
Output from mraic.pl version 1.4.4 by Johan Nylander
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13:28 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_8024.phylip" (19 taxa, 301 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	-862.7529	1818.1212	0.5179	0.5179
HKYIG	41	-862.0843	1819.4660	0.2644	0.7823
HKYI	40	-863.6335	1819.8824	0.2147	0.9971
GTRG	44	-863.1834	1829.8355	0.0015	0.9985
GTRI	44	-863.8276	1831.1240	0.0008	0.9993
GTRIG	45	-862.6416	1831.5185	0.0006	0.9999
K2PG	37	-876.7006	1838.0932	0.0000	1.0000
K2PI	37	-877.2478	1839.1877	0.0000	1.0000
K2PIG	38	-875.9939	1839.3008	0.0000	1.0000
SYMG	41	-875.1901	1845.6775	0.0000	1.0000
SYMI	41	-875.6529	1846.6030	0.0000	1.0000
SYMIG	42	-874.5117	1847.0233	0.0000	1.0000
HKY	39	-879.0189	1847.9918	0.0000	1.0000
F81G	39	-881.9081	1853.7701	0.0000	1.0000
F81IG	40	-880.8658	1854.3469	0.0000	1.0000
F81I	39	-882.3681	1854.6903	0.0000	1.0000
GTR	43	-879.9680	1860.6598	0.0000	1.0000
JC69G	36	-891.1143	1864.3195	0.0000	1.0000
JC69IG	37	-890.1655	1865.0229	0.0000	1.0000
JC69I	36	-891.8926	1865.8760	0.0000	1.0000
K2P	36	-895.4673	1873.0256	0.0000	1.0000
SYM	40	-893.6702	1879.9558	0.0000	1.0000
F81	38	-899.3941	1886.1011	0.0000	1.0000
JC69	35	-909.8832	1899.2758	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-862.7529	1805.5058	0.4634	0.4634
HKYIG	41	-862.0843	1806.1687	0.3326	0.7960
HKYI	40	-863.6335	1807.2670	0.1921	0.9881
GTRG	44	-863.1834	1814.3667	0.0055	0.9936
GTRIG	45	-862.6416	1815.2832	0.0035	0.9971
GTRI	44	-863.8276	1815.6553	0.0029	1.0000
K2PG	37	-876.7006	1827.4012	0.0000	1.0000
K2PIG	38	-875.9939	1827.9878	0.0000	1.0000
K2PI	37	-877.2478	1828.4957	0.0000	1.0000
SYMG	41	-875.1901	1832.3802	0.0000	1.0000
SYMIG	42	-874.5117	1833.0233	0.0000	1.0000
SYMI	41	-875.6529	1833.3057	0.0000	1.0000
HKY	39	-879.0189	1836.0378	0.0000	1.0000
F81IG	40	-880.8658	1841.7315	0.0000	1.0000
F81G	39	-881.9081	1841.8161	0.0000	1.0000
F81I	39	-882.3681	1842.7363	0.0000	1.0000
GTR	43	-879.9680	1845.9360	0.0000	1.0000
JC69G	36	-891.1143	1854.2286	0.0000	1.0000
JC69IG	37	-890.1655	1854.3309	0.0000	1.0000
JC69I	36	-891.8926	1855.7851	0.0000	1.0000
K2P	36	-895.4673	1862.9347	0.0000	1.0000
SYM	40	-893.6702	1867.3405	0.0000	1.0000
F81	38	-899.3941	1874.7881	0.0000	1.0000
JC69	35	-909.8832	1889.7664	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-862.7529	1953.7902	0.6516	0.6516
HKYI	40	-863.6335	1955.5514	0.2701	0.9216
HKYIG	41	-862.0843	1958.1602	0.0733	0.9949
K2PG	37	-876.7006	1964.5643	0.0030	0.9979
K2PI	37	-877.2478	1965.6587	0.0017	0.9996
K2PIG	38	-875.9939	1968.8580	0.0003	1.0000
GTRG	44	-863.1834	1977.4796	0.0000	1.0000
GTRI	44	-863.8276	1978.7682	0.0000	1.0000
HKY	39	-879.0189	1980.6151	0.0000	1.0000
GTRIG	45	-862.6416	1982.1032	0.0000	1.0000
SYMG	41	-875.1901	1984.3717	0.0000	1.0000
SYMI	41	-875.6529	1985.2973	0.0000	1.0000
F81G	39	-881.9081	1986.3934	0.0000	1.0000
F81I	39	-882.3681	1987.3136	0.0000	1.0000
JC69G	36	-891.1143	1987.6846	0.0000	1.0000
SYMIG	42	-874.5117	1988.7220	0.0000	1.0000
JC69I	36	-891.8926	1989.2411	0.0000	1.0000
F81IG	40	-880.8658	1990.0160	0.0000	1.0000
JC69IG	37	-890.1655	1991.4940	0.0000	1.0000
K2P	36	-895.4673	1996.3906	0.0000	1.0000
GTR	43	-879.9680	2005.3418	0.0000	1.0000
SYM	40	-893.6702	2015.6249	0.0000	1.0000
F81	38	-899.3941	2015.6583	0.0000	1.0000
JC69	35	-909.8832	2019.5152	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_8024.phylip = 1 - 301;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_8024.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_8024.phylip = 1 - 301;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_8024.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_8024.phylip = 1 - 301;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_8024.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

