
Output from mraic.pl version 1.4.4 by Johan Nylander
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13:23 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_11557.phylip" (19 taxa, 260 characters)

Minimum AIC  model: HKYG
Minimum AICc model: HKYG
Minimum BIC  model: K2PG


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	-845.6979	1786.3729	0.4235	0.4235
HKYI	40	-846.0311	1787.0393	0.3035	0.7270
HKYIG	41	-845.6962	1789.1905	0.1035	0.8305
GTRG	44	-842.3029	1791.0244	0.0414	0.8718
K2PG	37	-852.2129	1791.0924	0.0400	0.9118
K2PI	37	-852.6035	1791.8736	0.0271	0.9389
K2PIG	38	-851.3166	1792.0450	0.0248	0.9637
GTRI	44	-842.9442	1792.3070	0.0218	0.9855
GTRIG	45	-842.2692	1793.8843	0.0099	0.9954
SYMG	41	-849.7023	1797.2028	0.0019	0.9973
SYMI	41	-850.0453	1797.8888	0.0013	0.9987
SYMIG	42	-848.6236	1797.8924	0.0013	1.0000
HKY	39	-860.9416	1814.0649	0.0000	1.0000
JC69G	36	-865.1367	1814.2197	0.0000	1.0000
F81G	39	-861.1354	1814.4525	0.0000	1.0000
JC69I	36	-865.6123	1815.1708	0.0000	1.0000
F81I	39	-861.6313	1815.4444	0.0000	1.0000
JC69IG	37	-865.1021	1816.8709	0.0000	1.0000
F81IG	40	-861.0918	1817.1607	0.0000	1.0000
K2P	36	-866.9826	1817.9113	0.0000	1.0000
GTR	43	-858.8085	1821.1355	0.0000	1.0000
SYM	40	-864.5371	1824.0513	0.0000	1.0000
JC69	35	-879.6368	1840.5236	0.0000	1.0000
F81	38	-875.8532	1841.1181	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-845.6979	1771.3957	0.3104	0.3104
HKYI	40	-846.0311	1772.0622	0.2224	0.5328
GTRG	44	-842.3029	1772.6058	0.1695	0.7023
HKYIG	41	-845.6962	1773.3923	0.1144	0.8166
GTRI	44	-842.9442	1773.8884	0.0893	0.9059
GTRIG	45	-842.2692	1774.5385	0.0645	0.9704
K2PG	37	-852.2129	1778.4257	0.0092	0.9796
K2PIG	38	-851.3166	1778.6332	0.0083	0.9879
K2PI	37	-852.6035	1779.2070	0.0062	0.9942
SYMIG	42	-848.6236	1781.2472	0.0023	0.9964
SYMG	41	-849.7023	1781.4046	0.0021	0.9985
SYMI	41	-850.0453	1782.0906	0.0015	1.0000
HKY	39	-860.9416	1799.8831	0.0000	1.0000
F81G	39	-861.1354	1800.2707	0.0000	1.0000
F81I	39	-861.6313	1801.2626	0.0000	1.0000
F81IG	40	-861.0918	1802.1835	0.0000	1.0000
JC69G	36	-865.1367	1802.2735	0.0000	1.0000
JC69I	36	-865.6123	1803.2246	0.0000	1.0000
GTR	43	-858.8085	1803.6170	0.0000	1.0000
JC69IG	37	-865.1021	1804.2042	0.0000	1.0000
K2P	36	-866.9826	1805.9652	0.0000	1.0000
SYM	40	-864.5371	1809.0742	0.0000	1.0000
F81	38	-875.8532	1827.7063	0.0000	1.0000
JC69	35	-879.6368	1829.2736	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-852.2129	1910.1709	0.4727	0.4727
K2PI	37	-852.6035	1910.9522	0.3198	0.7925
HKYG	40	-845.6979	1913.8230	0.0761	0.8686
K2PIG	38	-851.3166	1913.9391	0.0718	0.9405
HKYI	40	-846.0311	1914.4894	0.0546	0.9950
HKYIG	41	-845.6962	1919.3803	0.0047	0.9997
SYMG	41	-849.7023	1927.3925	0.0001	0.9998
SYMI	41	-850.0453	1928.0786	0.0001	0.9999
GTRG	44	-842.3029	1929.2758	0.0000	0.9999
JC69G	36	-865.1367	1930.4580	0.0000	0.9999
GTRI	44	-842.9442	1930.5584	0.0000	1.0000
SYMIG	42	-848.6236	1930.7958	0.0000	1.0000
JC69I	36	-865.6123	1931.4092	0.0000	1.0000
K2P	36	-866.9826	1934.1497	0.0000	1.0000
GTRIG	45	-842.2692	1934.7691	0.0000	1.0000
JC69IG	37	-865.1021	1935.9495	0.0000	1.0000
HKY	39	-860.9416	1938.7497	0.0000	1.0000
F81G	39	-861.1354	1939.1373	0.0000	1.0000
F81I	39	-861.6313	1940.1292	0.0000	1.0000
F81IG	40	-861.0918	1944.6108	0.0000	1.0000
SYM	40	-864.5371	1951.5014	0.0000	1.0000
JC69	35	-879.6368	1953.8975	0.0000	1.0000
GTR	43	-858.8085	1956.7263	0.0000	1.0000
F81	38	-875.8532	1963.0122	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_11557.phylip = 1 - 260;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_11557.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_11557.phylip = 1 - 260;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_11557.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 (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_11557.phylip = 1 - 260;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_11557.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=gamma;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


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End of Output

