
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:20 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_32398.phylip" (19 taxa, 348 characters)

Minimum AIC  model: GTRIG
Minimum AICc model: GTRIG
Minimum BIC  model: HKYI


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
GTRIG	45	-872.5720	1848.8526	0.2791	0.2791
GTRG	44	-874.0337	1849.1366	0.2421	0.5212
GTRI	44	-874.1969	1849.4631	0.2056	0.7268
HKYI	40	-879.9635	1850.6110	0.1158	0.8427
HKYG	40	-880.0073	1850.6986	0.1109	0.9535
HKYIG	41	-879.5914	1852.4377	0.0465	1.0000
F81I	39	-896.3120	1880.7539	0.0000	1.0000
F81G	39	-896.3780	1880.8858	0.0000	1.0000
F81IG	40	-896.1727	1883.0294	0.0000	1.0000
GTR	43	-896.4246	1891.2966	0.0000	1.0000
HKY	39	-901.9189	1891.9677	0.0000	1.0000
K2PI	37	-905.1939	1893.4587	0.0000	1.0000
K2PG	37	-905.3386	1893.7482	0.0000	1.0000
K2PIG	38	-905.0666	1895.7255	0.0000	1.0000
SYMI	41	-903.0257	1899.3063	0.0000	1.0000
SYMG	41	-903.1327	1899.5202	0.0000	1.0000
SYMIG	42	-902.4666	1900.7758	0.0000	1.0000
JC69I	36	-918.4463	1917.4586	0.0000	1.0000
JC69G	36	-918.5443	1917.6545	0.0000	1.0000
JC69IG	37	-918.3416	1919.7542	0.0000	1.0000
F81	38	-917.9121	1921.4164	0.0000	1.0000
K2P	36	-927.6746	1935.9152	0.0000	1.0000
SYM	40	-925.1916	1941.0672	0.0000	1.0000
JC69	35	-940.3416	1958.7602	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRIG	45	-872.5720	1835.1440	0.4178	0.4178
GTRG	44	-874.0337	1836.0673	0.2633	0.6811
GTRI	44	-874.1969	1836.3938	0.2237	0.9048
HKYI	40	-879.9635	1839.9269	0.0382	0.9430
HKYG	40	-880.0073	1840.0145	0.0366	0.9796
HKYIG	41	-879.5914	1841.1828	0.0204	1.0000
F81I	39	-896.3120	1870.6240	0.0000	1.0000
F81G	39	-896.3780	1870.7559	0.0000	1.0000
F81IG	40	-896.1727	1872.3454	0.0000	1.0000
GTR	43	-896.4246	1878.8492	0.0000	1.0000
HKY	39	-901.9189	1881.8379	0.0000	1.0000
K2PI	37	-905.1939	1884.3878	0.0000	1.0000
K2PG	37	-905.3386	1884.6773	0.0000	1.0000
K2PIG	38	-905.0666	1886.1332	0.0000	1.0000
SYMI	41	-903.0257	1888.0514	0.0000	1.0000
SYMG	41	-903.1327	1888.2653	0.0000	1.0000
SYMIG	42	-902.4666	1888.9332	0.0000	1.0000
JC69I	36	-918.4463	1908.8927	0.0000	1.0000
JC69G	36	-918.5443	1909.0886	0.0000	1.0000
JC69IG	37	-918.3416	1910.6832	0.0000	1.0000
F81	38	-917.9121	1911.8241	0.0000	1.0000
K2P	36	-927.6746	1927.3493	0.0000	1.0000
SYM	40	-925.1916	1930.3832	0.0000	1.0000
JC69	35	-940.3416	1950.6832	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYI	40	-879.9635	1994.0150	0.4899	0.4899
HKYG	40	-880.0073	1994.1026	0.4689	0.9587
HKYIG	41	-879.5914	1999.1231	0.0381	0.9968
GTRG	44	-874.0337	2005.5642	0.0015	0.9984
GTRI	44	-874.1969	2005.8907	0.0013	0.9996
GTRIG	45	-872.5720	2008.4931	0.0004	1.0000
F81I	39	-896.3120	2020.8599	0.0000	1.0000
F81G	39	-896.3780	2020.9918	0.0000	1.0000
F81IG	40	-896.1727	2026.4335	0.0000	1.0000
K2PI	37	-905.1939	2026.9193	0.0000	1.0000
K2PG	37	-905.3386	2027.2088	0.0000	1.0000
HKY	39	-901.9189	2032.0738	0.0000	1.0000
K2PIG	38	-905.0666	2032.5169	0.0000	1.0000
GTR	43	-896.4246	2044.4939	0.0000	1.0000
SYMI	41	-903.0257	2045.9917	0.0000	1.0000
SYMG	41	-903.1327	2046.2056	0.0000	1.0000
JC69I	36	-918.4463	2047.5719	0.0000	1.0000
JC69G	36	-918.5443	2047.7678	0.0000	1.0000
SYMIG	42	-902.4666	2050.7257	0.0000	1.0000
JC69IG	37	-918.3416	2053.2147	0.0000	1.0000
F81	38	-917.9121	2058.2078	0.0000	1.0000
K2P	36	-927.6746	2066.0286	0.0000	1.0000
SYM	40	-925.1916	2084.4713	0.0000	1.0000
JC69	35	-940.3416	2085.5103	0.0000	1.0000



To specify default values for best AIC, AICc, or BIC models in MrBayes:

[Mrbayes block for the best AIC model (GTRIG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_32398.phylip = 1 - 348;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_32398.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best AICc model (GTRIG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_32398.phylip = 1 - 348;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_32398.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best BIC model (HKYI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_32398.phylip = 1 - 348;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_32398.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=propinv;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0) pinvarpr=Uniform(0.0,1.0);
END;


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End of Output

