
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:05 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/chr2_8114.phylip" (19 taxa, 294 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	-897.6742	1888.3129	0.2652	0.2652
K2PG	37	-901.8439	1888.6723	0.2216	0.4868
HKYIG	41	-896.9271	1889.5209	0.1450	0.6318
K2PIG	38	-901.0919	1889.8073	0.1256	0.7574
HKYI	40	-898.4403	1889.8449	0.1233	0.8807
K2PI	37	-902.6338	1890.2520	0.1006	0.9813
GTRG	44	-895.8515	1895.6066	0.0069	0.9882
GTRIG	45	-895.1081	1896.9097	0.0036	0.9918
GTRI	44	-896.7484	1897.4004	0.0028	0.9946
SYMG	41	-900.8971	1897.4609	0.0027	0.9974
SYMIG	42	-900.1637	1898.7178	0.0015	0.9988
SYMI	41	-901.7579	1899.1825	0.0012	1.0000
JC69G	36	-917.2347	1916.8353	0.0000	1.0000
F81G	39	-913.4783	1917.2400	0.0000	1.0000
JC69IG	37	-916.5863	1918.1569	0.0000	1.0000
JC69I	36	-918.0050	1918.3758	0.0000	1.0000
F81IG	40	-912.8282	1918.6207	0.0000	1.0000
F81I	39	-914.2402	1918.7638	0.0000	1.0000
HKY	39	-917.1607	1924.6049	0.0000	1.0000
K2P	36	-921.7094	1925.7846	0.0000	1.0000
GTR	43	-913.7377	1928.6114	0.0000	1.0000
SYM	40	-919.7593	1932.4831	0.0000	1.0000
F81	38	-932.5232	1952.6700	0.0000	1.0000
JC69	35	-936.5752	1952.9178	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-897.6742	1875.3485	0.3111	0.3111
HKYIG	41	-896.9271	1875.8543	0.2416	0.5527
HKYI	40	-898.4403	1876.8805	0.1446	0.6973
K2PG	37	-901.8439	1877.6879	0.0966	0.7939
K2PIG	38	-901.0919	1878.1838	0.0754	0.8693
K2PI	37	-902.6338	1879.2676	0.0438	0.9131
GTRG	44	-895.8515	1879.7030	0.0353	0.9484
GTRIG	45	-895.1081	1880.2161	0.0273	0.9756
GTRI	44	-896.7484	1881.4968	0.0144	0.9900
SYMG	41	-900.8971	1883.7942	0.0046	0.9946
SYMIG	42	-900.1637	1884.3274	0.0035	0.9981
SYMI	41	-901.7579	1885.5159	0.0019	1.0000
F81G	39	-913.4783	1904.9566	0.0000	1.0000
F81IG	40	-912.8282	1905.6563	0.0000	1.0000
JC69G	36	-917.2347	1906.4695	0.0000	1.0000
F81I	39	-914.2402	1906.4804	0.0000	1.0000
JC69IG	37	-916.5863	1907.1726	0.0000	1.0000
JC69I	36	-918.0050	1908.0100	0.0000	1.0000
HKY	39	-917.1607	1912.3214	0.0000	1.0000
GTR	43	-913.7377	1913.4754	0.0000	1.0000
K2P	36	-921.7094	1915.4188	0.0000	1.0000
SYM	40	-919.7593	1919.5186	0.0000	1.0000
F81	38	-932.5232	1941.0465	0.0000	1.0000
JC69	35	-936.5752	1943.1504	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-901.8439	2013.9804	0.6258	0.6258
K2PI	37	-902.6338	2015.5600	0.2840	0.9098
K2PIG	38	-901.0919	2018.1599	0.0774	0.9872
HKYG	40	-897.6742	2022.6917	0.0080	0.9952
HKYI	40	-898.4403	2024.2237	0.0037	0.9990
HKYIG	41	-896.9271	2026.8810	0.0010	1.0000
SYMG	41	-900.8971	2034.8210	0.0000	1.0000
SYMI	41	-901.7579	2036.5427	0.0000	1.0000
SYMIG	42	-900.1637	2039.0378	0.0000	1.0000
JC69G	36	-917.2347	2039.0784	0.0000	1.0000
JC69I	36	-918.0050	2040.6189	0.0000	1.0000
GTRG	44	-895.8515	2041.7805	0.0000	1.0000
JC69IG	37	-916.5863	2043.4650	0.0000	1.0000
GTRI	44	-896.7484	2043.5743	0.0000	1.0000
GTRIG	45	-895.1081	2045.9772	0.0000	1.0000
K2P	36	-921.7094	2048.0277	0.0000	1.0000
F81G	39	-913.4783	2048.6162	0.0000	1.0000
F81I	39	-914.2402	2050.1400	0.0000	1.0000
F81IG	40	-912.8282	2052.9995	0.0000	1.0000
HKY	39	-917.1607	2055.9810	0.0000	1.0000
SYM	40	-919.7593	2066.8618	0.0000	1.0000
GTR	43	-913.7377	2071.8693	0.0000	1.0000
JC69	35	-936.5752	2072.0757	0.0000	1.0000
F81	38	-932.5232	2081.0225	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/chr2_8114.phylip = 1 - 294;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_8114.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/chr2_8114.phylip = 1 - 294;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_8114.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/chr2_8114.phylip = 1 - 294;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_8114.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

