
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:41 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/chr2_24886.phylip" (19 taxa, 915 characters)

Minimum AIC  model: GTRIG
Minimum AICc model: GTRIG
Minimum BIC  model: HKYIG


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
GTRIG	45	-5124.5774	10343.9189	0.9542	0.9542
GTRG	44	-5128.7434	10350.0385	0.0447	0.9989
HKYIG	41	-5135.9021	10357.7493	0.0009	0.9999
GTRI	44	-5134.8788	10362.3093	0.0001	1.0000
HKYG	40	-5140.0011	10363.7550	0.0000	1.0000
HKYI	40	-5144.3618	10372.4765	0.0000	1.0000
K2PIG	38	-5207.3612	10494.1060	0.0000	1.0000
K2PG	37	-5210.0114	10497.2291	0.0000	1.0000
SYMIG	42	-5205.5917	10499.3257	0.0000	1.0000
SYMG	41	-5207.9680	10501.8809	0.0000	1.0000
K2PI	37	-5216.5692	10510.3447	0.0000	1.0000
SYMI	41	-5215.4717	10516.8885	0.0000	1.0000
GTR	43	-5237.4983	10565.3411	0.0000	1.0000
HKY	39	-5246.5950	10574.7557	0.0000	1.0000
F81IG	40	-5304.2269	10692.2066	0.0000	1.0000
F81G	39	-5308.1165	10697.7987	0.0000	1.0000
F81I	39	-5309.7525	10701.0707	0.0000	1.0000
K2P	36	-5316.6424	10708.3190	0.0000	1.0000
SYM	40	-5315.6995	10715.1518	0.0000	1.0000
JC69IG	37	-5342.2966	10761.7996	0.0000	1.0000
JC69G	36	-5344.9672	10764.9685	0.0000	1.0000
JC69I	36	-5348.5164	10772.0670	0.0000	1.0000
F81	38	-5404.5441	10888.4717	0.0000	1.0000
JC69	35	-5442.1248	10957.1164	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRIG	45	-5124.5774	10339.1548	0.9588	0.9588
GTRG	44	-5128.7434	10345.4868	0.0404	0.9993
HKYIG	41	-5135.9021	10353.8043	0.0006	0.9999
GTRI	44	-5134.8788	10357.7576	0.0001	1.0000
HKYG	40	-5140.0011	10360.0022	0.0000	1.0000
HKYI	40	-5144.3618	10368.7236	0.0000	1.0000
K2PIG	38	-5207.3612	10490.7225	0.0000	1.0000
K2PG	37	-5210.0114	10494.0228	0.0000	1.0000
SYMIG	42	-5205.5917	10495.1835	0.0000	1.0000
SYMG	41	-5207.9680	10497.9359	0.0000	1.0000
K2PI	37	-5216.5692	10507.1383	0.0000	1.0000
SYMI	41	-5215.4717	10512.9434	0.0000	1.0000
GTR	43	-5237.4983	10560.9966	0.0000	1.0000
HKY	39	-5246.5950	10571.1900	0.0000	1.0000
F81IG	40	-5304.2269	10688.4538	0.0000	1.0000
F81G	39	-5308.1165	10694.2330	0.0000	1.0000
F81I	39	-5309.7525	10697.5049	0.0000	1.0000
K2P	36	-5316.6424	10705.2848	0.0000	1.0000
SYM	40	-5315.6995	10711.3990	0.0000	1.0000
JC69IG	37	-5342.2966	10758.5932	0.0000	1.0000
JC69G	36	-5344.9672	10761.9343	0.0000	1.0000
JC69I	36	-5348.5164	10769.0328	0.0000	1.0000
F81	38	-5404.5441	10885.0881	0.0000	1.0000
JC69	35	-5442.1248	10954.2495	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYIG	41	-5135.9021	10551.3802	0.6047	0.6047
HKYG	40	-5140.0011	10552.7591	0.3035	0.9081
GTRIG	45	-5124.5774	10556.0064	0.0598	0.9680
GTRG	44	-5128.7434	10557.5194	0.0281	0.9961
HKYI	40	-5144.3618	10561.4806	0.0039	0.9999
GTRI	44	-5134.8788	10569.7902	0.0001	1.0000
K2PG	37	-5210.0114	10672.3230	0.0000	1.0000
K2PIG	38	-5207.3612	10673.8416	0.0000	1.0000
K2PI	37	-5216.5692	10685.4385	0.0000	1.0000
SYMG	41	-5207.9680	10695.5118	0.0000	1.0000
SYMIG	42	-5205.5917	10697.5783	0.0000	1.0000
SYMI	41	-5215.4717	10710.5193	0.0000	1.0000
HKY	39	-5246.5950	10759.1280	0.0000	1.0000
GTR	43	-5237.4983	10768.2104	0.0000	1.0000
K2P	36	-5316.6424	10878.7661	0.0000	1.0000
F81IG	40	-5304.2269	10881.2107	0.0000	1.0000
F81G	39	-5308.1165	10882.1711	0.0000	1.0000
F81I	39	-5309.7525	10885.4430	0.0000	1.0000
SYM	40	-5315.6995	10904.1559	0.0000	1.0000
JC69G	36	-5344.9672	10935.4156	0.0000	1.0000
JC69IG	37	-5342.2966	10936.8934	0.0000	1.0000
JC69I	36	-5348.5164	10942.5141	0.0000	1.0000
F81	38	-5404.5441	11068.2072	0.0000	1.0000
JC69	35	-5442.1248	11122.9119	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_24886.phylip = 1 - 915;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_24886.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_24886.phylip = 1 - 915;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_24886.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_24886.phylip = 1 - 915;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_24886.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;


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End of Output

