
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
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_17883.phylip" (19 taxa, 761 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	-1974.8681	4043.2670	0.4120	0.4120
GTRIG	45	-1974.0635	4043.9171	0.2977	0.7097
GTRI	44	-1976.0703	4045.6713	0.1238	0.8335
HKYG	40	-1980.9591	4046.4738	0.0829	0.9164
HKYIG	41	-1980.2387	4047.2674	0.0557	0.9722
HKYI	40	-1982.0611	4048.6778	0.0275	0.9997
K2PG	37	-1990.9720	4059.8333	0.0001	0.9998
K2PIG	38	-1990.2531	4060.6114	0.0001	0.9999
SYMG	41	-1987.4742	4061.7385	0.0000	0.9999
K2PI	37	-1992.0088	4061.9070	0.0000	1.0000
SYMIG	42	-1986.7215	4062.4736	0.0000	1.0000
SYMI	41	-1988.5519	4063.8938	0.0000	1.0000
GTR	43	-1996.2353	4083.7481	0.0000	1.0000
HKY	39	-2001.6138	4085.5550	0.0000	1.0000
K2P	36	-2011.8691	4099.4177	0.0000	1.0000
F81G	39	-2009.4242	4101.1758	0.0000	1.0000
SYM	40	-2008.5720	4101.6995	0.0000	1.0000
F81IG	40	-2008.7220	4101.9996	0.0000	1.0000
F81I	39	-2010.5115	4103.3503	0.0000	1.0000
JC69G	36	-2018.5383	4112.7562	0.0000	1.0000
JC69IG	37	-2017.8312	4113.5518	0.0000	1.0000
JC69I	36	-2019.6173	4114.9141	0.0000	1.0000
F81	38	-2029.7563	4139.6178	0.0000	1.0000
JC69	35	-2039.0033	4151.4825	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1974.8681	4037.7363	0.4199	0.4199
GTRIG	45	-1974.0635	4038.1269	0.3454	0.7653
GTRI	44	-1976.0703	4040.1406	0.1262	0.8915
HKYG	40	-1980.9591	4041.9182	0.0519	0.9434
HKYIG	41	-1980.2387	4042.4774	0.0392	0.9826
HKYI	40	-1982.0611	4044.1222	0.0172	0.9998
K2PG	37	-1990.9720	4055.9440	0.0000	0.9999
K2PIG	38	-1990.2531	4056.5061	0.0000	0.9999
SYMG	41	-1987.4742	4056.9485	0.0000	1.0000
SYMIG	42	-1986.7215	4057.4430	0.0000	1.0000
K2PI	37	-1992.0088	4058.0176	0.0000	1.0000
SYMI	41	-1988.5519	4059.1039	0.0000	1.0000
GTR	43	-1996.2353	4078.4705	0.0000	1.0000
HKY	39	-2001.6138	4081.2276	0.0000	1.0000
K2P	36	-2011.8691	4095.7381	0.0000	1.0000
F81G	39	-2009.4242	4096.8485	0.0000	1.0000
SYM	40	-2008.5720	4097.1439	0.0000	1.0000
F81IG	40	-2008.7220	4097.4441	0.0000	1.0000
F81I	39	-2010.5115	4099.0229	0.0000	1.0000
JC69G	36	-2018.5383	4109.0767	0.0000	1.0000
JC69IG	37	-2017.8312	4109.6625	0.0000	1.0000
JC69I	36	-2019.6173	4111.2345	0.0000	1.0000
F81	38	-2029.7563	4135.5125	0.0000	1.0000
JC69	35	-2039.0033	4148.0066	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1980.9591	4227.3035	0.3633	0.3633
K2PG	37	-1990.9720	4227.4254	0.3419	0.7052
K2PI	37	-1992.0088	4229.4991	0.1212	0.8264
HKYI	40	-1982.0611	4229.5076	0.1207	0.9471
HKYIG	41	-1980.2387	4232.4973	0.0271	0.9742
K2PIG	38	-1990.2531	4232.6222	0.0254	0.9996
GTRG	44	-1974.8681	4241.6601	0.0003	0.9999
GTRI	44	-1976.0703	4244.0644	0.0001	0.9999
GTRIG	45	-1974.0635	4246.6854	0.0000	1.0000
SYMG	41	-1987.4742	4246.9684	0.0000	1.0000
SYMI	41	-1988.5519	4249.1238	0.0000	1.0000
SYMIG	42	-1986.7215	4252.0976	0.0000	1.0000
HKY	39	-2001.6138	4261.9783	0.0000	1.0000
K2P	36	-2011.8691	4262.5849	0.0000	1.0000
JC69G	36	-2018.5383	4275.9235	0.0000	1.0000
F81G	39	-2009.4242	4277.5992	0.0000	1.0000
GTR	43	-1996.2353	4277.7598	0.0000	1.0000
JC69I	36	-2019.6173	4278.0813	0.0000	1.0000
F81I	39	-2010.5115	4279.7736	0.0000	1.0000
JC69IG	37	-2017.8312	4281.1439	0.0000	1.0000
SYM	40	-2008.5720	4282.5292	0.0000	1.0000
F81IG	40	-2008.7220	4282.8294	0.0000	1.0000
JC69	35	-2039.0033	4310.2188	0.0000	1.0000
F81	38	-2029.7563	4311.6286	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_17883.phylip = 1 - 761;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_17883.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_17883.phylip = 1 - 761;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_17883.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_17883.phylip = 1 - 761;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_17883.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

