYMI	41	-1715.0249	3684.6844	0.0005	0.9999
SYMIG	42	-1714.0159	3688.8769	0.0001	1.0000
JC69G	36	-1753.2095	3730.0007	0.0000	1.0000
JC69I	36	-1754.4934	3732.5685	0.0000	1.0000
F81G	39	-1746.4726	3735.1587	0.0000	1.0000
F81I	39	-1747.1826	3736.5786	0.0000	1.0000
JC69IG	37	-1753.4760	3736.7441	0.0000	1.0000
F81IG	40	-1746.5425	3741.5090	0.0000	1.0000
HKY	39	-1750.1626	3742.5386	0.0000	1.0000
K2P	36	-1759.7051	3742.9918	0.0000	1.0000
GTR	43	-1738.2862	3743.6281	0.0000	1.0000
SYM	40	-1752.3394	3753.1028	0.0000	1.0000
JC69	35	-1790.5906	3798.5522	0.0000	1.0000
F81	38	-1782.8889	3801.7806	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/chr11_3350.phylip = 1 - 498;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_3350.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/chr11_3350.phylip = 1 - 498;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_3350.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/chr11_3350.phylip = 1 - 498;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_3350.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

