
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:50 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_12017.phylip" (19 taxa, 315 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
Minimum BIC  model: K2PI


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	-899.1903	1901.0474	0.5799	0.5799
GTRI	44	-900.2190	1903.1046	0.2073	0.7872
GTRIG	45	-899.7404	1904.8712	0.0857	0.8729
GTR	43	-903.3885	1906.7401	0.0337	0.9065
HKYI	40	-907.3973	1906.7654	0.0332	0.9398
HKYG	40	-907.5055	1906.9818	0.0298	0.9696
HKYIG	41	-907.4000	1909.4154	0.0088	0.9784
K2PI	37	-912.9940	1910.1397	0.0062	0.9846
K2PG	37	-913.1649	1910.4814	0.0052	0.9898
SYMG	41	-908.0121	1910.6396	0.0048	0.9946
HKY	39	-911.6130	1912.5715	0.0018	0.9964
K2PIG	38	-913.1771	1913.0933	0.0014	0.9978
SYMI	41	-909.3618	1913.3390	0.0012	0.9990
SYMIG	42	-909.0720	1915.4234	0.0004	0.9995
SYM	40	-912.1082	1916.1872	0.0003	0.9998
K2P	36	-917.6024	1916.7875	0.0002	1.0000
F81G	39	-917.6112	1924.5678	0.0000	1.0000
JC69G	36	-922.5913	1926.7654	0.0000	1.0000
F81I	39	-918.8232	1926.9918	0.0000	1.0000
F81IG	40	-918.6820	1929.3347	0.0000	1.0000
JC69I	36	-923.9623	1929.5074	0.0000	1.0000
F81	38	-921.6969	1930.1329	0.0000	1.0000
JC69IG	37	-923.8534	1931.8584	0.0000	1.0000
JC69	35	-926.9304	1932.8931	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-899.1903	1886.3807	0.6055	0.6055
GTRI	44	-900.2190	1888.4380	0.2165	0.8220
GTRIG	45	-899.7404	1889.4809	0.1285	0.9505
GTR	43	-903.3885	1892.7770	0.0247	0.9752
HKYI	40	-907.3973	1894.7946	0.0090	0.9842
HKYG	40	-907.5055	1895.0110	0.0081	0.9923
HKYIG	41	-907.4000	1896.8000	0.0033	0.9956
SYMG	41	-908.0121	1898.0242	0.0018	0.9974
K2PI	37	-912.9940	1899.9881	0.0007	0.9981
K2PG	37	-913.1649	1900.3298	0.0006	0.9986
SYMI	41	-909.3618	1900.7236	0.0005	0.9991
HKY	39	-911.6130	1901.2261	0.0004	0.9995
SYMIG	42	-909.0720	1902.1439	0.0002	0.9997
K2PIG	38	-913.1771	1902.3542	0.0002	0.9999
SYM	40	-912.1082	1904.2164	0.0001	1.0000
K2P	36	-917.6024	1907.2047	0.0000	1.0000
F81G	39	-917.6112	1913.2224	0.0000	1.0000
F81I	39	-918.8232	1915.6463	0.0000	1.0000
JC69G	36	-922.5913	1917.1826	0.0000	1.0000
F81IG	40	-918.6820	1917.3639	0.0000	1.0000
F81	38	-921.6969	1919.3938	0.0000	1.0000
JC69I	36	-923.9623	1919.9246	0.0000	1.0000
JC69IG	37	-923.8534	1921.7068	0.0000	1.0000
JC69	35	-926.9304	1923.8609	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PI	37	-912.9940	2038.8332	0.4586	0.4586
K2PG	37	-913.1649	2039.1750	0.3865	0.8451
K2P	36	-917.6024	2042.2973	0.0811	0.9262
HKYI	40	-907.3973	2044.8975	0.0221	0.9483
K2PIG	38	-913.1771	2044.9520	0.0215	0.9699
HKYG	40	-907.5055	2045.1139	0.0198	0.9897
HKY	39	-911.6130	2047.5764	0.0058	0.9955
HKYIG	41	-907.4000	2050.6555	0.0012	0.9967
GTRG	44	-899.1903	2051.4939	0.0008	0.9976
SYMG	41	-908.0121	2051.8797	0.0007	0.9982
JC69G	36	-922.5913	2052.2753	0.0006	0.9988
GTRI	44	-900.2190	2053.5512	0.0003	0.9991
GTR	43	-903.3885	2054.1376	0.0002	0.9993
SYM	40	-912.1082	2054.3193	0.0002	0.9995
SYMI	41	-909.3618	2054.5791	0.0002	0.9997
JC69I	36	-923.9623	2055.0173	0.0001	0.9998
JC69	35	-926.9304	2055.2009	0.0001	0.9999
GTRIG	45	-899.7404	2058.3466	0.0000	1.0000
F81G	39	-917.6112	2059.5727	0.0000	1.0000
SYMIG	42	-909.0720	2059.7520	0.0000	1.0000
JC69IG	37	-923.8534	2060.5520	0.0000	1.0000
F81	38	-921.6969	2061.9916	0.0000	1.0000
F81I	39	-918.8232	2061.9967	0.0000	1.0000
F81IG	40	-918.6820	2067.4668	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/chr2_12017.phylip = 1 - 315;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_12017.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/chr2_12017.phylip = 1 - 315;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_12017.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 (K2PI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_12017.phylip = 1 - 315;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_12017.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=propinv;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0) pinvarpr=Uniform(0.0,1.0);
END;


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End of Output

