
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:54 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/chr7_1412.phylip" (19 taxa, 274 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
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
GTRG	44	-883.9909	1873.2744	0.4474	0.4474
GTRIG	45	-883.1793	1874.5165	0.2404	0.6879
GTRI	44	-885.8152	1876.9230	0.0722	0.7601
SYMG	41	-890.2282	1877.3012	0.0597	0.8198
HKYG	40	-891.7953	1877.6678	0.0497	0.8696
HKYIG	41	-890.5586	1877.9619	0.0429	0.9125
SYMIG	42	-889.5646	1878.7656	0.0287	0.9412
K2PG	37	-896.8650	1879.6452	0.0185	0.9597
SYMI	41	-891.7097	1880.2641	0.0136	0.9733
K2PIG	38	-896.0090	1880.6307	0.0113	0.9846
HKYI	40	-893.3138	1880.7049	0.0109	0.9955
K2PI	37	-898.2838	1882.4828	0.0045	1.0000
GTR	43	-908.4867	1919.4256	0.0000	1.0000
SYM	40	-912.9292	1919.9357	0.0000	1.0000
HKY	39	-915.6969	1922.7271	0.0000	1.0000
K2P	36	-920.0634	1923.3673	0.0000	1.0000
JC69G	36	-927.4974	1938.2353	0.0000	1.0000
F81G	39	-923.5697	1938.4728	0.0000	1.0000
JC69IG	37	-926.9264	1939.7680	0.0000	1.0000
F81IG	40	-922.9692	1940.0157	0.0000	1.0000
JC69I	36	-928.7635	1940.7675	0.0000	1.0000
F81I	39	-924.8171	1940.9676	0.0000	1.0000
JC69	35	-949.3184	1979.2251	0.0000	1.0000
F81	38	-945.6118	1979.8364	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-883.9909	1855.9818	0.4701	0.4701
GTRIG	45	-883.1793	1856.3586	0.3894	0.8595
GTRI	44	-885.8152	1859.6305	0.0758	0.9353
SYMG	41	-890.2282	1862.4564	0.0185	0.9538
HKYIG	41	-890.5586	1863.1171	0.0133	0.9671
SYMIG	42	-889.5646	1863.1293	0.0132	0.9803
HKYG	40	-891.7953	1863.5906	0.0105	0.9907
SYMI	41	-891.7097	1865.4193	0.0042	0.9949
HKYI	40	-893.3138	1866.6276	0.0023	0.9972
K2PG	37	-896.8650	1867.7299	0.0013	0.9985
K2PIG	38	-896.0090	1868.0179	0.0011	0.9997
K2PI	37	-898.2838	1870.5675	0.0003	1.0000
GTR	43	-908.4867	1902.9734	0.0000	1.0000
SYM	40	-912.9292	1905.8585	0.0000	1.0000
HKY	39	-915.6969	1909.3938	0.0000	1.0000
K2P	36	-920.0634	1912.1268	0.0000	1.0000
F81G	39	-923.5697	1925.1395	0.0000	1.0000
F81IG	40	-922.9692	1925.9384	0.0000	1.0000
JC69G	36	-927.4974	1926.9948	0.0000	1.0000
F81I	39	-924.8171	1927.6342	0.0000	1.0000
JC69IG	37	-926.9264	1927.8527	0.0000	1.0000
JC69I	36	-928.7635	1929.5270	0.0000	1.0000
F81	38	-945.6118	1967.2236	0.0000	1.0000
JC69	35	-949.3184	1968.6369	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-896.8650	2001.4156	0.6899	0.6899
K2PI	37	-898.2838	2004.2533	0.1670	0.8569
K2PIG	38	-896.0090	2005.3168	0.0981	0.9550
HKYG	40	-891.7953	2008.1157	0.0242	0.9792
SYMG	41	-890.2282	2010.5946	0.0070	0.9862
HKYI	40	-893.3138	2011.1527	0.0053	0.9915
HKYIG	41	-890.5586	2011.2554	0.0050	0.9966
SYMI	41	-891.7097	2013.5576	0.0016	0.9982
SYMIG	42	-889.5646	2014.8806	0.0008	0.9990
GTRG	44	-883.9909	2014.9594	0.0008	0.9998
GTRI	44	-885.8152	2018.6081	0.0001	0.9999
GTRIG	45	-883.1793	2018.9494	0.0001	1.0000
K2P	36	-920.0634	2042.1994	0.0000	1.0000
HKY	39	-915.6969	2050.3058	0.0000	1.0000
SYM	40	-912.9292	2050.3836	0.0000	1.0000
JC69G	36	-927.4974	2057.0674	0.0000	1.0000
GTR	43	-908.4867	2058.3379	0.0000	1.0000
JC69I	36	-928.7635	2059.5996	0.0000	1.0000
JC69IG	37	-926.9264	2061.5385	0.0000	1.0000
F81G	39	-923.5697	2066.0515	0.0000	1.0000
F81I	39	-924.8171	2068.5462	0.0000	1.0000
F81IG	40	-922.9692	2070.4636	0.0000	1.0000
JC69	35	-949.3184	2095.0963	0.0000	1.0000
F81	38	-945.6118	2104.5225	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/chr7_1412.phylip = 1 - 274;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_1412.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/chr7_1412.phylip = 1 - 274;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_1412.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 (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_1412.phylip = 1 - 274;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_1412.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

