
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:39 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_17686.phylip" (19 taxa, 666 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
Minimum BIC  model: GTRG


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	-2060.1283	4214.6334	0.6187	0.6187
GTRIG	45	-2059.5519	4215.7812	0.3485	0.9672
GTRI	44	-2063.0712	4220.5192	0.0326	0.9998
HKYG	40	-2073.1693	4231.5866	0.0001	0.9999
HKYIG	41	-2072.6655	4232.8502	0.0001	1.0000
HKYI	40	-2075.5131	4236.2742	0.0000	1.0000
GTR	43	-2092.5715	4277.2265	0.0000	1.0000
HKY	39	-2100.4801	4283.9443	0.0000	1.0000
K2PG	37	-2107.8411	4294.1599	0.0000	1.0000
SYMG	41	-2103.7626	4295.0444	0.0000	1.0000
K2PIG	38	-2107.3119	4295.3510	0.0000	1.0000
SYMIG	42	-2103.2327	4296.2631	0.0000	1.0000
K2PI	37	-2110.0685	4298.6147	0.0000	1.0000
SYMI	41	-2106.0161	4299.5514	0.0000	1.0000
F81G	39	-2124.0438	4331.0717	0.0000	1.0000
F81IG	40	-2123.4628	4332.1735	0.0000	1.0000
F81I	39	-2126.8814	4336.7468	0.0000	1.0000
K2P	36	-2135.1906	4346.6165	0.0000	1.0000
SYM	40	-2133.6674	4352.5827	0.0000	1.0000
JC69G	36	-2150.9679	4378.1710	0.0000	1.0000
JC69IG	37	-2150.3629	4379.2035	0.0000	1.0000
F81	38	-2151.5108	4383.7489	0.0000	1.0000
JC69I	36	-2153.7593	4383.7539	0.0000	1.0000
JC69	35	-2178.9238	4431.8475	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2060.1283	4208.2566	0.5856	0.5856
GTRIG	45	-2059.5519	4209.1038	0.3834	0.9690
GTRI	44	-2063.0712	4214.1424	0.0309	0.9999
HKYG	40	-2073.1693	4226.3386	0.0001	1.0000
HKYIG	41	-2072.6655	4227.3310	0.0000	1.0000
HKYI	40	-2075.5131	4231.0262	0.0000	1.0000
GTR	43	-2092.5715	4271.1429	0.0000	1.0000
HKY	39	-2100.4801	4278.9603	0.0000	1.0000
SYMG	41	-2103.7626	4289.5251	0.0000	1.0000
K2PG	37	-2107.8411	4289.6822	0.0000	1.0000
SYMIG	42	-2103.2327	4290.4654	0.0000	1.0000
K2PIG	38	-2107.3119	4290.6238	0.0000	1.0000
SYMI	41	-2106.0161	4294.0322	0.0000	1.0000
K2PI	37	-2110.0685	4294.1370	0.0000	1.0000
F81G	39	-2124.0438	4326.0876	0.0000	1.0000
F81IG	40	-2123.4628	4326.9255	0.0000	1.0000
F81I	39	-2126.8814	4331.7628	0.0000	1.0000
K2P	36	-2135.1906	4342.3812	0.0000	1.0000
SYM	40	-2133.6674	4347.3347	0.0000	1.0000
JC69G	36	-2150.9679	4373.9357	0.0000	1.0000
JC69IG	37	-2150.3629	4374.7258	0.0000	1.0000
F81	38	-2151.5108	4379.0216	0.0000	1.0000
JC69I	36	-2153.7593	4379.5186	0.0000	1.0000
JC69	35	-2178.9238	4427.8475	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
GTRG	44	-2060.1283	4406.3134	0.4468	0.4468
HKYG	40	-2073.1693	4406.3902	0.4300	0.8768
HKYI	40	-2075.5131	4411.0778	0.0413	0.9181
GTRIG	45	-2059.5519	4411.6618	0.0308	0.9489
HKYIG	41	-2072.6655	4411.8839	0.0276	0.9764
GTRI	44	-2063.0712	4412.1991	0.0236	1.0000
HKY	39	-2100.4801	4454.5106	0.0000	1.0000
K2PG	37	-2107.8411	4456.2299	0.0000	1.0000
K2PI	37	-2110.0685	4460.6848	0.0000	1.0000
K2PIG	38	-2107.3119	4461.6728	0.0000	1.0000
GTR	43	-2092.5715	4464.6984	0.0000	1.0000
SYMG	41	-2103.7626	4474.0780	0.0000	1.0000
SYMI	41	-2106.0161	4478.5851	0.0000	1.0000
SYMIG	42	-2103.2327	4479.5195	0.0000	1.0000
F81G	39	-2124.0438	4501.6379	0.0000	1.0000
K2P	36	-2135.1906	4504.4276	0.0000	1.0000
F81IG	40	-2123.4628	4506.9771	0.0000	1.0000
F81I	39	-2126.8814	4507.3131	0.0000	1.0000
SYM	40	-2133.6674	4527.3863	0.0000	1.0000
JC69G	36	-2150.9679	4535.9822	0.0000	1.0000
JC69IG	37	-2150.3629	4541.2735	0.0000	1.0000
JC69I	36	-2153.7593	4541.5650	0.0000	1.0000
F81	38	-2151.5108	4550.0706	0.0000	1.0000
JC69	35	-2178.9238	4585.3927	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/chr2_17686.phylip = 1 - 666;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_17686.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/chr2_17686.phylip = 1 - 666;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_17686.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 (GTRG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_17686.phylip = 1 - 666;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_17686.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;


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End of Output

