
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:30 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/chr22_640.phylip" (19 taxa, 605 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	-2139.2456	4373.5627	0.6752	0.6752
GTRIG	45	-2139.1879	4375.7819	0.2226	0.8979
GTRI	44	-2141.1593	4377.3900	0.0996	0.9975
HKYG	40	-2149.8828	4385.5812	0.0017	0.9992
HKYIG	41	-2149.8159	4387.7490	0.0006	0.9997
HKYI	40	-2151.6641	4389.1438	0.0003	1.0000
GTR	43	-2157.6120	4407.9690	0.0000	1.0000
K2PG	37	-2167.2529	4413.4652	0.0000	1.0000
SYMG	41	-2162.8455	4413.8082	0.0000	1.0000
K2PIG	38	-2167.1683	4415.5733	0.0000	1.0000
SYMIG	42	-2162.7753	4415.9777	0.0000	1.0000
K2PI	37	-2169.0990	4417.1573	0.0000	1.0000
SYMI	41	-2164.6111	4417.3394	0.0000	1.0000
HKY	39	-2167.9525	4419.4271	0.0000	1.0000
SYM	40	-2181.0490	4447.9136	0.0000	1.0000
K2P	36	-2186.3483	4449.3867	0.0000	1.0000
F81G	39	-2223.5023	4530.5267	0.0000	1.0000
F81IG	40	-2223.4402	4532.6960	0.0000	1.0000
F81I	39	-2224.6580	4532.8381	0.0000	1.0000
JC69G	36	-2236.0527	4548.7956	0.0000	1.0000
JC69IG	37	-2235.9513	4550.8621	0.0000	1.0000
JC69I	36	-2237.2311	4551.1524	0.0000	1.0000
F81	38	-2240.3443	4561.9253	0.0000	1.0000
JC69	35	-2253.6375	4581.7038	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2139.2456	4366.4913	0.6496	0.6496
GTRIG	45	-2139.1879	4368.3758	0.2532	0.9028
GTRI	44	-2141.1593	4370.3185	0.0958	0.9987
HKYG	40	-2149.8828	4379.7656	0.0009	0.9995
HKYIG	41	-2149.8159	4381.6318	0.0003	0.9999
HKYI	40	-2151.6641	4383.3282	0.0001	1.0000
GTR	43	-2157.6120	4401.2239	0.0000	1.0000
SYMG	41	-2162.8455	4407.6910	0.0000	1.0000
K2PG	37	-2167.2529	4408.5058	0.0000	1.0000
SYMIG	42	-2162.7753	4409.5506	0.0000	1.0000
K2PIG	38	-2167.1683	4410.3365	0.0000	1.0000
SYMI	41	-2164.6111	4411.2222	0.0000	1.0000
K2PI	37	-2169.0990	4412.1979	0.0000	1.0000
HKY	39	-2167.9525	4413.9049	0.0000	1.0000
SYM	40	-2181.0490	4442.0980	0.0000	1.0000
K2P	36	-2186.3483	4444.6965	0.0000	1.0000
F81G	39	-2223.5023	4525.0045	0.0000	1.0000
F81IG	40	-2223.4402	4526.8804	0.0000	1.0000
F81I	39	-2224.6580	4527.3160	0.0000	1.0000
JC69G	36	-2236.0527	4544.1055	0.0000	1.0000
JC69IG	37	-2235.9513	4545.9027	0.0000	1.0000
JC69I	36	-2237.2311	4546.4623	0.0000	1.0000
F81	38	-2240.3443	4556.6885	0.0000	1.0000
JC69	35	-2253.6375	4577.2750	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2149.8828	4555.9747	0.7419	0.7419
HKYI	40	-2151.6641	4559.5374	0.1249	0.8668
GTRG	44	-2139.2456	4560.3213	0.0844	0.9513
HKYIG	41	-2149.8159	4562.2462	0.0322	0.9835
GTRI	44	-2141.1593	4564.1486	0.0125	0.9960
GTRIG	45	-2139.1879	4566.6111	0.0036	0.9996
K2PG	37	-2167.2529	4571.4992	0.0003	0.9999
K2PI	37	-2169.0990	4575.1914	0.0000	1.0000
K2PIG	38	-2167.1683	4577.7352	0.0000	1.0000
HKY	39	-2167.9525	4585.7088	0.0000	1.0000
SYMG	41	-2162.8455	4588.3054	0.0000	1.0000
GTR	43	-2157.6120	4590.6488	0.0000	1.0000
SYMI	41	-2164.6111	4591.8365	0.0000	1.0000
SYMIG	42	-2162.7753	4594.5702	0.0000	1.0000
K2P	36	-2186.3483	4603.2848	0.0000	1.0000
SYM	40	-2181.0490	4618.3071	0.0000	1.0000
F81G	39	-2223.5023	4696.8084	0.0000	1.0000
F81I	39	-2224.6580	4699.1199	0.0000	1.0000
JC69G	36	-2236.0527	4702.6937	0.0000	1.0000
F81IG	40	-2223.4402	4703.0896	0.0000	1.0000
JC69I	36	-2237.2311	4705.0505	0.0000	1.0000
JC69IG	37	-2235.9513	4708.8962	0.0000	1.0000
F81	38	-2240.3443	4724.0872	0.0000	1.0000
JC69	35	-2253.6375	4731.4580	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/chr22_640.phylip = 1 - 605;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr22_640.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/chr22_640.phylip = 1 - 605;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr22_640.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/chr22_640.phylip = 1 - 605;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr22_640.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

