
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:23 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/chr5_11206.phylip" (19 taxa, 302 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	-944.2280	1991.8646	0.6926	0.6926
HKYG	40	-950.9501	1994.4673	0.1885	0.8811
GTRI	44	-946.4787	1996.3660	0.0729	0.9540
HKYI	40	-953.1305	1998.8281	0.0213	0.9753
GTRIG	45	-946.4451	1999.0620	0.0189	0.9942
HKYIG	41	-953.1043	2001.4548	0.0057	1.0000
GTR	43	-956.2084	2013.0835	0.0000	1.0000
K2PG	37	-965.1193	2014.8901	0.0000	1.0000
HKY	39	-962.9692	2015.8468	0.0000	1.0000
SYMG	41	-962.4801	2020.2064	0.0000	1.0000
K2PI	37	-967.8000	2020.2516	0.0000	1.0000
K2PIG	38	-967.2720	2021.8140	0.0000	1.0000
F81G	39	-965.9745	2021.8573	0.0000	1.0000
F81I	39	-966.4850	2022.8784	0.0000	1.0000
SYMI	41	-964.8426	2024.9313	0.0000	1.0000
F81IG	40	-966.1872	2024.9414	0.0000	1.0000
SYMIG	42	-964.5672	2027.0803	0.0000	1.0000
K2P	36	-978.0372	2038.1273	0.0000	1.0000
JC69G	36	-979.1466	2040.3461	0.0000	1.0000
JC69I	36	-979.7783	2041.6095	0.0000	1.0000
SYM	40	-974.5855	2041.7380	0.0000	1.0000
JC69IG	37	-979.0968	2042.8451	0.0000	1.0000
F81	38	-977.9784	2043.2267	0.0000	1.0000
JC69	35	-991.7369	2062.9474	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-944.2280	1976.4560	0.8187	0.8187
GTRI	44	-946.4787	1980.9575	0.0862	0.9050
HKYG	40	-950.9501	1981.9003	0.0538	0.9588
GTRIG	45	-946.4451	1982.8901	0.0328	0.9916
HKYI	40	-953.1305	1986.2610	0.0061	0.9977
HKYIG	41	-953.1043	1988.2087	0.0023	1.0000
GTR	43	-956.2084	1998.4168	0.0000	1.0000
HKY	39	-962.9692	2003.9384	0.0000	1.0000
K2PG	37	-965.1193	2004.2386	0.0000	1.0000
SYMG	41	-962.4801	2006.9603	0.0000	1.0000
K2PI	37	-967.8000	2009.6000	0.0000	1.0000
F81G	39	-965.9745	2009.9489	0.0000	1.0000
K2PIG	38	-967.2720	2010.5441	0.0000	1.0000
F81I	39	-966.4850	2010.9700	0.0000	1.0000
SYMI	41	-964.8426	2011.6851	0.0000	1.0000
F81IG	40	-966.1872	2012.3744	0.0000	1.0000
SYMIG	42	-964.5672	2013.1344	0.0000	1.0000
K2P	36	-978.0372	2028.0745	0.0000	1.0000
SYM	40	-974.5855	2029.1710	0.0000	1.0000
JC69G	36	-979.1466	2030.2933	0.0000	1.0000
JC69I	36	-979.7783	2031.5566	0.0000	1.0000
F81	38	-977.9784	2031.9568	0.0000	1.0000
JC69IG	37	-979.0968	2032.1936	0.0000	1.0000
JC69	35	-991.7369	2053.4737	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-950.9501	2130.3174	0.8819	0.8819
HKYI	40	-953.1305	2134.6781	0.0997	0.9816
GTRG	44	-944.2280	2139.7148	0.0080	0.9896
HKYIG	41	-953.1043	2140.3362	0.0059	0.9955
K2PG	37	-965.1193	2141.5244	0.0032	0.9988
GTRI	44	-946.4787	2144.2162	0.0008	0.9996
K2PI	37	-967.8000	2146.8858	0.0002	0.9998
HKY	39	-962.9692	2148.6451	0.0001	0.9999
GTRIG	45	-946.4451	2149.8593	0.0001	1.0000
K2PIG	38	-967.2720	2151.5403	0.0000	1.0000
F81G	39	-965.9745	2154.6556	0.0000	1.0000
F81I	39	-966.4850	2155.6767	0.0000	1.0000
GTR	43	-956.2084	2157.9652	0.0000	1.0000
SYMG	41	-962.4801	2159.0878	0.0000	1.0000
F81IG	40	-966.1872	2160.7915	0.0000	1.0000
K2P	36	-978.0372	2161.6499	0.0000	1.0000
SYMI	41	-964.8426	2163.8126	0.0000	1.0000
JC69G	36	-979.1466	2163.8687	0.0000	1.0000
JC69I	36	-979.7783	2165.1320	0.0000	1.0000
SYMIG	42	-964.5672	2168.9723	0.0000	1.0000
JC69IG	37	-979.0968	2169.4794	0.0000	1.0000
F81	38	-977.9784	2172.9530	0.0000	1.0000
SYM	40	-974.5855	2177.5881	0.0000	1.0000
JC69	35	-991.7369	2183.3387	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/chr5_11206.phylip = 1 - 302;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_11206.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/chr5_11206.phylip = 1 - 302;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_11206.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/chr5_11206.phylip = 1 - 302;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_11206.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

