
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:32 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_5908.phylip" (19 taxa, 744 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	-3574.5962	7242.8577	0.4221	0.4221
HKYG	40	-3579.3323	7243.3304	0.3332	0.7553
GTRIG	45	-3574.5961	7245.1234	0.1360	0.8913
HKYIG	41	-3579.3322	7245.5705	0.1087	1.0000
HKYI	40	-3590.5295	7265.7248	0.0000	1.0000
GTRI	44	-3586.4288	7266.5228	0.0000	1.0000
K2PG	37	-3621.4074	7320.7978	0.0000	1.0000
K2PIG	38	-3621.4119	7323.0281	0.0000	1.0000
SYMG	41	-3619.0459	7324.9978	0.0000	1.0000
SYMIG	42	-3619.0557	7327.2641	0.0000	1.0000
SYMI	41	-3626.8381	7340.5822	0.0000	1.0000
K2PI	37	-3634.8550	7347.6930	0.0000	1.0000
HKY	39	-3634.0600	7350.5519	0.0000	1.0000
GTR	43	-3630.5489	7352.5034	0.0000	1.0000
F81G	39	-3657.7773	7397.9863	0.0000	1.0000
F81IG	40	-3657.7772	7400.2202	0.0000	1.0000
F81I	39	-3665.7323	7413.8964	0.0000	1.0000
K2P	36	-3670.7015	7417.1710	0.0000	1.0000
SYM	40	-3668.0926	7420.8509	0.0000	1.0000
JC69G	36	-3688.4336	7452.6353	0.0000	1.0000
JC69IG	37	-3688.4336	7454.8502	0.0000	1.0000
JC69I	36	-3696.3542	7468.4765	0.0000	1.0000
F81	38	-3706.7714	7493.7471	0.0000	1.0000
JC69	35	-3735.4201	7544.3995	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-3574.5962	7237.1924	0.4943	0.4943
HKYG	40	-3579.3323	7238.6647	0.2367	0.7310
GTRIG	45	-3574.5961	7239.1922	0.1819	0.9129
HKYIG	41	-3579.3322	7240.6645	0.0871	1.0000
GTRI	44	-3586.4288	7260.8576	0.0000	1.0000
HKYI	40	-3590.5295	7261.0591	0.0000	1.0000
K2PG	37	-3621.4074	7316.8148	0.0000	1.0000
K2PIG	38	-3621.4119	7318.8238	0.0000	1.0000
SYMG	41	-3619.0459	7320.0919	0.0000	1.0000
SYMIG	42	-3619.0557	7322.1114	0.0000	1.0000
SYMI	41	-3626.8381	7335.6763	0.0000	1.0000
K2PI	37	-3634.8550	7343.7100	0.0000	1.0000
HKY	39	-3634.0600	7346.1201	0.0000	1.0000
GTR	43	-3630.5489	7347.0977	0.0000	1.0000
F81G	39	-3657.7773	7393.5545	0.0000	1.0000
F81IG	40	-3657.7772	7395.5544	0.0000	1.0000
F81I	39	-3665.7323	7409.4645	0.0000	1.0000
K2P	36	-3670.7015	7413.4030	0.0000	1.0000
SYM	40	-3668.0926	7416.1852	0.0000	1.0000
JC69G	36	-3688.4336	7448.8673	0.0000	1.0000
JC69IG	37	-3688.4336	7450.8672	0.0000	1.0000
JC69I	36	-3696.3542	7464.7084	0.0000	1.0000
F81	38	-3706.7714	7489.5428	0.0000	1.0000
JC69	35	-3735.4201	7540.8401	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-3579.3323	7423.1463	0.9644	0.9644
HKYIG	41	-3579.3322	7429.7582	0.0354	0.9998
GTRG	44	-3574.5962	7440.1222	0.0002	1.0000
HKYI	40	-3590.5295	7445.5407	0.0000	1.0000
GTRIG	45	-3574.5961	7446.7340	0.0000	1.0000
GTRI	44	-3586.4288	7463.7874	0.0000	1.0000
K2PG	37	-3621.4074	7487.4603	0.0000	1.0000
K2PIG	38	-3621.4119	7494.0814	0.0000	1.0000
SYMG	41	-3619.0459	7509.1855	0.0000	1.0000
K2PI	37	-3634.8550	7514.3555	0.0000	1.0000
SYMIG	42	-3619.0557	7515.8172	0.0000	1.0000
SYMI	41	-3626.8381	7524.7699	0.0000	1.0000
HKY	39	-3634.0600	7525.9897	0.0000	1.0000
GTR	43	-3630.5489	7545.4155	0.0000	1.0000
F81G	39	-3657.7773	7573.4241	0.0000	1.0000
K2P	36	-3670.7015	7579.4364	0.0000	1.0000
F81IG	40	-3657.7772	7580.0361	0.0000	1.0000
F81I	39	-3665.7323	7589.3341	0.0000	1.0000
SYM	40	-3668.0926	7600.6668	0.0000	1.0000
JC69G	36	-3688.4336	7614.9008	0.0000	1.0000
JC69IG	37	-3688.4336	7621.5127	0.0000	1.0000
JC69I	36	-3696.3542	7630.7419	0.0000	1.0000
F81	38	-3706.7714	7664.8004	0.0000	1.0000
JC69	35	-3735.4201	7702.2616	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/chr12_5908.phylip = 1 - 744;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr12_5908.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/chr12_5908.phylip = 1 - 744;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr12_5908.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/chr12_5908.phylip = 1 - 744;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr12_5908.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

