
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
13:25 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/chrZ_5682.phylip" (19 taxa, 296 characters)

Minimum AIC  model: HKYG
Minimum AICc model: HKYG
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
HKYG	40	-893.3665	1879.5958	0.4399	0.4399
HKYI	40	-893.9225	1880.7077	0.2523	0.6922
HKYIG	41	-893.1033	1881.7656	0.1487	0.8409
GTRG	44	-889.6861	1883.1491	0.0744	0.9153
GTRI	44	-889.9087	1883.5942	0.0596	0.9749
GTRIG	45	-889.3807	1885.3215	0.0251	1.0000
HKY	39	-910.1368	1910.4611	0.0000	1.0000
GTR	43	-906.6261	1914.2681	0.0000	1.0000
K2PG	37	-917.0530	1919.0051	0.0000	1.0000
K2PI	37	-917.2385	1919.3763	0.0000	1.0000
K2PIG	38	-916.8420	1921.2172	0.0000	1.0000
SYMG	41	-916.5986	1928.7563	0.0000	1.0000
SYMI	41	-916.6871	1928.9332	0.0000	1.0000
SYMIG	42	-916.3736	1931.0239	0.0000	1.0000
F81G	39	-927.1630	1944.5134	0.0000	1.0000
F81I	39	-927.1760	1944.5394	0.0000	1.0000
F81IG	40	-926.8478	1946.5583	0.0000	1.0000
K2P	36	-934.8185	1951.9227	0.0000	1.0000
SYM	40	-934.2486	1961.3600	0.0000	1.0000
F81	38	-942.9614	1973.4560	0.0000	1.0000
JC69G	36	-953.5463	1989.3784	0.0000	1.0000
JC69I	36	-953.6167	1989.5190	0.0000	1.0000
JC69IG	37	-953.2838	1991.4668	0.0000	1.0000
JC69	35	-969.7569	2019.2061	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-893.3665	1866.7330	0.2686	0.2686
GTRG	44	-889.6861	1867.3722	0.1951	0.4637
GTRI	44	-889.9087	1867.8173	0.1562	0.6199
HKYI	40	-893.9225	1867.8449	0.1541	0.7740
HKYIG	41	-893.1033	1868.2065	0.1286	0.9026
GTRIG	45	-889.3807	1868.7615	0.0974	1.0000
HKY	39	-910.1368	1898.2736	0.0000	1.0000
GTR	43	-906.6261	1899.2522	0.0000	1.0000
K2PG	37	-917.0530	1908.1059	0.0000	1.0000
K2PI	37	-917.2385	1908.4771	0.0000	1.0000
K2PIG	38	-916.8420	1909.6841	0.0000	1.0000
SYMG	41	-916.5986	1915.1972	0.0000	1.0000
SYMI	41	-916.6871	1915.3742	0.0000	1.0000
SYMIG	42	-916.3736	1916.7473	0.0000	1.0000
F81G	39	-927.1630	1932.3259	0.0000	1.0000
F81I	39	-927.1760	1932.3519	0.0000	1.0000
F81IG	40	-926.8478	1933.6955	0.0000	1.0000
K2P	36	-934.8185	1941.6369	0.0000	1.0000
SYM	40	-934.2486	1948.4973	0.0000	1.0000
F81	38	-942.9614	1961.9229	0.0000	1.0000
JC69G	36	-953.5463	1979.0926	0.0000	1.0000
JC69I	36	-953.6167	1979.2333	0.0000	1.0000
JC69IG	37	-953.2838	1980.5676	0.0000	1.0000
JC69	35	-969.7569	2009.5138	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-893.3665	2014.3474	0.6061	0.6061
HKYI	40	-893.9225	2015.4593	0.3476	0.9536
HKYIG	41	-893.1033	2019.5113	0.0458	0.9995
GTRG	44	-889.6861	2029.7480	0.0003	0.9998
GTRI	44	-889.9087	2030.1932	0.0002	1.0000
GTRIG	45	-889.3807	2034.8276	0.0000	1.0000
HKY	39	-910.1368	2042.1976	0.0000	1.0000
K2PG	37	-917.0530	2044.6492	0.0000	1.0000
K2PI	37	-917.2385	2045.0204	0.0000	1.0000
K2PIG	38	-916.8420	2049.9177	0.0000	1.0000
GTR	43	-906.6261	2057.9377	0.0000	1.0000
SYMG	41	-916.5986	2066.5019	0.0000	1.0000
SYMI	41	-916.6871	2066.6789	0.0000	1.0000
SYMIG	42	-916.3736	2071.7424	0.0000	1.0000
K2P	36	-934.8185	2074.4899	0.0000	1.0000
F81G	39	-927.1630	2076.2500	0.0000	1.0000
F81I	39	-927.1760	2076.2760	0.0000	1.0000
F81IG	40	-926.8478	2081.3099	0.0000	1.0000
SYM	40	-934.2486	2096.1117	0.0000	1.0000
F81	38	-942.9614	2102.1565	0.0000	1.0000
JC69G	36	-953.5463	2111.9456	0.0000	1.0000
JC69I	36	-953.6167	2112.0862	0.0000	1.0000
JC69IG	37	-953.2838	2117.1109	0.0000	1.0000
JC69	35	-969.7569	2138.6764	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_5682.phylip = 1 - 296;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_5682.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;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_5682.phylip = 1 - 296;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_5682.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;


[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/chrZ_5682.phylip = 1 - 296;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_5682.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

