
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:14 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_24825.phylip" (19 taxa, 367 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	-939.5346	1979.3674	0.2792	0.2792
GTRI	44	-939.8571	1980.0124	0.2022	0.4814
HKYG	40	-945.0411	1980.1435	0.1894	0.6708
HKYI	40	-945.2486	1980.5585	0.1539	0.8248
GTRIG	45	-939.2629	1981.4229	0.0999	0.9247
HKYIG	41	-944.6951	1981.9871	0.0753	1.0000
K2PG	37	-962.1085	2006.7642	0.0000	1.0000
K2PI	37	-962.1544	2006.8559	0.0000	1.0000
K2PIG	38	-961.8886	2008.8137	0.0000	1.0000
SYMG	41	-958.7508	2010.0985	0.0000	1.0000
SYMI	41	-958.7996	2010.1961	0.0000	1.0000
GTR	43	-956.2434	2010.2019	0.0000	1.0000
F81G	39	-961.6368	2010.8148	0.0000	1.0000
F81I	39	-961.8060	2011.1532	0.0000	1.0000
SYMIG	42	-958.6878	2012.5237	0.0000	1.0000
F81IG	40	-961.2834	2012.6280	0.0000	1.0000
HKY	39	-963.1006	2013.7425	0.0000	1.0000
JC69G	36	-977.5791	2035.2308	0.0000	1.0000
JC69I	36	-977.6648	2035.4023	0.0000	1.0000
JC69IG	37	-977.3498	2037.2468	0.0000	1.0000
K2P	36	-982.0643	2044.2014	0.0000	1.0000
F81	38	-979.8274	2044.6914	0.0000	1.0000
SYM	40	-977.6668	2045.3949	0.0000	1.0000
JC69	35	-996.6394	2070.8921	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-939.5346	1967.0692	0.3671	0.3671
GTRI	44	-939.8571	1967.7142	0.2659	0.6330
GTRIG	45	-939.2629	1968.5257	0.1772	0.8102
HKYG	40	-945.0411	1970.0822	0.0814	0.8916
HKYI	40	-945.2486	1970.4972	0.0661	0.9577
HKYIG	41	-944.6951	1971.3902	0.0423	1.0000
K2PG	37	-962.1085	1998.2171	0.0000	1.0000
K2PI	37	-962.1544	1998.3088	0.0000	1.0000
GTR	43	-956.2434	1998.4868	0.0000	1.0000
SYMG	41	-958.7508	1999.5016	0.0000	1.0000
SYMI	41	-958.7996	1999.5991	0.0000	1.0000
K2PIG	38	-961.8886	1999.7771	0.0000	1.0000
F81G	39	-961.6368	2001.2735	0.0000	1.0000
SYMIG	42	-958.6878	2001.3755	0.0000	1.0000
F81I	39	-961.8060	2001.6120	0.0000	1.0000
F81IG	40	-961.2834	2002.5667	0.0000	1.0000
HKY	39	-963.1006	2004.2012	0.0000	1.0000
JC69G	36	-977.5791	2027.1581	0.0000	1.0000
JC69I	36	-977.6648	2027.3295	0.0000	1.0000
JC69IG	37	-977.3498	2028.6996	0.0000	1.0000
SYM	40	-977.6668	2035.3335	0.0000	1.0000
F81	38	-979.8274	2035.6549	0.0000	1.0000
K2P	36	-982.0643	2036.1287	0.0000	1.0000
JC69	35	-996.6394	2063.2788	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-945.0411	2126.2966	0.5290	0.5290
HKYI	40	-945.2486	2126.7117	0.4299	0.9589
HKYIG	41	-944.6951	2131.5101	0.0390	0.9980
GTRG	44	-939.5346	2138.9051	0.0010	0.9989
GTRI	44	-939.8571	2139.5501	0.0007	0.9996
K2PG	37	-962.1085	2142.7154	0.0001	0.9998
K2PI	37	-962.1544	2142.8071	0.0001	0.9999
GTRIG	45	-939.2629	2144.2670	0.0001	1.0000
K2PIG	38	-961.8886	2148.1809	0.0000	1.0000
F81G	39	-961.6368	2153.5827	0.0000	1.0000
F81I	39	-961.8060	2153.9211	0.0000	1.0000
HKY	39	-963.1006	2156.5103	0.0000	1.0000
F81IG	40	-961.2834	2158.7812	0.0000	1.0000
SYMG	41	-958.7508	2159.6214	0.0000	1.0000
SYMI	41	-958.7996	2159.7190	0.0000	1.0000
SYMIG	42	-958.6878	2165.4007	0.0000	1.0000
GTR	43	-956.2434	2166.4173	0.0000	1.0000
JC69G	36	-977.5791	2167.7511	0.0000	1.0000
JC69I	36	-977.6648	2167.9226	0.0000	1.0000
JC69IG	37	-977.3498	2173.1980	0.0000	1.0000
K2P	36	-982.0643	2176.7217	0.0000	1.0000
F81	38	-979.8274	2184.0586	0.0000	1.0000
SYM	40	-977.6668	2191.5480	0.0000	1.0000
JC69	35	-996.6394	2199.9664	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_24825.phylip = 1 - 367;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_24825.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_24825.phylip = 1 - 367;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_24825.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/chr2_24825.phylip = 1 - 367;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_24825.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;


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End of Output

