
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:07 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/chr19_346.phylip" (19 taxa, 386 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	-885.0210	1859.5493	0.4230	0.4230
HKYI	40	-885.4319	1860.3710	0.2805	0.7035
HKYIG	41	-884.9011	1861.8138	0.1363	0.8398
GTRG	44	-881.6945	1863.0019	0.0753	0.9151
GTRI	44	-882.0828	1863.7784	0.0510	0.9661
GTRIG	45	-881.6001	1865.3767	0.0230	0.9891
HKY	39	-890.1009	1867.2191	0.0091	0.9982
GTR	43	-886.7172	1870.4988	0.0018	1.0000
K2PG	37	-904.9882	1892.0568	0.0000	1.0000
K2PI	37	-905.3978	1892.8760	0.0000	1.0000
K2PIG	38	-904.8332	1894.2081	0.0000	1.0000
F81G	39	-906.0259	1899.0692	0.0000	1.0000
SYMG	41	-903.7247	1899.4611	0.0000	1.0000
F81I	39	-906.4560	1899.9294	0.0000	1.0000
K2P	36	-910.2931	1900.2195	0.0000	1.0000
SYMI	41	-904.1785	1900.3686	0.0000	1.0000
F81IG	40	-905.9113	1901.3298	0.0000	1.0000
SYMIG	42	-903.5926	1901.7158	0.0000	1.0000
F81	38	-910.8293	1906.2003	0.0000	1.0000
SYM	40	-908.6298	1906.7668	0.0000	1.0000
JC69G	36	-923.5662	1926.7657	0.0000	1.0000
JC69I	36	-924.0042	1927.6416	0.0000	1.0000
JC69IG	37	-923.4279	1928.9363	0.0000	1.0000
JC69	35	-928.5454	1934.2909	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-885.0210	1850.0420	0.3159	0.3159
HKYI	40	-885.4319	1850.8638	0.2094	0.5253
GTRG	44	-881.6945	1851.3890	0.1611	0.6864
HKYIG	41	-884.9011	1851.8022	0.1310	0.8174
GTRI	44	-882.0828	1852.1655	0.1092	0.9267
GTRIG	45	-881.6001	1853.2002	0.0651	0.9918
HKY	39	-890.1009	1858.2017	0.0053	0.9971
GTR	43	-886.7172	1859.4345	0.0029	1.0000
K2PG	37	-904.9882	1883.9763	0.0000	1.0000
K2PI	37	-905.3978	1884.7956	0.0000	1.0000
K2PIG	38	-904.8332	1885.6663	0.0000	1.0000
SYMG	41	-903.7247	1889.4495	0.0000	1.0000
F81G	39	-906.0259	1890.0519	0.0000	1.0000
SYMI	41	-904.1785	1890.3569	0.0000	1.0000
F81I	39	-906.4560	1890.9121	0.0000	1.0000
SYMIG	42	-903.5926	1891.1852	0.0000	1.0000
F81IG	40	-905.9113	1891.8226	0.0000	1.0000
K2P	36	-910.2931	1892.5863	0.0000	1.0000
SYM	40	-908.6298	1897.2595	0.0000	1.0000
F81	38	-910.8293	1897.6585	0.0000	1.0000
JC69G	36	-923.5662	1919.1324	0.0000	1.0000
JC69I	36	-924.0042	1920.0084	0.0000	1.0000
JC69IG	37	-923.4279	1920.8558	0.0000	1.0000
JC69	35	-928.5454	1927.0909	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-885.0210	2008.2755	0.5426	0.5426
HKYI	40	-885.4319	2009.0973	0.3598	0.9023
HKY	39	-890.1009	2012.4794	0.0663	0.9687
HKYIG	41	-884.9011	2013.9915	0.0311	0.9998
GTRG	44	-881.6945	2025.4458	0.0001	0.9999
GTRI	44	-882.0828	2026.2224	0.0001	1.0000
GTR	43	-886.7172	2029.5355	0.0000	1.0000
K2PG	37	-904.9882	2030.3423	0.0000	1.0000
K2PI	37	-905.3978	2031.1615	0.0000	1.0000
GTRIG	45	-881.6001	2031.2129	0.0000	1.0000
K2P	36	-910.2931	2034.9964	0.0000	1.0000
K2PIG	38	-904.8332	2035.9881	0.0000	1.0000
F81G	39	-906.0259	2044.3296	0.0000	1.0000
F81I	39	-906.4560	2045.1897	0.0000	1.0000
F81	38	-910.8293	2047.9803	0.0000	1.0000
F81IG	40	-905.9113	2050.0561	0.0000	1.0000
SYMG	41	-903.7247	2051.6388	0.0000	1.0000
SYMI	41	-904.1785	2052.5463	0.0000	1.0000
SYM	40	-908.6298	2055.4930	0.0000	1.0000
SYMIG	42	-903.5926	2057.3304	0.0000	1.0000
JC69G	36	-923.5662	2061.5426	0.0000	1.0000
JC69I	36	-924.0042	2062.4185	0.0000	1.0000
JC69	35	-928.5454	2065.5452	0.0000	1.0000
JC69IG	37	-923.4279	2067.2218	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/chr19_346.phylip = 1 - 386;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr19_346.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/chr19_346.phylip = 1 - 386;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr19_346.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/chr19_346.phylip = 1 - 386;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr19_346.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

