
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:47 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_11740.phylip" (19 taxa, 607 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	-2114.6220	4324.2903	0.3481	0.3481
HKYG	40	-2119.3509	4324.4968	0.3140	0.6621
GTRIG	45	-2114.4087	4326.1971	0.1342	0.7963
HKYIG	41	-2119.1741	4326.4437	0.1186	0.9149
HKYI	40	-2121.2181	4328.2313	0.0485	0.9635
GTRI	44	-2116.8762	4328.7987	0.0365	1.0000
K2PG	37	-2137.8194	4354.5808	0.0000	1.0000
K2PIG	38	-2137.6481	4356.5146	0.0000	1.0000
K2PI	37	-2139.4073	4357.7565	0.0000	1.0000
SYMG	41	-2136.0685	4360.2327	0.0000	1.0000
SYMIG	42	-2135.8961	4362.1964	0.0000	1.0000
SYMI	41	-2137.7094	4363.5145	0.0000	1.0000
HKY	39	-2146.5373	4376.5772	0.0000	1.0000
GTR	43	-2142.1113	4376.9438	0.0000	1.0000
K2P	36	-2165.7351	4408.1440	0.0000	1.0000
F81G	39	-2163.4602	4410.4231	0.0000	1.0000
F81IG	40	-2163.3120	4412.4191	0.0000	1.0000
SYM	40	-2163.7441	4413.2833	0.0000	1.0000
F81I	39	-2165.0260	4413.5545	0.0000	1.0000
JC69G	36	-2178.6847	4434.0430	0.0000	1.0000
JC69IG	37	-2178.5500	4436.0421	0.0000	1.0000
JC69I	36	-2180.1401	4436.9539	0.0000	1.0000
F81	38	-2189.4258	4460.0699	0.0000	1.0000
JC69	35	-2205.1091	4484.6315	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2114.6220	4317.2440	0.4293	0.4293
HKYG	40	-2119.3509	4318.7018	0.2071	0.6365
GTRIG	45	-2114.4087	4318.8174	0.1955	0.8320
HKYIG	41	-2119.1741	4320.3481	0.0909	0.9229
GTRI	44	-2116.8762	4321.7525	0.0451	0.9680
HKYI	40	-2121.2181	4322.4363	0.0320	1.0000
K2PG	37	-2137.8194	4349.6388	0.0000	1.0000
K2PIG	38	-2137.6481	4351.2963	0.0000	1.0000
K2PI	37	-2139.4073	4352.8145	0.0000	1.0000
SYMG	41	-2136.0685	4354.1371	0.0000	1.0000
SYMIG	42	-2135.8961	4355.7921	0.0000	1.0000
SYMI	41	-2137.7094	4357.4189	0.0000	1.0000
GTR	43	-2142.1113	4370.2227	0.0000	1.0000
HKY	39	-2146.5373	4371.0745	0.0000	1.0000
K2P	36	-2165.7351	4403.4703	0.0000	1.0000
F81G	39	-2163.4602	4404.9204	0.0000	1.0000
F81IG	40	-2163.3120	4406.6240	0.0000	1.0000
SYM	40	-2163.7441	4407.4882	0.0000	1.0000
F81I	39	-2165.0260	4408.0519	0.0000	1.0000
JC69G	36	-2178.6847	4429.3693	0.0000	1.0000
JC69IG	37	-2178.5500	4431.1001	0.0000	1.0000
JC69I	36	-2180.1401	4432.2802	0.0000	1.0000
F81	38	-2189.4258	4454.8516	0.0000	1.0000
JC69	35	-2205.1091	4480.2182	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2119.3509	4495.0429	0.8309	0.8309
HKYI	40	-2121.2181	4498.7774	0.1284	0.9593
HKYIG	41	-2119.1741	4501.0978	0.0402	0.9996
GTRG	44	-2114.6220	4511.2193	0.0003	0.9998
K2PG	37	-2137.8194	4512.7543	0.0001	0.9999
GTRI	44	-2116.8762	4515.7277	0.0000	1.0000
K2PI	37	-2139.4073	4515.9301	0.0000	1.0000
GTRIG	45	-2114.4087	4517.2012	0.0000	1.0000
K2PIG	38	-2137.6481	4518.8204	0.0000	1.0000
SYMG	41	-2136.0685	4534.8868	0.0000	1.0000
SYMI	41	-2137.7094	4538.1686	0.0000	1.0000
SYMIG	42	-2135.8961	4540.9503	0.0000	1.0000
HKY	39	-2146.5373	4543.0071	0.0000	1.0000
GTR	43	-2142.1113	4559.7894	0.0000	1.0000
K2P	36	-2165.7351	4562.1773	0.0000	1.0000
F81G	39	-2163.4602	4576.8530	0.0000	1.0000
F81I	39	-2165.0260	4579.9845	0.0000	1.0000
F81IG	40	-2163.3120	4582.9652	0.0000	1.0000
SYM	40	-2163.7441	4583.8294	0.0000	1.0000
JC69G	36	-2178.6847	4588.0763	0.0000	1.0000
JC69I	36	-2180.1401	4590.9873	0.0000	1.0000
JC69IG	37	-2178.5500	4594.2156	0.0000	1.0000
F81	38	-2189.4258	4622.3757	0.0000	1.0000
JC69	35	-2205.1091	4634.5167	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_11740.phylip = 1 - 607;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_11740.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_11740.phylip = 1 - 607;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_11740.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/chr2_11740.phylip = 1 - 607;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_11740.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

