
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:26 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/chr4_4009.phylip" (19 taxa, 590 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	-1980.6553	4056.5767	0.7394	0.7394
GTRIG	45	-1980.6414	4058.8931	0.2322	0.9716
GTRI	44	-1984.4626	4064.1913	0.0164	0.9881
HKYG	40	-1989.7649	4065.5043	0.0085	0.9966
HKYIG	41	-1989.7251	4067.7350	0.0028	0.9994
HKYI	40	-1992.3548	4070.6842	0.0006	1.0000
GTR	43	-2002.0479	4097.0261	0.0000	1.0000
HKY	39	-2010.5130	4104.6987	0.0000	1.0000
K2PG	37	-2014.8793	4108.8528	0.0000	1.0000
K2PIG	38	-2014.7833	4110.9460	0.0000	1.0000
SYMG	41	-2012.3521	4112.9889	0.0000	1.0000
K2PI	37	-2017.7127	4114.5196	0.0000	1.0000
SYMIG	42	-2013.7344	4118.0721	0.0000	1.0000
SYMI	41	-2015.9832	4120.2511	0.0000	1.0000
F81IG	40	-2019.4899	4124.9542	0.0000	1.0000
F81I	39	-2021.4393	4126.5513	0.0000	1.0000
F81G	39	-2021.7473	4127.1673	0.0000	1.0000
K2P	36	-2035.2515	4147.3204	0.0000	1.0000
SYM	40	-2031.8474	4149.6693	0.0000	1.0000
JC69IG	37	-2040.6696	4160.4334	0.0000	1.0000
JC69I	36	-2042.0221	4160.8616	0.0000	1.0000
JC69G	36	-2042.4347	4161.6867	0.0000	1.0000
F81	38	-2040.5312	4162.4416	0.0000	1.0000
JC69	35	-2061.2373	4197.0233	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1980.6553	4049.3106	0.7122	0.7122
GTRIG	45	-1980.6414	4051.2828	0.2657	0.9779
GTRI	44	-1984.4626	4056.9253	0.0158	0.9937
HKYG	40	-1989.7649	4059.5298	0.0043	0.9980
HKYIG	41	-1989.7251	4061.4503	0.0016	0.9997
HKYI	40	-1992.3548	4064.7097	0.0003	1.0000
GTR	43	-2002.0479	4090.0957	0.0000	1.0000
HKY	39	-2010.5130	4099.0260	0.0000	1.0000
K2PG	37	-2014.8793	4103.7586	0.0000	1.0000
K2PIG	38	-2014.7833	4105.5666	0.0000	1.0000
SYMG	41	-2012.3521	4106.7042	0.0000	1.0000
K2PI	37	-2017.7127	4109.4254	0.0000	1.0000
SYMIG	42	-2013.7344	4111.4688	0.0000	1.0000
SYMI	41	-2015.9832	4113.9665	0.0000	1.0000
F81IG	40	-2019.4899	4118.9797	0.0000	1.0000
F81I	39	-2021.4393	4120.8785	0.0000	1.0000
F81G	39	-2021.7473	4121.4946	0.0000	1.0000
K2P	36	-2035.2515	4142.5031	0.0000	1.0000
SYM	40	-2031.8474	4143.6948	0.0000	1.0000
JC69IG	37	-2040.6696	4155.3392	0.0000	1.0000
JC69I	36	-2042.0221	4156.0442	0.0000	1.0000
JC69G	36	-2042.4347	4156.8693	0.0000	1.0000
F81	38	-2040.5312	4157.0623	0.0000	1.0000
JC69	35	-2061.2373	4192.4746	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1989.7649	4234.7347	0.8730	0.8730
HKYI	40	-1992.3548	4239.9146	0.0655	0.9385
HKYIG	41	-1989.7251	4241.0353	0.0374	0.9759
GTRG	44	-1980.6553	4242.0360	0.0227	0.9985
GTRIG	45	-1980.6414	4248.3883	0.0009	0.9995
GTRI	44	-1984.4626	4249.6507	0.0005	1.0000
K2PG	37	-2014.8793	4265.8231	0.0000	1.0000
HKY	39	-2010.5130	4269.8508	0.0000	1.0000
K2PI	37	-2017.7127	4271.4899	0.0000	1.0000
K2PIG	38	-2014.7833	4272.0113	0.0000	1.0000
GTR	43	-2002.0479	4278.4410	0.0000	1.0000
SYMG	41	-2012.3521	4286.2893	0.0000	1.0000
F81I	39	-2021.4393	4291.7033	0.0000	1.0000
F81G	39	-2021.7473	4292.3194	0.0000	1.0000
SYMI	41	-2015.9832	4293.5515	0.0000	1.0000
F81IG	40	-2019.4899	4294.1846	0.0000	1.0000
SYMIG	42	-2013.7344	4295.4339	0.0000	1.0000
K2P	36	-2035.2515	4300.1875	0.0000	1.0000
JC69I	36	-2042.0221	4313.7286	0.0000	1.0000
JC69G	36	-2042.4347	4314.5537	0.0000	1.0000
JC69IG	37	-2040.6696	4317.4037	0.0000	1.0000
SYM	40	-2031.8474	4318.8997	0.0000	1.0000
F81	38	-2040.5312	4323.5070	0.0000	1.0000
JC69	35	-2061.2373	4345.7788	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/chr4_4009.phylip = 1 - 590;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_4009.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/chr4_4009.phylip = 1 - 590;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_4009.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/chr4_4009.phylip = 1 - 590;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_4009.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

