
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:44 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/chr5_10216.phylip" (19 taxa, 1102 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	-5117.6912	10327.1288	0.7216	0.7216
GTRIG	45	-5117.5800	10329.0805	0.2719	0.9935
HKYG	40	-5127.0610	10337.2135	0.0047	0.9982
HKYIG	41	-5126.9325	10339.1141	0.0018	1.0000
GTRI	44	-5129.3342	10350.4148	0.0000	1.0000
HKYI	40	-5137.8938	10358.8790	0.0000	1.0000
SYMG	41	-5143.0787	10371.4065	0.0000	1.0000
SYMIG	42	-5142.7114	10372.8335	0.0000	1.0000
K2PG	37	-5154.6595	10385.9619	0.0000	1.0000
K2PIG	38	-5154.4904	10387.7692	0.0000	1.0000
SYMI	41	-5152.1719	10389.5928	0.0000	1.0000
K2PI	37	-5164.6914	10406.0257	0.0000	1.0000
GTR	43	-5210.7099	10510.9963	0.0000	1.0000
HKY	39	-5222.1149	10525.1677	0.0000	1.0000
SYM	40	-5226.5148	10536.1210	0.0000	1.0000
K2P	36	-5249.4142	10573.3298	0.0000	1.0000
F81G	39	-5265.1173	10611.1725	0.0000	1.0000
F81IG	40	-5265.0900	10613.2715	0.0000	1.0000
F81I	39	-5276.4241	10633.7860	0.0000	1.0000
JC69G	36	-5292.8943	10660.2901	0.0000	1.0000
JC69IG	37	-5292.8225	10662.2879	0.0000	1.0000
JC69I	36	-5302.2483	10678.9981	0.0000	1.0000
F81	38	-5350.8531	10780.4946	0.0000	1.0000
JC69	35	-5374.8639	10822.0917	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-5117.6912	10323.3823	0.7054	0.7054
GTRIG	45	-5117.5800	10325.1601	0.2900	0.9953
HKYG	40	-5127.0610	10334.1221	0.0033	0.9986
HKYIG	41	-5126.9325	10335.8651	0.0014	1.0000
GTRI	44	-5129.3342	10346.6683	0.0000	1.0000
HKYI	40	-5137.8938	10355.7876	0.0000	1.0000
SYMG	41	-5143.0787	10368.1574	0.0000	1.0000
SYMIG	42	-5142.7114	10369.4227	0.0000	1.0000
K2PG	37	-5154.6595	10383.3190	0.0000	1.0000
K2PIG	38	-5154.4904	10384.9809	0.0000	1.0000
SYMI	41	-5152.1719	10386.3438	0.0000	1.0000
K2PI	37	-5164.6914	10403.3828	0.0000	1.0000
GTR	43	-5210.7099	10507.4197	0.0000	1.0000
HKY	39	-5222.1149	10522.2299	0.0000	1.0000
SYM	40	-5226.5148	10533.0296	0.0000	1.0000
K2P	36	-5249.4142	10570.8284	0.0000	1.0000
F81G	39	-5265.1173	10608.2346	0.0000	1.0000
F81IG	40	-5265.0900	10610.1801	0.0000	1.0000
F81I	39	-5276.4241	10630.8482	0.0000	1.0000
JC69G	36	-5292.8943	10657.7887	0.0000	1.0000
JC69IG	37	-5292.8225	10659.6451	0.0000	1.0000
JC69I	36	-5302.2483	10676.4967	0.0000	1.0000
F81	38	-5350.8531	10777.7063	0.0000	1.0000
JC69	35	-5374.8639	10819.7277	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-5127.0610	10534.3173	0.9576	0.9576
HKYIG	41	-5126.9325	10541.0652	0.0328	0.9904
GTRG	44	-5117.6912	10543.5971	0.0092	0.9997
GTRIG	45	-5117.5800	10550.3797	0.0003	1.0000
HKYI	40	-5137.8938	10555.9829	0.0000	1.0000
GTRI	44	-5129.3342	10566.8831	0.0000	1.0000
K2PG	37	-5154.6595	10568.4997	0.0000	1.0000
SYMG	41	-5143.0787	10573.3576	0.0000	1.0000
K2PIG	38	-5154.4904	10575.1664	0.0000	1.0000
SYMIG	42	-5142.7114	10579.6278	0.0000	1.0000
K2PI	37	-5164.6914	10588.5635	0.0000	1.0000
SYMI	41	-5152.1719	10591.5439	0.0000	1.0000
HKY	39	-5222.1149	10717.4203	0.0000	1.0000
GTR	43	-5210.7099	10722.6296	0.0000	1.0000
SYM	40	-5226.5148	10733.2249	0.0000	1.0000
K2P	36	-5249.4142	10751.0042	0.0000	1.0000
F81G	39	-5265.1173	10803.4250	0.0000	1.0000
F81IG	40	-5265.0900	10810.3754	0.0000	1.0000
F81I	39	-5276.4241	10826.0386	0.0000	1.0000
JC69G	36	-5292.8943	10837.9644	0.0000	1.0000
JC69IG	37	-5292.8225	10844.8257	0.0000	1.0000
JC69I	36	-5302.2483	10856.6725	0.0000	1.0000
F81	38	-5350.8531	10967.8918	0.0000	1.0000
JC69	35	-5374.8639	10994.8986	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/chr5_10216.phylip = 1 - 1102;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_10216.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/chr5_10216.phylip = 1 - 1102;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_10216.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/chr5_10216.phylip = 1 - 1102;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_10216.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

