
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:21 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_24963.phylip" (19 taxa, 939 characters)

Minimum AIC  model: HKYIG
Minimum AICc model: HKYIG
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
HKYIG	41	-3136.8279	6359.4953	0.5812	0.5812
HKYG	40	-3138.5533	6360.7592	0.3089	0.8901
GTRIG	45	-3134.6590	6363.9541	0.0625	0.9526
GTRG	44	-3136.1844	6364.7984	0.0410	0.9936
HKYI	40	-3142.5133	6368.6791	0.0059	0.9995
GTRI	44	-3140.5928	6373.6151	0.0005	1.0000
SYMIG	42	-3153.9689	6395.9691	0.0000	1.0000
K2PIG	38	-3158.8688	6397.0310	0.0000	1.0000
SYMG	41	-3155.7076	6397.2547	0.0000	1.0000
K2PG	37	-3160.7436	6398.6081	0.0000	1.0000
SYMI	41	-3159.7203	6405.2801	0.0000	1.0000
K2PI	37	-3164.3194	6405.7599	0.0000	1.0000
F81IG	40	-3213.9408	6511.5343	0.0000	1.0000
F81G	39	-3215.3986	6512.2677	0.0000	1.0000
F81I	39	-3218.6467	6518.7639	0.0000	1.0000
JC69IG	37	-3232.7351	6542.5913	0.0000	1.0000
JC69G	36	-3234.1967	6543.3468	0.0000	1.0000
JC69I	36	-3237.1870	6549.3275	0.0000	1.0000
HKY	39	-3233.9987	6549.4679	0.0000	1.0000
GTR	43	-3232.4731	6555.1741	0.0000	1.0000
K2P	36	-3254.0817	6583.1168	0.0000	1.0000
SYM	40	-3250.0803	6583.8131	0.0000	1.0000
F81	38	-3304.6616	6688.6165	0.0000	1.0000
JC69	35	-3322.6131	6718.0170	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYIG	41	-3136.8279	6355.6558	0.5716	0.5716
HKYG	40	-3138.5533	6357.1066	0.2767	0.8483
GTRIG	45	-3134.6590	6359.3180	0.0916	0.9399
GTRG	44	-3136.1844	6360.3689	0.0542	0.9941
HKYI	40	-3142.5133	6365.0265	0.0053	0.9993
GTRI	44	-3140.5928	6369.1856	0.0007	1.0000
SYMIG	42	-3153.9689	6391.9379	0.0000	1.0000
SYMG	41	-3155.7076	6393.4152	0.0000	1.0000
K2PIG	38	-3158.8688	6393.7376	0.0000	1.0000
K2PG	37	-3160.7436	6395.4871	0.0000	1.0000
SYMI	41	-3159.7203	6401.4406	0.0000	1.0000
K2PI	37	-3164.3194	6402.6389	0.0000	1.0000
F81IG	40	-3213.9408	6507.8817	0.0000	1.0000
F81G	39	-3215.3986	6508.7971	0.0000	1.0000
F81I	39	-3218.6467	6515.2933	0.0000	1.0000
JC69IG	37	-3232.7351	6539.4703	0.0000	1.0000
JC69G	36	-3234.1967	6540.3933	0.0000	1.0000
HKY	39	-3233.9987	6545.9973	0.0000	1.0000
JC69I	36	-3237.1870	6546.3741	0.0000	1.0000
GTR	43	-3232.4731	6550.9462	0.0000	1.0000
SYM	40	-3250.0803	6580.1606	0.0000	1.0000
K2P	36	-3254.0817	6580.1634	0.0000	1.0000
F81	38	-3304.6616	6685.3232	0.0000	1.0000
JC69	35	-3322.6131	6715.2263	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-3138.5533	6550.8993	0.8317	0.8317
HKYIG	41	-3136.8279	6554.2933	0.1524	0.9841
HKYI	40	-3142.5133	6558.8191	0.0159	1.0000
GTRG	44	-3136.1844	6573.5408	0.0000	1.0000
K2PG	37	-3160.7436	6574.7453	0.0000	1.0000
GTRIG	45	-3134.6590	6577.3347	0.0000	1.0000
K2PIG	38	-3158.8688	6577.8406	0.0000	1.0000
K2PI	37	-3164.3194	6581.8971	0.0000	1.0000
GTRI	44	-3140.5928	6582.3574	0.0000	1.0000
SYMG	41	-3155.7076	6592.0526	0.0000	1.0000
SYMIG	42	-3153.9689	6595.4202	0.0000	1.0000
SYMI	41	-3159.7203	6600.0781	0.0000	1.0000
F81G	39	-3215.3986	6697.7449	0.0000	1.0000
F81IG	40	-3213.9408	6701.6743	0.0000	1.0000
F81I	39	-3218.6467	6704.2411	0.0000	1.0000
JC69G	36	-3234.1967	6714.8067	0.0000	1.0000
JC69IG	37	-3232.7351	6718.7285	0.0000	1.0000
JC69I	36	-3237.1870	6720.7875	0.0000	1.0000
HKY	39	-3233.9987	6734.9451	0.0000	1.0000
K2P	36	-3254.0817	6754.5767	0.0000	1.0000
GTR	43	-3232.4731	6759.2732	0.0000	1.0000
SYM	40	-3250.0803	6773.9532	0.0000	1.0000
F81	38	-3304.6616	6869.4262	0.0000	1.0000
JC69	35	-3322.6131	6884.7948	0.0000	1.0000



To specify default values for best AIC, AICc, or BIC models in MrBayes:

[Mrbayes block for the best AIC model (HKYIG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_24963.phylip = 1 - 939;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_24963.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best AICc model (HKYIG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_24963.phylip = 1 - 939;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_24963.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
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_24963.phylip = 1 - 939;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_24963.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

