
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:11 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_32307.phylip" (19 taxa, 294 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	-826.9000	1757.7037	0.6730	0.6730
HKYG	40	-833.1166	1759.1975	0.3189	0.9918
HKYIG	41	-836.1775	1768.0216	0.0039	0.9957
HKYI	40	-837.8357	1768.6358	0.0028	0.9985
GTRIG	45	-832.1921	1771.0777	0.0008	0.9994
GTRI	44	-834.4867	1772.8771	0.0003	0.9997
K2PG	37	-844.1723	1773.3290	0.0003	1.0000
SYMG	41	-841.5250	1778.7166	0.0000	1.0000
K2PIG	38	-848.7589	1785.1414	0.0000	1.0000
K2PI	37	-850.2942	1785.5728	0.0000	1.0000
SYMIG	42	-845.4568	1789.3040	0.0000	1.0000
SYMI	41	-847.2976	1790.2619	0.0000	1.0000
F81G	39	-850.6672	1791.6178	0.0000	1.0000
HKY	39	-850.9027	1792.0888	0.0000	1.0000
GTR	43	-847.0992	1795.3343	0.0000	1.0000
F81I	39	-854.4664	1799.2162	0.0000	1.0000
F81IG	40	-853.1454	1799.2552	0.0000	1.0000
JC69G	36	-860.7713	1803.9083	0.0000	1.0000
K2P	36	-862.2637	1806.8932	0.0000	1.0000
SYM	40	-858.6181	1810.2006	0.0000	1.0000
JC69IG	37	-864.4527	1813.8897	0.0000	1.0000
JC69I	36	-865.8215	1814.0088	0.0000	1.0000
F81	38	-867.8589	1823.3412	0.0000	1.0000
JC69	35	-877.8690	1835.5053	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-826.9000	1741.8001	0.8975	0.8975
HKYG	40	-833.1166	1746.2331	0.0978	0.9953
HKYIG	41	-836.1775	1754.3549	0.0017	0.9970
GTRIG	45	-832.1921	1754.3841	0.0017	0.9986
HKYI	40	-837.8357	1755.6714	0.0009	0.9995
GTRI	44	-834.4867	1756.9735	0.0005	1.0000
K2PG	37	-844.1723	1762.3446	0.0000	1.0000
SYMG	41	-841.5250	1765.0500	0.0000	1.0000
K2PIG	38	-848.7589	1773.5179	0.0000	1.0000
K2PI	37	-850.2942	1774.5885	0.0000	1.0000
SYMIG	42	-845.4568	1774.9136	0.0000	1.0000
SYMI	41	-847.2976	1776.5952	0.0000	1.0000
F81G	39	-850.6672	1779.3344	0.0000	1.0000
HKY	39	-850.9027	1779.8053	0.0000	1.0000
GTR	43	-847.0992	1780.1983	0.0000	1.0000
F81IG	40	-853.1454	1786.2908	0.0000	1.0000
F81I	39	-854.4664	1786.9328	0.0000	1.0000
JC69G	36	-860.7713	1793.5425	0.0000	1.0000
K2P	36	-862.2637	1796.5275	0.0000	1.0000
SYM	40	-858.6181	1797.2362	0.0000	1.0000
JC69IG	37	-864.4527	1802.9054	0.0000	1.0000
JC69I	36	-865.8215	1803.6431	0.0000	1.0000
F81	38	-867.8589	1811.7177	0.0000	1.0000
JC69	35	-877.8690	1825.7379	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-833.1166	1893.5763	0.9113	0.9113
K2PG	37	-844.1723	1898.6370	0.0726	0.9839
HKYI	40	-837.8357	1903.0146	0.0081	0.9920
GTRG	44	-826.9000	1903.8776	0.0053	0.9973
HKYIG	41	-836.1775	1905.3817	0.0025	0.9998
K2PI	37	-850.2942	1910.8809	0.0002	0.9999
K2PIG	38	-848.7589	1913.4939	0.0000	1.0000
SYMG	41	-841.5250	1916.0767	0.0000	1.0000
GTRI	44	-834.4867	1919.0510	0.0000	1.0000
GTRIG	45	-832.1921	1920.1452	0.0000	1.0000
F81G	39	-850.6672	1922.9940	0.0000	1.0000
HKY	39	-850.9027	1923.4650	0.0000	1.0000
JC69G	36	-860.7713	1926.1514	0.0000	1.0000
SYMI	41	-847.2976	1927.6220	0.0000	1.0000
K2P	36	-862.2637	1929.1364	0.0000	1.0000
SYMIG	42	-845.4568	1929.6239	0.0000	1.0000
F81I	39	-854.4664	1930.5924	0.0000	1.0000
F81IG	40	-853.1454	1933.6340	0.0000	1.0000
JC69I	36	-865.8215	1936.2519	0.0000	1.0000
GTR	43	-847.0992	1938.5923	0.0000	1.0000
JC69IG	37	-864.4527	1939.1978	0.0000	1.0000
SYM	40	-858.6181	1944.5794	0.0000	1.0000
F81	38	-867.8589	1951.6938	0.0000	1.0000
JC69	35	-877.8690	1954.6632	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/chr1_32307.phylip = 1 - 294;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_32307.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/chr1_32307.phylip = 1 - 294;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_32307.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/chr1_32307.phylip = 1 - 294;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_32307.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;


-------------------------------------------------------------
End of Output

