
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:38 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/chr24_2269.phylip" (19 taxa, 620 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
Minimum BIC  model: K2PG


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	-2109.2520	4313.3909	0.6362	0.6362
GTRIG	45	-2108.8880	4314.9885	0.2862	0.9225
SYMIG	42	-2114.4931	4319.2461	0.0341	0.9565
GTRI	44	-2112.7061	4320.2992	0.0201	0.9766
K2PG	37	-2121.7015	4322.2346	0.0076	0.9843
HKYG	40	-2118.6663	4322.9975	0.0052	0.9895
K2PIG	38	-2121.2456	4323.5927	0.0039	0.9934
HKYIG	41	-2118.2396	4324.4378	0.0025	0.9959
SYMI	41	-2118.4109	4324.7802	0.0021	0.9980
SYMG	41	-2118.6358	4325.2301	0.0017	0.9997
K2PI	37	-2125.6890	4330.2097	0.0001	0.9999
HKYI	40	-2122.4979	4330.6608	0.0001	1.0000
GTR	43	-2154.7261	4402.0217	0.0000	1.0000
SYM	40	-2159.8252	4405.3152	0.0000	1.0000
K2P	36	-2167.9170	4412.4034	0.0000	1.0000
HKY	39	-2164.8028	4412.9849	0.0000	1.0000
JC69G	36	-2205.3782	4487.3258	0.0000	1.0000
JC69IG	37	-2205.0836	4488.9989	0.0000	1.0000
F81G	39	-2203.5556	4490.4904	0.0000	1.0000
F81IG	40	-2203.2663	4492.1976	0.0000	1.0000
JC69I	36	-2209.1082	4494.7859	0.0000	1.0000
F81I	39	-2207.7126	4498.8044	0.0000	1.0000
JC69	35	-2243.4316	4561.1783	0.0000	1.0000
F81	38	-2241.5567	4564.2149	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2109.2520	4306.5040	0.6181	0.6181
GTRIG	45	-2108.8880	4307.7760	0.3272	0.9453
SYMIG	42	-2114.4931	4312.9861	0.0242	0.9695
GTRI	44	-2112.7061	4313.4123	0.0195	0.9890
HKYG	40	-2118.6663	4317.3325	0.0028	0.9918
K2PG	37	-2121.7015	4317.4030	0.0027	0.9944
HKYIG	41	-2118.2396	4318.4793	0.0016	0.9960
K2PIG	38	-2121.2456	4318.4912	0.0015	0.9975
SYMI	41	-2118.4109	4318.8217	0.0013	0.9988
SYMG	41	-2118.6358	4319.2716	0.0010	0.9999
HKYI	40	-2122.4979	4324.9959	0.0001	1.0000
K2PI	37	-2125.6890	4325.3781	0.0000	1.0000
GTR	43	-2154.7261	4395.4522	0.0000	1.0000
SYM	40	-2159.8252	4399.6503	0.0000	1.0000
HKY	39	-2164.8028	4407.6056	0.0000	1.0000
K2P	36	-2167.9170	4407.8339	0.0000	1.0000
JC69G	36	-2205.3782	4482.7564	0.0000	1.0000
JC69IG	37	-2205.0836	4484.1672	0.0000	1.0000
F81G	39	-2203.5556	4485.1111	0.0000	1.0000
F81IG	40	-2203.2663	4486.5327	0.0000	1.0000
JC69I	36	-2209.1082	4490.2165	0.0000	1.0000
F81I	39	-2207.7126	4493.4251	0.0000	1.0000
JC69	35	-2243.4316	4556.8633	0.0000	1.0000
F81	38	-2241.5567	4559.1134	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-2121.7015	4481.3026	0.9228	0.9228
K2PIG	38	-2121.2456	4486.8205	0.0585	0.9813
K2PI	37	-2125.6890	4489.2777	0.0171	0.9984
HKYG	40	-2118.6663	4494.5213	0.0012	0.9996
SYMIG	42	-2114.4931	4499.0343	0.0001	0.9997
HKYIG	41	-2118.2396	4500.0978	0.0001	0.9998
SYMI	41	-2118.4109	4500.4402	0.0001	0.9999
SYMG	41	-2118.6358	4500.8901	0.0001	0.9999
GTRG	44	-2109.2520	4501.4116	0.0000	1.0000
HKYI	40	-2122.4979	4502.1846	0.0000	1.0000
GTRIG	45	-2108.8880	4507.1134	0.0000	1.0000
GTRI	44	-2112.7061	4508.3199	0.0000	1.0000
K2P	36	-2167.9170	4567.3038	0.0000	1.0000
SYM	40	-2159.8252	4576.8391	0.0000	1.0000
HKY	39	-2164.8028	4580.3646	0.0000	1.0000
GTR	43	-2154.7261	4585.9302	0.0000	1.0000
JC69G	36	-2205.3782	4642.2263	0.0000	1.0000
JC69IG	37	-2205.0836	4648.0669	0.0000	1.0000
JC69I	36	-2209.1082	4649.6864	0.0000	1.0000
F81G	39	-2203.5556	4657.8702	0.0000	1.0000
F81IG	40	-2203.2663	4663.7214	0.0000	1.0000
F81I	39	-2207.7126	4666.1842	0.0000	1.0000
JC69	35	-2243.4316	4711.9035	0.0000	1.0000
F81	38	-2241.5567	4727.4427	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/chr24_2269.phylip = 1 - 620;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr24_2269.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/chr24_2269.phylip = 1 - 620;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr24_2269.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 (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr24_2269.phylip = 1 - 620;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr24_2269.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=gamma;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


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End of Output

