
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:21 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/chr1_32424.phylip" (19 taxa, 393 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	-978.0182	2055.4157	0.4781	0.4781
GTRI	44	-978.6248	2056.6290	0.2607	0.7388
GTRIG	45	-977.6404	2057.2117	0.1948	0.9336
HKYG	40	-985.7840	2060.8862	0.0310	0.9646
HKYI	40	-985.9971	2061.3123	0.0251	0.9897
HKYIG	41	-985.6366	2063.0852	0.0103	1.0000
GTR	43	-994.3342	2085.5107	0.0000	1.0000
HKY	39	-1002.0419	2090.9223	0.0000	1.0000
F81G	39	-1009.4821	2105.8028	0.0000	1.0000
F81I	39	-1009.4832	2105.8049	0.0000	1.0000
K2PG	37	-1012.7369	2107.3950	0.0000	1.0000
K2PI	37	-1012.7551	2107.4313	0.0000	1.0000
F81IG	40	-1009.4820	2108.2821	0.0000	1.0000
K2PIG	38	-1012.7361	2109.8451	0.0000	1.0000
SYMG	41	-1009.8478	2111.5076	0.0000	1.0000
SYMI	41	-1009.9189	2111.6498	0.0000	1.0000
SYMIG	42	-1009.8285	2113.9769	0.0000	1.0000
F81	38	-1024.7771	2133.9270	0.0000	1.0000
K2P	36	-1030.0078	2139.4988	0.0000	1.0000
SYM	40	-1026.4090	2142.1363	0.0000	1.0000
JC69I	36	-1032.8358	2145.1547	0.0000	1.0000
JC69G	36	-1032.8856	2145.2544	0.0000	1.0000
JC69IG	37	-1032.8855	2147.6921	0.0000	1.0000
JC69	35	-1048.7818	2174.6224	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-978.0182	2044.0364	0.4687	0.4687
GTRI	44	-978.6248	2045.2496	0.2555	0.7242
GTRIG	45	-977.6404	2045.2809	0.2516	0.9758
HKYG	40	-985.7840	2051.5680	0.0108	0.9866
HKYI	40	-985.9971	2051.9942	0.0088	0.9954
HKYIG	41	-985.6366	2053.2733	0.0046	1.0000
GTR	43	-994.3342	2074.6683	0.0000	1.0000
HKY	39	-1002.0419	2082.0837	0.0000	1.0000
F81G	39	-1009.4821	2096.9643	0.0000	1.0000
F81I	39	-1009.4832	2096.9664	0.0000	1.0000
F81IG	40	-1009.4820	2098.9640	0.0000	1.0000
K2PG	37	-1012.7369	2099.4738	0.0000	1.0000
K2PI	37	-1012.7551	2099.5102	0.0000	1.0000
K2PIG	38	-1012.7361	2101.4722	0.0000	1.0000
SYMG	41	-1009.8478	2101.6956	0.0000	1.0000
SYMI	41	-1009.9189	2101.8378	0.0000	1.0000
SYMIG	42	-1009.8285	2103.6569	0.0000	1.0000
F81	38	-1024.7771	2125.5541	0.0000	1.0000
K2P	36	-1030.0078	2132.0157	0.0000	1.0000
SYM	40	-1026.4090	2132.8181	0.0000	1.0000
JC69I	36	-1032.8358	2137.6715	0.0000	1.0000
JC69G	36	-1032.8856	2137.7713	0.0000	1.0000
JC69IG	37	-1032.8855	2139.7710	0.0000	1.0000
JC69	35	-1048.7818	2167.5635	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-985.7840	2210.5204	0.5287	0.5287
HKYI	40	-985.9971	2210.9465	0.4273	0.9560
HKYIG	41	-985.6366	2216.1995	0.0309	0.9869
GTRG	44	-978.0182	2218.8840	0.0081	0.9950
GTRI	44	-978.6248	2220.0973	0.0044	0.9994
GTRIG	45	-977.6404	2224.1023	0.0006	1.0000
HKY	39	-1002.0419	2237.0623	0.0000	1.0000
GTR	43	-994.3342	2245.5422	0.0000	1.0000
K2PG	37	-1012.7369	2246.5048	0.0000	1.0000
K2PI	37	-1012.7551	2246.5412	0.0000	1.0000
F81G	39	-1009.4821	2251.9428	0.0000	1.0000
F81I	39	-1009.4832	2251.9450	0.0000	1.0000
K2PIG	38	-1012.7361	2252.4770	0.0000	1.0000
F81IG	40	-1009.4820	2257.9163	0.0000	1.0000
SYMG	41	-1009.8478	2264.6218	0.0000	1.0000
SYMI	41	-1009.9189	2264.7640	0.0000	1.0000
SYMIG	42	-1009.8285	2270.5569	0.0000	1.0000
K2P	36	-1030.0078	2275.0728	0.0000	1.0000
F81	38	-1024.7771	2276.5589	0.0000	1.0000
JC69I	36	-1032.8358	2280.7287	0.0000	1.0000
JC69G	36	-1032.8856	2280.8284	0.0000	1.0000
JC69IG	37	-1032.8855	2286.8019	0.0000	1.0000
SYM	40	-1026.4090	2291.7705	0.0000	1.0000
JC69	35	-1048.7818	2306.6469	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/chr1_32424.phylip = 1 - 393;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_32424.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/chr1_32424.phylip = 1 - 393;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_32424.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/chr1_32424.phylip = 1 - 393;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_32424.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

