
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:49 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_25881.phylip" (19 taxa, 579 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	-1976.1450	4038.3867	0.9287	0.9287
GTRG	44	-1974.3484	4044.1126	0.0530	0.9818
HKYIG	41	-1979.0670	4046.5474	0.0157	0.9975
HKYI	40	-1982.4301	4050.9568	0.0017	0.9992
GTRIG	45	-1977.4743	4052.7160	0.0007	0.9999
GTRI	44	-1980.9236	4057.2629	0.0001	1.0000
K2PG	37	-1994.2757	4067.7491	0.0000	1.0000
K2PI	37	-1996.2081	4071.6140	0.0000	1.0000
SYMG	41	-1993.6838	4075.7809	0.0000	1.0000
K2PIG	38	-1998.1213	4077.7316	0.0000	1.0000
SYMI	41	-1995.5858	4079.5849	0.0000	1.0000
SYMIG	42	-1997.1982	4085.1352	0.0000	1.0000
HKY	39	-2016.2253	4116.2390	0.0000	1.0000
GTR	43	-2014.0850	4121.2429	0.0000	1.0000
F81G	39	-2020.5918	4124.9721	0.0000	1.0000
F81IG	40	-2019.9876	4126.0718	0.0000	1.0000
F81I	39	-2023.8111	4131.4106	0.0000	1.0000
JC69G	36	-2034.6766	4146.2683	0.0000	1.0000
JC69IG	37	-2035.9532	4151.1041	0.0000	1.0000
SYM	40	-2033.2442	4152.5851	0.0000	1.0000
JC69I	36	-2039.1973	4155.3097	0.0000	1.0000
K2P	36	-2039.4056	4155.7264	0.0000	1.0000
F81	38	-2058.0200	4197.5289	0.0000	1.0000
JC69	35	-2075.9954	4226.6318	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-1976.1450	4032.2900	0.8818	0.8818
GTRG	44	-1974.3484	4036.6968	0.0974	0.9792
HKYIG	41	-1979.0670	4040.1340	0.0175	0.9966
HKYI	40	-1982.4301	4044.8601	0.0016	0.9983
GTRIG	45	-1977.4743	4044.9486	0.0016	0.9999
GTRI	44	-1980.9236	4049.8472	0.0001	1.0000
K2PG	37	-1994.2757	4062.5513	0.0000	1.0000
K2PI	37	-1996.2081	4066.4162	0.0000	1.0000
SYMG	41	-1993.6838	4069.3675	0.0000	1.0000
K2PIG	38	-1998.1213	4072.2427	0.0000	1.0000
SYMI	41	-1995.5858	4073.1715	0.0000	1.0000
SYMIG	42	-1997.1982	4078.3964	0.0000	1.0000
HKY	39	-2016.2253	4110.4505	0.0000	1.0000
GTR	43	-2014.0850	4114.1700	0.0000	1.0000
F81G	39	-2020.5918	4119.1836	0.0000	1.0000
F81IG	40	-2019.9876	4119.9751	0.0000	1.0000
F81I	39	-2023.8111	4125.6221	0.0000	1.0000
JC69G	36	-2034.6766	4141.3532	0.0000	1.0000
JC69IG	37	-2035.9532	4145.9064	0.0000	1.0000
SYM	40	-2033.2442	4146.4884	0.0000	1.0000
JC69I	36	-2039.1973	4150.3946	0.0000	1.0000
K2P	36	-2039.4056	4150.8112	0.0000	1.0000
F81	38	-2058.0200	4192.0400	0.0000	1.0000
JC69	35	-2075.9954	4221.9909	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1976.1450	4206.7421	0.9957	0.9957
HKYIG	41	-1979.0670	4218.9474	0.0022	0.9979
HKYI	40	-1982.4301	4219.3122	0.0019	0.9998
K2PG	37	-1994.2757	4223.9195	0.0002	1.0000
K2PI	37	-1996.2081	4227.7844	0.0000	1.0000
GTRG	44	-1974.3484	4228.5941	0.0000	1.0000
K2PIG	38	-1998.1213	4237.9722	0.0000	1.0000
GTRIG	45	-1977.4743	4241.2072	0.0000	1.0000
GTRI	44	-1980.9236	4241.7445	0.0000	1.0000
SYMG	41	-1993.6838	4248.1809	0.0000	1.0000
SYMI	41	-1995.5858	4251.9849	0.0000	1.0000
SYMIG	42	-1997.1982	4261.5711	0.0000	1.0000
HKY	39	-2016.2253	4280.5413	0.0000	1.0000
F81G	39	-2020.5918	4289.2744	0.0000	1.0000
F81IG	40	-2019.9876	4294.4272	0.0000	1.0000
F81I	39	-2023.8111	4295.7129	0.0000	1.0000
JC69G	36	-2034.6766	4298.3600	0.0000	1.0000
GTR	43	-2014.0850	4301.7060	0.0000	1.0000
JC69IG	37	-2035.9532	4307.2746	0.0000	1.0000
JC69I	36	-2039.1973	4307.4014	0.0000	1.0000
K2P	36	-2039.4056	4307.8181	0.0000	1.0000
SYM	40	-2033.2442	4320.9405	0.0000	1.0000
F81	38	-2058.0200	4357.7695	0.0000	1.0000
JC69	35	-2075.9954	4374.6365	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/chr2_25881.phylip = 1 - 579;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_25881.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/chr2_25881.phylip = 1 - 579;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_25881.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/chr2_25881.phylip = 1 - 579;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_25881.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

