
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:12 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/chr11_4735.phylip" (19 taxa, 267 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	-877.7910	1861.4198	0.5647	0.5647
HKYG	40	-884.9244	1864.3620	0.1297	0.6944
GTRI	44	-879.2742	1864.3863	0.1281	0.8225
GTRIG	45	-877.9668	1864.6667	0.1114	0.9338
HKYIG	41	-884.9105	1867.1276	0.0325	0.9664
HKYI	40	-886.3484	1867.2102	0.0312	0.9976
K2PG	37	-893.9822	1874.2440	0.0009	0.9985
HKY	39	-891.4707	1874.6859	0.0007	0.9993
GTR	43	-886.6562	1876.2811	0.0003	0.9996
SYMI	41	-890.2072	1877.7211	0.0002	0.9998
K2PI	37	-895.8452	1877.9698	0.0001	0.9999
K2PIG	38	-895.3295	1879.6591	0.0001	1.0000
SYMG	41	-891.8892	1881.0851	0.0000	1.0000
SYMIG	42	-892.1499	1884.4248	0.0000	1.0000
K2P	36	-902.3829	1888.3485	0.0000	1.0000
SYM	40	-900.3203	1895.1538	0.0000	1.0000
F81G	39	-917.7083	1927.1611	0.0000	1.0000
F81I	39	-917.7636	1927.2717	0.0000	1.0000
F81IG	40	-918.0293	1930.5719	0.0000	1.0000
JC69I	36	-924.0583	1931.6993	0.0000	1.0000
JC69G	36	-925.2369	1934.0564	0.0000	1.0000
JC69IG	37	-926.3291	1938.9378	0.0000	1.0000
F81	38	-925.4056	1939.8111	0.0000	1.0000
JC69	35	-933.4642	1947.8375	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-877.7910	1843.5820	0.6225	0.6225
GTRIG	45	-877.9668	1845.9337	0.1921	0.8145
GTRI	44	-879.2742	1846.5484	0.1412	0.9557
HKYG	40	-884.9244	1849.8487	0.0271	0.9829
HKYIG	41	-884.9105	1851.8209	0.0101	0.9930
HKYI	40	-886.3484	1852.6969	0.0065	0.9995
GTR	43	-886.6562	1859.3125	0.0002	0.9998
HKY	39	-891.4707	1860.9414	0.0001	0.9999
K2PG	37	-893.9822	1861.9645	0.0001	0.9999
SYMI	41	-890.2072	1862.4145	0.0001	1.0000
K2PI	37	-895.8452	1865.6903	0.0000	1.0000
SYMG	41	-891.8892	1865.7785	0.0000	1.0000
K2PIG	38	-895.3295	1866.6591	0.0000	1.0000
SYMIG	42	-892.1499	1868.2998	0.0000	1.0000
K2P	36	-902.3829	1876.7659	0.0000	1.0000
SYM	40	-900.3203	1880.6405	0.0000	1.0000
F81G	39	-917.7083	1913.4166	0.0000	1.0000
F81I	39	-917.7636	1913.5272	0.0000	1.0000
F81IG	40	-918.0293	1916.0586	0.0000	1.0000
JC69I	36	-924.0583	1920.1167	0.0000	1.0000
JC69G	36	-925.2369	1922.4738	0.0000	1.0000
JC69IG	37	-926.3291	1926.6583	0.0000	1.0000
F81	38	-925.4056	1926.8111	0.0000	1.0000
JC69	35	-933.4642	1936.9284	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-884.9244	1993.3387	0.5139	0.5139
K2PG	37	-893.9822	1994.6927	0.2611	0.7750
HKYI	40	-886.3484	1996.1868	0.1237	0.8987
K2PI	37	-895.8452	1998.4185	0.0405	0.9392
HKYIG	41	-884.9105	1998.8981	0.0319	0.9711
HKY	39	-891.4707	2000.8441	0.0121	0.9831
GTRG	44	-877.7910	2001.4209	0.0090	0.9922
K2PIG	38	-895.3295	2002.9745	0.0042	0.9963
GTRI	44	-879.2742	2004.3874	0.0020	0.9984
K2P	36	-902.3829	2005.9068	0.0010	0.9993
GTRIG	45	-877.9668	2007.3599	0.0005	0.9998
SYMI	41	-890.2072	2009.4917	0.0002	0.9999
SYMG	41	-891.8892	2012.8557	0.0000	1.0000
GTR	43	-886.6562	2013.5642	0.0000	1.0000
SYMIG	42	-892.1499	2018.9643	0.0000	1.0000
SYM	40	-900.3203	2024.1305	0.0000	1.0000
JC69I	36	-924.0583	2049.2576	0.0000	1.0000
JC69G	36	-925.2369	2051.6148	0.0000	1.0000
F81G	39	-917.7083	2053.3193	0.0000	1.0000
F81I	39	-917.7636	2053.4299	0.0000	1.0000
JC69IG	37	-926.3291	2059.3865	0.0000	1.0000
F81IG	40	-918.0293	2059.5486	0.0000	1.0000
JC69	35	-933.4642	2062.4821	0.0000	1.0000
F81	38	-925.4056	2063.1266	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/chr11_4735.phylip = 1 - 267;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_4735.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/chr11_4735.phylip = 1 - 267;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_4735.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/chr11_4735.phylip = 1 - 267;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_4735.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

