
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:18 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/chr5_1649.phylip" (19 taxa, 619 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	-1984.8653	4064.6295	0.6523	0.6523
GTRIG	45	-1984.6453	4066.5157	0.2540	0.9063
GTRI	44	-1986.8112	4068.5213	0.0932	0.9994
HKYG	40	-1997.0919	4079.8586	0.0003	0.9998
HKYIG	41	-1996.8673	4081.7034	0.0001	0.9999
HKYI	40	-1998.9140	4083.5028	0.0001	0.9999
SYMG	41	-1998.2099	4084.3885	0.0000	1.0000
SYMIG	42	-1998.0159	4086.3026	0.0000	1.0000
SYMI	41	-1999.9268	4087.8225	0.0000	1.0000
K2PG	37	-2006.9045	4092.6490	0.0000	1.0000
K2PIG	38	-2006.6645	4094.4394	0.0000	1.0000
K2PI	37	-2008.6539	4096.1477	0.0000	1.0000
GTR	43	-2006.8576	4106.2960	0.0000	1.0000
HKY	39	-2019.9487	4123.2860	0.0000	1.0000
SYM	40	-2020.6432	4126.9612	0.0000	1.0000
K2P	36	-2031.0713	4138.7199	0.0000	1.0000
F81G	39	-2055.4484	4194.2853	0.0000	1.0000
F81IG	40	-2055.2736	4196.2220	0.0000	1.0000
F81I	39	-2057.0018	4197.3922	0.0000	1.0000
JC69G	36	-2063.9079	4204.3931	0.0000	1.0000
JC69IG	37	-2063.7322	4206.3043	0.0000	1.0000
JC69I	36	-2065.5622	4207.7017	0.0000	1.0000
F81	38	-2077.4239	4235.9582	0.0000	1.0000
JC69	35	-2086.4389	4247.2002	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1984.8653	4057.7306	0.6243	0.6243
GTRIG	45	-1984.6453	4059.2906	0.2862	0.9105
GTRI	44	-1986.8112	4061.6224	0.0892	0.9997
HKYG	40	-1997.0919	4074.1838	0.0002	0.9999
HKYIG	41	-1996.8673	4075.7346	0.0001	0.9999
HKYI	40	-1998.9140	4077.8280	0.0000	1.0000
SYMG	41	-1998.2099	4078.4197	0.0000	1.0000
SYMIG	42	-1998.0159	4080.0317	0.0000	1.0000
SYMI	41	-1999.9268	4081.8537	0.0000	1.0000
K2PG	37	-2006.9045	4087.8091	0.0000	1.0000
K2PIG	38	-2006.6645	4089.3290	0.0000	1.0000
K2PI	37	-2008.6539	4091.3077	0.0000	1.0000
GTR	43	-2006.8576	4099.7151	0.0000	1.0000
HKY	39	-2019.9487	4117.8974	0.0000	1.0000
SYM	40	-2020.6432	4121.2864	0.0000	1.0000
K2P	36	-2031.0713	4134.1425	0.0000	1.0000
F81G	39	-2055.4484	4188.8967	0.0000	1.0000
F81IG	40	-2055.2736	4190.5473	0.0000	1.0000
F81I	39	-2057.0018	4192.0036	0.0000	1.0000
JC69G	36	-2063.9079	4199.8158	0.0000	1.0000
JC69IG	37	-2063.7322	4201.4643	0.0000	1.0000
JC69I	36	-2065.5622	4203.1244	0.0000	1.0000
F81	38	-2077.4239	4230.8479	0.0000	1.0000
JC69	35	-2086.4389	4242.8777	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1997.0919	4251.3081	0.3452	0.3452
K2PG	37	-2006.9045	4251.6490	0.2911	0.6363
GTRG	44	-1984.8653	4252.5672	0.1839	0.8203
HKYI	40	-1998.9140	4254.9523	0.0558	0.8761
K2PI	37	-2008.6539	4255.1476	0.0506	0.9267
GTRI	44	-1986.8112	4256.4590	0.0263	0.9530
HKYIG	41	-1996.8673	4257.2869	0.0174	0.9703
K2PIG	38	-2006.6645	4257.5970	0.0149	0.9852
GTRIG	45	-1984.6453	4258.5553	0.0092	0.9944
SYMG	41	-1998.2099	4259.9721	0.0045	0.9990
SYMI	41	-1999.9268	4263.4060	0.0008	0.9998
SYMIG	42	-1998.0159	4266.0122	0.0002	1.0000
GTR	43	-2006.8576	4290.1236	0.0000	1.0000
HKY	39	-2019.9487	4290.5935	0.0000	1.0000
K2P	36	-2031.0713	4293.5543	0.0000	1.0000
SYM	40	-2020.6432	4298.4107	0.0000	1.0000
JC69G	36	-2063.9079	4359.2276	0.0000	1.0000
F81G	39	-2055.4484	4361.5928	0.0000	1.0000
JC69I	36	-2065.5622	4362.5362	0.0000	1.0000
F81I	39	-2057.0018	4364.6997	0.0000	1.0000
JC69IG	37	-2063.7322	4365.3042	0.0000	1.0000
F81IG	40	-2055.2736	4367.6715	0.0000	1.0000
JC69	35	-2086.4389	4397.8614	0.0000	1.0000
F81	38	-2077.4239	4399.1159	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/chr5_1649.phylip = 1 - 619;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_1649.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/chr5_1649.phylip = 1 - 619;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_1649.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/chr5_1649.phylip = 1 - 619;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_1649.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

