
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:05 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/chr13_2847.phylip" (19 taxa, 611 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	-2061.6375	4218.2715	0.4941	0.4941
GTRIG	45	-2060.6970	4218.7214	0.3946	0.8888
HKYG	40	-2068.6434	4223.0411	0.0455	0.9343
HKYIG	41	-2067.7819	4223.6166	0.0341	0.9684
GTRI	44	-2064.5149	4224.0263	0.0278	0.9962
HKYI	40	-2071.5042	4228.7628	0.0026	0.9988
K2PG	37	-2076.5422	4231.9919	0.0005	0.9993
K2PIG	38	-2075.6437	4232.4693	0.0004	0.9997
SYMIG	42	-2071.7929	4233.9450	0.0002	0.9999
K2PI	37	-2079.5626	4238.0326	0.0000	1.0000
SYMG	41	-2075.2473	4238.5474	0.0000	1.0000
SYMI	41	-2075.6083	4239.2694	0.0000	1.0000
GTR	43	-2106.1125	4304.8988	0.0000	1.0000
HKY	39	-2113.8221	4311.1084	0.0000	1.0000
SYM	40	-2118.0107	4321.7759	0.0000	1.0000
K2P	36	-2122.6461	4321.9332	0.0000	1.0000
F81G	39	-2133.3082	4350.0805	0.0000	1.0000
F81IG	40	-2132.5325	4350.8194	0.0000	1.0000
F81I	39	-2136.2257	4355.9155	0.0000	1.0000
JC69G	36	-2139.6912	4356.0236	0.0000	1.0000
JC69IG	37	-2138.8890	4356.6855	0.0000	1.0000
JC69I	36	-2142.7076	4362.0562	0.0000	1.0000
F81	38	-2173.1328	4427.4474	0.0000	1.0000
JC69	35	-2179.9907	4434.3640	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2061.6375	4211.2751	0.4773	0.4773
GTRIG	45	-2060.6970	4211.3939	0.4498	0.9271
GTRI	44	-2064.5149	4217.0299	0.0269	0.9540
HKYG	40	-2068.6434	4217.2867	0.0236	0.9776
HKYIG	41	-2067.7819	4217.5638	0.0206	0.9981
HKYI	40	-2071.5042	4223.0084	0.0014	0.9995
K2PG	37	-2076.5422	4227.0844	0.0002	0.9997
K2PIG	38	-2075.6437	4227.2875	0.0002	0.9998
SYMIG	42	-2071.7929	4227.5859	0.0001	1.0000
SYMG	41	-2075.2473	4232.4947	0.0000	1.0000
K2PI	37	-2079.5626	4233.1251	0.0000	1.0000
SYMI	41	-2075.6083	4233.2167	0.0000	1.0000
GTR	43	-2106.1125	4298.2250	0.0000	1.0000
HKY	39	-2113.8221	4305.6443	0.0000	1.0000
SYM	40	-2118.0107	4316.0215	0.0000	1.0000
K2P	36	-2122.6461	4317.2921	0.0000	1.0000
F81G	39	-2133.3082	4344.6164	0.0000	1.0000
F81IG	40	-2132.5325	4345.0650	0.0000	1.0000
F81I	39	-2136.2257	4350.4514	0.0000	1.0000
JC69G	36	-2139.6912	4351.3825	0.0000	1.0000
JC69IG	37	-2138.8890	4351.7780	0.0000	1.0000
JC69I	36	-2142.7076	4357.4151	0.0000	1.0000
F81	38	-2173.1328	4422.2655	0.0000	1.0000
JC69	35	-2179.9907	4429.9814	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-2076.5422	4390.4430	0.7383	0.7383
HKYG	40	-2068.6434	4393.8906	0.1317	0.8700
K2PIG	38	-2075.6437	4395.0611	0.0734	0.9434
K2PI	37	-2079.5626	4396.4837	0.0360	0.9794
HKYIG	41	-2067.7819	4398.5828	0.0126	0.9920
HKYI	40	-2071.5042	4399.6123	0.0075	0.9995
GTRG	44	-2061.6375	4405.5393	0.0004	0.9999
GTRIG	45	-2060.6970	4410.0733	0.0000	1.0000
GTRI	44	-2064.5149	4411.2941	0.0000	1.0000
SYMIG	42	-2071.7929	4413.0199	0.0000	1.0000
SYMG	41	-2075.2473	4413.5137	0.0000	1.0000
SYMI	41	-2075.6083	4414.2357	0.0000	1.0000
K2P	36	-2122.6461	4476.2356	0.0000	1.0000
HKY	39	-2113.8221	4477.8330	0.0000	1.0000
GTR	43	-2106.1125	4488.0742	0.0000	1.0000
SYM	40	-2118.0107	4492.6254	0.0000	1.0000
JC69G	36	-2139.6912	4510.3260	0.0000	1.0000
JC69IG	37	-2138.8890	4515.1365	0.0000	1.0000
JC69I	36	-2142.7076	4516.3586	0.0000	1.0000
F81G	39	-2133.3082	4516.8052	0.0000	1.0000
F81IG	40	-2132.5325	4521.6689	0.0000	1.0000
F81I	39	-2136.2257	4522.6402	0.0000	1.0000
JC69	35	-2179.9907	4584.5098	0.0000	1.0000
F81	38	-2173.1328	4590.0392	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/chr13_2847.phylip = 1 - 611;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr13_2847.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/chr13_2847.phylip = 1 - 611;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr13_2847.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/chr13_2847.phylip = 1 - 611;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr13_2847.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

