
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:29 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/chr6_7862.phylip" (19 taxa, 869 characters)

Minimum AIC  model: HKYI
Minimum AICc model: HKYI
Minimum BIC  model: HKYI


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
HKYI	40	-2063.2276	4210.4167	0.4414	0.4414
HKYG	40	-2063.5662	4211.0938	0.3146	0.7559
HKYIG	41	-2063.5662	4213.2967	0.1046	0.8605
GTRI	44	-2060.6390	4214.0839	0.0705	0.9311
GTRG	44	-2060.9462	4214.6982	0.0519	0.9829
GTRIG	45	-2060.9462	4216.9228	0.0171	1.0000
F81I	39	-2078.6233	4239.0102	0.0000	1.0000
F81G	39	-2078.8692	4239.5020	0.0000	1.0000
HKY	39	-2079.8339	4241.4314	0.0000	1.0000
F81IG	40	-2078.8691	4241.6996	0.0000	1.0000
GTR	43	-2077.5776	4245.7418	0.0000	1.0000
K2PI	37	-2086.0673	4249.5184	0.0000	1.0000
K2PG	37	-2086.4252	4250.2343	0.0000	1.0000
K2PIG	38	-2086.4252	4252.4215	0.0000	1.0000
SYMI	41	-2083.5334	4253.2312	0.0000	1.0000
SYMG	41	-2083.9116	4253.9877	0.0000	1.0000
SYMIG	42	-2083.9116	4256.1961	0.0000	1.0000
F81	38	-2094.5128	4268.5967	0.0000	1.0000
JC69I	36	-2099.6870	4274.5760	0.0000	1.0000
JC69G	36	-2099.9529	4275.1078	0.0000	1.0000
JC69IG	37	-2099.9529	4277.2896	0.0000	1.0000
K2P	36	-2102.1628	4279.5275	0.0000	1.0000
SYM	40	-2099.6008	4283.1629	0.0000	1.0000
JC69	35	-2115.4976	4304.0205	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYI	40	-2063.2276	4206.4553	0.4058	0.4058
HKYG	40	-2063.5662	4207.1324	0.2893	0.6951
HKYIG	41	-2063.5662	4209.1323	0.1064	0.8015
GTRI	44	-2060.6390	4209.2781	0.0989	0.9005
GTRG	44	-2060.9462	4209.8924	0.0728	0.9732
GTRIG	45	-2060.9462	4211.8924	0.0268	1.0000
F81I	39	-2078.6233	4235.2466	0.0000	1.0000
F81G	39	-2078.8692	4235.7384	0.0000	1.0000
HKY	39	-2079.8339	4237.6678	0.0000	1.0000
F81IG	40	-2078.8691	4237.7382	0.0000	1.0000
GTR	43	-2077.5776	4241.1552	0.0000	1.0000
K2PI	37	-2086.0673	4246.1346	0.0000	1.0000
K2PG	37	-2086.4252	4246.8504	0.0000	1.0000
K2PIG	38	-2086.4252	4248.8504	0.0000	1.0000
SYMI	41	-2083.5334	4249.0668	0.0000	1.0000
SYMG	41	-2083.9116	4249.8232	0.0000	1.0000
SYMIG	42	-2083.9116	4251.8232	0.0000	1.0000
F81	38	-2094.5128	4265.0257	0.0000	1.0000
JC69I	36	-2099.6870	4271.3741	0.0000	1.0000
JC69G	36	-2099.9529	4271.9058	0.0000	1.0000
JC69IG	37	-2099.9529	4273.9058	0.0000	1.0000
K2P	36	-2102.1628	4276.3256	0.0000	1.0000
SYM	40	-2099.6008	4279.2016	0.0000	1.0000
JC69	35	-2115.4976	4300.9953	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYI	40	-2063.2276	4397.1490	0.5757	0.5757
HKYG	40	-2063.5662	4397.8262	0.4104	0.9861
HKYIG	41	-2063.5662	4404.5934	0.0139	1.0000
GTRI	44	-2060.6390	4419.0412	0.0000	1.0000
GTRG	44	-2060.9462	4419.6555	0.0000	1.0000
F81I	39	-2078.6233	4421.1730	0.0000	1.0000
F81G	39	-2078.8692	4421.6648	0.0000	1.0000
K2PI	37	-2086.0673	4422.5263	0.0000	1.0000
K2PG	37	-2086.4252	4423.2421	0.0000	1.0000
HKY	39	-2079.8339	4423.5942	0.0000	1.0000
GTRIG	45	-2060.9462	4426.4228	0.0000	1.0000
F81IG	40	-2078.8691	4428.4320	0.0000	1.0000
K2PIG	38	-2086.4252	4430.0095	0.0000	1.0000
JC69I	36	-2099.6870	4442.9984	0.0000	1.0000
JC69G	36	-2099.9529	4443.5302	0.0000	1.0000
SYMI	41	-2083.5334	4444.5278	0.0000	1.0000
SYMG	41	-2083.9116	4445.2843	0.0000	1.0000
GTR	43	-2077.5776	4446.1509	0.0000	1.0000
F81	38	-2094.5128	4446.1847	0.0000	1.0000
K2P	36	-2102.1628	4447.9500	0.0000	1.0000
JC69IG	37	-2099.9529	4450.2975	0.0000	1.0000
SYMIG	42	-2083.9116	4452.0516	0.0000	1.0000
JC69	35	-2115.4976	4467.8523	0.0000	1.0000
SYM	40	-2099.6008	4469.8953	0.0000	1.0000



To specify default values for best AIC, AICc, or BIC models in MrBayes:

[Mrbayes block for the best AIC model (HKYI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_7862.phylip = 1 - 869;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_7862.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=propinv;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best AICc model (HKYI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_7862.phylip = 1 - 869;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_7862.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=propinv;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best BIC model (HKYI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_7862.phylip = 1 - 869;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_7862.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=propinv;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0) pinvarpr=Uniform(0.0,1.0);
END;


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End of Output

