
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:58 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/chr6_5992.phylip" (19 taxa, 336 characters)

Minimum AIC  model: HKYG
Minimum AICc model: HKYG
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
HKYG	40	-951.3011	1993.7209	0.4824	0.4824
HKYI	40	-951.5944	1994.3075	0.3597	0.8421
HKYIG	41	-951.2306	1996.1756	0.1414	0.9835
GTRG	44	-950.1678	2001.9438	0.0079	0.9914
GTRI	44	-950.4399	2002.4881	0.0060	0.9974
GTRIG	45	-950.1143	2004.5044	0.0022	0.9996
K2PG	37	-963.0001	2009.4364	0.0002	0.9998
K2PI	37	-963.2300	2009.8961	0.0001	0.9999
K2PIG	38	-962.9338	2011.8475	0.0001	1.0000
SYMG	41	-961.7773	2017.2689	0.0000	1.0000
SYMI	41	-962.1254	2017.9651	0.0000	1.0000
SYMIG	42	-961.5914	2019.5103	0.0000	1.0000
HKY	39	-969.8645	2028.2696	0.0000	1.0000
GTR	43	-968.3923	2035.7435	0.0000	1.0000
F81G	39	-973.9659	2036.4723	0.0000	1.0000
F81I	39	-974.0786	2036.6978	0.0000	1.0000
K2P	36	-978.6586	2038.2269	0.0000	1.0000
F81IG	40	-973.9656	2039.0498	0.0000	1.0000
SYM	40	-977.1572	2045.4330	0.0000	1.0000
JC69G	36	-983.6254	2048.1605	0.0000	1.0000
JC69I	36	-986.4796	2053.8688	0.0000	1.0000
JC69IG	37	-986.3092	2056.0547	0.0000	1.0000
F81	38	-992.2097	2070.3991	0.0000	1.0000
JC69	35	-1000.0972	2078.5943	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-951.3011	1982.6023	0.4418	0.4418
HKYI	40	-951.5944	1983.1889	0.3295	0.7714
HKYIG	41	-951.2306	1984.4613	0.1744	0.9458
GTRG	44	-950.1678	1988.3355	0.0251	0.9709
GTRI	44	-950.4399	1988.8799	0.0191	0.9901
GTRIG	45	-950.1143	1990.2285	0.0098	0.9998
K2PG	37	-963.0001	2000.0002	0.0001	0.9999
K2PI	37	-963.2300	2000.4599	0.0001	1.0000
K2PIG	38	-962.9338	2001.8677	0.0000	1.0000
SYMG	41	-961.7773	2005.5546	0.0000	1.0000
SYMI	41	-962.1254	2006.2509	0.0000	1.0000
SYMIG	42	-961.5914	2007.1827	0.0000	1.0000
HKY	39	-969.8645	2017.7290	0.0000	1.0000
GTR	43	-968.3923	2022.7846	0.0000	1.0000
F81G	39	-973.9659	2025.9317	0.0000	1.0000
F81I	39	-974.0786	2026.1572	0.0000	1.0000
F81IG	40	-973.9656	2027.9311	0.0000	1.0000
K2P	36	-978.6586	2029.3172	0.0000	1.0000
SYM	40	-977.1572	2034.3144	0.0000	1.0000
JC69G	36	-983.6254	2039.2508	0.0000	1.0000
JC69I	36	-986.4796	2044.9591	0.0000	1.0000
JC69IG	37	-986.3092	2046.6185	0.0000	1.0000
F81	38	-992.2097	2060.4193	0.0000	1.0000
JC69	35	-1000.0972	2070.1943	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-951.3011	2135.2867	0.5266	0.5266
HKYI	40	-951.5944	2135.8733	0.3927	0.9193
HKYIG	41	-951.2306	2140.9628	0.0308	0.9501
K2PG	37	-963.0001	2141.2333	0.0269	0.9770
K2PI	37	-963.2300	2141.6930	0.0214	0.9984
K2PIG	38	-962.9338	2146.9179	0.0016	1.0000
GTRG	44	-950.1678	2156.2884	0.0000	1.0000
GTRI	44	-950.4399	2156.8328	0.0000	1.0000
GTRIG	45	-950.1143	2161.9985	0.0000	1.0000
SYMG	41	-961.7773	2162.0562	0.0000	1.0000
SYMI	41	-962.1254	2162.7524	0.0000	1.0000
HKY	39	-969.8645	2166.5964	0.0000	1.0000
K2P	36	-978.6586	2166.7332	0.0000	1.0000
SYMIG	42	-961.5914	2167.5014	0.0000	1.0000
F81G	39	-973.9659	2174.7991	0.0000	1.0000
F81I	39	-974.0786	2175.0246	0.0000	1.0000
JC69G	36	-983.6254	2176.6668	0.0000	1.0000
F81IG	40	-973.9656	2180.6156	0.0000	1.0000
JC69I	36	-986.4796	2182.3751	0.0000	1.0000
GTR	43	-968.3923	2186.9204	0.0000	1.0000
SYM	40	-977.1572	2186.9988	0.0000	1.0000
JC69IG	37	-986.3092	2187.8516	0.0000	1.0000
JC69	35	-1000.0972	2203.7932	0.0000	1.0000
F81	38	-992.2097	2205.4695	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/chr6_5992.phylip = 1 - 336;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_5992.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/chr6_5992.phylip = 1 - 336;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_5992.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 (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_5992.phylip = 1 - 336;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_5992.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

