
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:06 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/chr3_338.phylip" (19 taxa, 370 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	-931.3209	1962.8264	0.5318	0.5318
GTRIG	45	-930.7384	1964.2547	0.2604	0.7921
GTRI	44	-932.3044	1964.7934	0.1989	0.9910
HKYG	40	-941.2430	1972.4556	0.0043	0.9953
HKYI	40	-941.6905	1973.3505	0.0028	0.9980
HKYIG	41	-940.7677	1974.0354	0.0020	1.0000
GTR	43	-945.2152	1988.0378	0.0000	1.0000
HKY	39	-956.6056	2000.6658	0.0000	1.0000
F81G	39	-956.9493	2001.3532	0.0000	1.0000
F81I	39	-957.3348	2002.1241	0.0000	1.0000
F81IG	40	-956.5654	2003.1005	0.0000	1.0000
SYMG	41	-964.2962	2021.0924	0.0000	1.0000
SYMI	41	-964.7071	2021.9141	0.0000	1.0000
SYMIG	42	-963.6873	2022.4205	0.0000	1.0000
K2PG	37	-970.2134	2022.8966	0.0000	1.0000
K2PI	37	-970.4833	2023.4365	0.0000	1.0000
K2PIG	38	-969.6936	2024.3419	0.0000	1.0000
F81	38	-971.9326	2028.8198	0.0000	1.0000
JC69G	36	-983.1358	2046.2716	0.0000	1.0000
JC69I	36	-983.4683	2046.9366	0.0000	1.0000
JC69IG	37	-982.7254	2047.9206	0.0000	1.0000
SYM	40	-980.3011	2050.5718	0.0000	1.0000
K2P	36	-987.2127	2054.4253	0.0000	1.0000
JC69	35	-998.8679	2075.2807	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-931.3209	1950.6418	0.4905	0.4905
GTRIG	45	-930.7384	1951.4769	0.3231	0.8136
GTRI	44	-932.3044	1952.6088	0.1835	0.9971
HKYG	40	-941.2430	1962.4860	0.0013	0.9984
HKYI	40	-941.6905	1963.3809	0.0008	0.9992
HKYIG	41	-940.7677	1963.5354	0.0008	1.0000
GTR	43	-945.2152	1976.4305	0.0000	1.0000
HKY	39	-956.6056	1991.2113	0.0000	1.0000
F81G	39	-956.9493	1991.8987	0.0000	1.0000
F81I	39	-957.3348	1992.6696	0.0000	1.0000
F81IG	40	-956.5654	1993.1309	0.0000	1.0000
SYMG	41	-964.2962	2010.5924	0.0000	1.0000
SYMIG	42	-963.6873	2011.3746	0.0000	1.0000
SYMI	41	-964.7071	2011.4141	0.0000	1.0000
K2PG	37	-970.2134	2014.4267	0.0000	1.0000
K2PI	37	-970.4833	2014.9666	0.0000	1.0000
K2PIG	38	-969.6936	2015.3872	0.0000	1.0000
F81	38	-971.9326	2019.8652	0.0000	1.0000
JC69G	36	-983.1358	2038.2716	0.0000	1.0000
JC69I	36	-983.4683	2038.9366	0.0000	1.0000
JC69IG	37	-982.7254	2039.4507	0.0000	1.0000
SYM	40	-980.3011	2040.6022	0.0000	1.0000
K2P	36	-987.2127	2046.4253	0.0000	1.0000
JC69	35	-998.8679	2067.7357	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-941.2430	2119.0261	0.5151	0.5151
HKYI	40	-941.6905	2119.9210	0.3293	0.8444
GTRG	44	-931.3209	2122.8359	0.0767	0.9211
HKYIG	41	-940.7677	2123.9890	0.0431	0.9642
GTRI	44	-932.3044	2124.8030	0.0287	0.9929
GTRIG	45	-930.7384	2127.5845	0.0071	1.0000
HKY	39	-956.6056	2143.8379	0.0000	1.0000
F81G	39	-956.9493	2144.5253	0.0000	1.0000
GTR	43	-945.2152	2144.7111	0.0000	1.0000
F81I	39	-957.3348	2145.2962	0.0000	1.0000
F81IG	40	-956.5654	2149.6710	0.0000	1.0000
K2PG	37	-970.2134	2159.2263	0.0000	1.0000
K2PI	37	-970.4833	2159.7662	0.0000	1.0000
K2PIG	38	-969.6936	2164.1003	0.0000	1.0000
F81	38	-971.9326	2168.5783	0.0000	1.0000
SYMG	41	-964.2962	2171.0460	0.0000	1.0000
SYMI	41	-964.7071	2171.8678	0.0000	1.0000
SYMIG	42	-963.6873	2175.7418	0.0000	1.0000
JC69G	36	-983.1358	2179.1577	0.0000	1.0000
JC69I	36	-983.4683	2179.8227	0.0000	1.0000
JC69IG	37	-982.7254	2184.2504	0.0000	1.0000
K2P	36	-987.2127	2187.3114	0.0000	1.0000
SYM	40	-980.3011	2197.1424	0.0000	1.0000
JC69	35	-998.8679	2204.7083	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/chr3_338.phylip = 1 - 370;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_338.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/chr3_338.phylip = 1 - 370;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_338.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/chr3_338.phylip = 1 - 370;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_338.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

