
Output from mraic.pl version 1.4.4 by Johan Nylander
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13:11 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/chrUn_random_9893.phylip" (19 taxa, 600 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	-1995.5099	4086.1550	0.3815	0.3815
GTRI	44	-1995.6393	4086.4137	0.3352	0.7167
GTRIG	45	-1995.5099	4088.4928	0.1185	0.8353
HKYG	40	-2001.6748	4089.2173	0.0825	0.9178
HKYI	40	-2002.0603	4089.9882	0.0561	0.9739
HKYIG	41	-2001.6748	4091.5216	0.0261	1.0000
K2PG	37	-2031.6499	4142.3033	0.0000	1.0000
K2PI	37	-2032.2292	4143.4620	0.0000	1.0000
K2PIG	38	-2031.6525	4144.5884	0.0000	1.0000
SYMG	41	-2028.8023	4145.7767	0.0000	1.0000
SYMI	41	-2029.2140	4146.6001	0.0000	1.0000
SYMIG	42	-2028.8088	4148.1023	0.0000	1.0000
GTR	43	-2031.0149	4154.8355	0.0000	1.0000
HKY	39	-2035.9326	4155.4366	0.0000	1.0000
F81G	39	-2053.7354	4191.0422	0.0000	1.0000
F81I	39	-2053.9263	4191.4240	0.0000	1.0000
F81IG	40	-2053.7354	4193.3384	0.0000	1.0000
K2P	36	-2063.2962	4203.3241	0.0000	1.0000
SYM	40	-2060.0086	4205.8849	0.0000	1.0000
JC69G	36	-2076.1949	4229.1216	0.0000	1.0000
JC69I	36	-2076.2757	4229.2833	0.0000	1.0000
JC69IG	37	-2079.5980	4238.1995	0.0000	1.0000
F81	38	-2084.4544	4250.1923	0.0000	1.0000
JC69	35	-2105.7355	4285.9390	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1995.5099	4079.0199	0.4030	0.4030
GTRI	44	-1995.6393	4079.2786	0.3541	0.7570
GTRIG	45	-1995.5099	4081.0199	0.1482	0.9053
HKYG	40	-2001.6748	4083.3496	0.0462	0.9515
HKYI	40	-2002.0603	4084.1205	0.0315	0.9830
HKYIG	41	-2001.6748	4085.3496	0.0170	1.0000
K2PG	37	-2031.6499	4137.2997	0.0000	1.0000
K2PI	37	-2032.2292	4138.4584	0.0000	1.0000
K2PIG	38	-2031.6525	4139.3049	0.0000	1.0000
SYMG	41	-2028.8023	4139.6047	0.0000	1.0000
SYMI	41	-2029.2140	4140.4281	0.0000	1.0000
SYMIG	42	-2028.8088	4141.6176	0.0000	1.0000
GTR	43	-2031.0149	4148.0297	0.0000	1.0000
HKY	39	-2035.9326	4149.8652	0.0000	1.0000
F81G	39	-2053.7354	4185.4708	0.0000	1.0000
F81I	39	-2053.9263	4185.8526	0.0000	1.0000
F81IG	40	-2053.7354	4187.4708	0.0000	1.0000
K2P	36	-2063.2962	4198.5923	0.0000	1.0000
SYM	40	-2060.0086	4200.0173	0.0000	1.0000
JC69G	36	-2076.1949	4224.3898	0.0000	1.0000
JC69I	36	-2076.2757	4224.5515	0.0000	1.0000
JC69IG	37	-2079.5980	4233.1960	0.0000	1.0000
F81	38	-2084.4544	4244.9088	0.0000	1.0000
JC69	35	-2105.7355	4281.4709	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2001.6748	4259.2268	0.5802	0.5802
HKYI	40	-2002.0603	4259.9977	0.3946	0.9748
HKYIG	41	-2001.6748	4265.6237	0.0237	0.9985
GTRG	44	-1995.5099	4272.4848	0.0008	0.9993
GTRI	44	-1995.6393	4272.7435	0.0007	1.0000
GTRIG	45	-1995.5099	4278.8817	0.0000	1.0000
K2PG	37	-2031.6499	4299.9861	0.0000	1.0000
K2PI	37	-2032.2292	4301.1448	0.0000	1.0000
K2PIG	38	-2031.6525	4306.3883	0.0000	1.0000
SYMG	41	-2028.8023	4319.8788	0.0000	1.0000
SYMI	41	-2029.2140	4320.7022	0.0000	1.0000
HKY	39	-2035.9326	4321.3454	0.0000	1.0000
SYMIG	42	-2028.8088	4326.2886	0.0000	1.0000
GTR	43	-2031.0149	4337.0977	0.0000	1.0000
K2P	36	-2063.2962	4356.8818	0.0000	1.0000
F81G	39	-2053.7354	4356.9510	0.0000	1.0000
F81I	39	-2053.9263	4357.3328	0.0000	1.0000
F81IG	40	-2053.7354	4363.3480	0.0000	1.0000
SYM	40	-2060.0086	4375.8944	0.0000	1.0000
JC69G	36	-2076.1949	4382.6793	0.0000	1.0000
JC69I	36	-2076.2757	4382.8410	0.0000	1.0000
JC69IG	37	-2079.5980	4395.8824	0.0000	1.0000
F81	38	-2084.4544	4411.9922	0.0000	1.0000
JC69	35	-2105.7355	4435.3635	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/chrUn_random_9893.phylip = 1 - 600;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrUn_random_9893.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/chrUn_random_9893.phylip = 1 - 600;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrUn_random_9893.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/chrUn_random_9893.phylip = 1 - 600;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrUn_random_9893.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

