
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:12 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/chr3_5834.phylip" (19 taxa, 268 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	-838.4633	1782.6845	0.6355	0.6355
GTRI	44	-839.7082	1785.1743	0.1830	0.8185
GTRIG	45	-838.3284	1785.3055	0.1714	0.9898
HKYG	40	-848.9498	1792.3489	0.0051	0.9949
HKYI	40	-849.3368	1793.1230	0.0034	0.9983
HKYIG	41	-848.8985	1795.0359	0.0013	0.9997
GTR	43	-848.1442	1799.1812	0.0002	0.9998
SYMG	41	-851.8947	1801.0284	0.0001	0.9999
SYMI	41	-852.5840	1802.4070	0.0000	0.9999
K2PG	37	-858.4967	1803.2195	0.0000	1.0000
SYMIG	42	-851.8089	1803.6712	0.0000	1.0000
K2PI	37	-858.8076	1803.8412	0.0000	1.0000
K2PIG	38	-858.4542	1805.8516	0.0000	1.0000
HKY	39	-857.3528	1806.3898	0.0000	1.0000
SYM	40	-860.2755	1815.0003	0.0000	1.0000
K2P	36	-866.6709	1816.8743	0.0000	1.0000
F81G	39	-863.2483	1818.1809	0.0000	1.0000
F81I	39	-863.9909	1819.6660	0.0000	1.0000
F81IG	40	-863.1855	1820.8203	0.0000	1.0000
JC69G	36	-870.8211	1825.1747	0.0000	1.0000
JC69I	36	-871.4528	1826.4380	0.0000	1.0000
JC69IG	37	-870.7630	1827.7521	0.0000	1.0000
F81	38	-870.8793	1830.7018	0.0000	1.0000
JC69	35	-878.4113	1837.6847	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-838.4633	1764.9267	0.5840	0.5840
GTRIG	45	-838.3284	1766.6568	0.2459	0.8299
GTRI	44	-839.7082	1767.4165	0.1682	0.9980
HKYG	40	-848.9498	1777.8996	0.0009	0.9989
HKYI	40	-849.3368	1778.6737	0.0006	0.9995
HKYIG	41	-848.8985	1779.7969	0.0003	0.9999
GTR	43	-848.1442	1782.2884	0.0001	1.0000
SYMG	41	-851.8947	1785.7894	0.0000	1.0000
SYMI	41	-852.5840	1787.1680	0.0000	1.0000
SYMIG	42	-851.8089	1787.6178	0.0000	1.0000
K2PG	37	-858.4967	1790.9934	0.0000	1.0000
K2PI	37	-858.8076	1791.6152	0.0000	1.0000
HKY	39	-857.3528	1792.7056	0.0000	1.0000
K2PIG	38	-858.4542	1792.9083	0.0000	1.0000
SYM	40	-860.2755	1800.5510	0.0000	1.0000
F81G	39	-863.2483	1804.4967	0.0000	1.0000
K2P	36	-866.6709	1805.3418	0.0000	1.0000
F81I	39	-863.9909	1805.9818	0.0000	1.0000
F81IG	40	-863.1855	1806.3710	0.0000	1.0000
JC69G	36	-870.8211	1813.6422	0.0000	1.0000
JC69I	36	-871.4528	1814.9055	0.0000	1.0000
JC69IG	37	-870.7630	1815.5260	0.0000	1.0000
F81	38	-870.8793	1817.7585	0.0000	1.0000
JC69	35	-878.4113	1826.8226	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-848.9498	1921.5390	0.3340	0.3340
HKYI	40	-849.3368	1922.3131	0.2268	0.5607
GTRG	44	-838.4633	1922.9301	0.1666	0.7273
K2PG	37	-858.4967	1923.8600	0.1046	0.8320
K2PI	37	-858.8076	1924.4817	0.0767	0.9087
GTRI	44	-839.7082	1925.4199	0.0480	0.9566
HKYIG	41	-848.8985	1927.0274	0.0215	0.9781
GTRIG	45	-838.3284	1928.2512	0.0116	0.9897
K2PIG	38	-858.4542	1929.3658	0.0067	0.9964
HKY	39	-857.3528	1932.7541	0.0012	0.9976
SYMG	41	-851.8947	1933.0199	0.0011	0.9987
SYMI	41	-852.5840	1934.3985	0.0005	0.9993
K2P	36	-866.6709	1934.6174	0.0005	0.9997
GTR	43	-848.1442	1936.7008	0.0002	0.9999
SYMIG	42	-851.8089	1938.4393	0.0001	1.0000
JC69G	36	-870.8211	1942.9177	0.0000	1.0000
JC69I	36	-871.4528	1944.1811	0.0000	1.0000
SYM	40	-860.2755	1944.1904	0.0000	1.0000
F81G	39	-863.2483	1944.5452	0.0000	1.0000
F81I	39	-863.9909	1946.0303	0.0000	1.0000
JC69IG	37	-870.7630	1948.3925	0.0000	1.0000
F81IG	40	-863.1855	1950.0105	0.0000	1.0000
JC69	35	-878.4113	1952.5071	0.0000	1.0000
F81	38	-870.8793	1954.2160	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/chr3_5834.phylip = 1 - 268;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_5834.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/chr3_5834.phylip = 1 - 268;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_5834.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/chr3_5834.phylip = 1 - 268;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_5834.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

