
Output from mraic.pl version 1.4.4 by Johan Nylander
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13:18 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/chr7_5163.phylip" (19 taxa, 831 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	-2076.5161	4246.0704	0.5129	0.5129
GTRIG	45	-2076.3146	4247.9030	0.2052	0.7180
GTRI	44	-2078.0269	4249.0921	0.1132	0.8313
HKYG	40	-2082.6043	4249.3604	0.0990	0.9302
HKYIG	41	-2082.3264	4251.0178	0.0432	0.9735
HKYI	40	-2083.9334	4252.0188	0.0262	0.9997
GTR	43	-2085.1686	4261.1453	0.0003	0.9999
HKY	39	-2091.2417	4264.4277	0.0001	1.0000
SYMG	41	-2101.3223	4289.0097	0.0000	1.0000
K2PG	37	-2105.9516	4289.4492	0.0000	1.0000
SYMI	41	-2102.2528	4290.8706	0.0000	1.0000
K2PI	37	-2106.7221	4290.9903	0.0000	1.0000
F81G	39	-2105.3619	4292.6683	0.0000	1.0000
SYMIG	42	-2102.6074	4293.7987	0.0000	1.0000
F81IG	40	-2105.0949	4294.3416	0.0000	1.0000
K2PIG	38	-2107.5138	4294.7699	0.0000	1.0000
F81I	39	-2106.6381	4295.2206	0.0000	1.0000
F81	38	-2111.4844	4302.7113	0.0000	1.0000
SYM	40	-2111.5191	4307.1901	0.0000	1.0000
K2P	36	-2116.6016	4308.5584	0.0000	1.0000
JC69G	36	-2123.6116	4322.5783	0.0000	1.0000
JC69I	36	-2124.3519	4324.0590	0.0000	1.0000
JC69IG	37	-2123.5019	4324.5499	0.0000	1.0000
JC69	35	-2134.0948	4341.3594	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2076.5161	4241.0323	0.5296	0.5296
GTRIG	45	-2076.3146	4242.6291	0.2383	0.7679
GTRI	44	-2078.0269	4244.0539	0.1169	0.8848
HKYG	40	-2082.6043	4245.2085	0.0656	0.9505
HKYIG	41	-2082.3264	4246.6527	0.0319	0.9823
HKYI	40	-2083.9334	4247.8669	0.0174	0.9997
GTR	43	-2085.1686	4256.3372	0.0003	1.0000
HKY	39	-2091.2417	4260.4833	0.0000	1.0000
SYMG	41	-2101.3223	4284.6446	0.0000	1.0000
K2PG	37	-2105.9516	4285.9032	0.0000	1.0000
SYMI	41	-2102.2528	4286.5056	0.0000	1.0000
K2PI	37	-2106.7221	4287.4443	0.0000	1.0000
F81G	39	-2105.3619	4288.7239	0.0000	1.0000
SYMIG	42	-2102.6074	4289.2149	0.0000	1.0000
F81IG	40	-2105.0949	4290.1897	0.0000	1.0000
K2PIG	38	-2107.5138	4291.0275	0.0000	1.0000
F81I	39	-2106.6381	4291.2762	0.0000	1.0000
F81	38	-2111.4844	4298.9688	0.0000	1.0000
SYM	40	-2111.5191	4303.0382	0.0000	1.0000
K2P	36	-2116.6016	4305.2033	0.0000	1.0000
JC69G	36	-2123.6116	4319.2231	0.0000	1.0000
JC69I	36	-2124.3519	4320.7039	0.0000	1.0000
JC69IG	37	-2123.5019	4321.0039	0.0000	1.0000
JC69	35	-2134.0948	4338.1896	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2082.6043	4434.1137	0.7596	0.7596
HKYI	40	-2083.9334	4436.7721	0.2011	0.9607
HKYIG	41	-2082.3264	4440.2806	0.0348	0.9955
HKY	39	-2091.2417	4444.6659	0.0039	0.9994
GTRG	44	-2076.5161	4448.8280	0.0005	0.9999
GTRI	44	-2078.0269	4451.8496	0.0001	1.0000
GTRIG	45	-2076.3146	4455.1475	0.0000	1.0000
GTR	43	-2085.1686	4459.4103	0.0000	1.0000
K2PG	37	-2105.9516	4460.6405	0.0000	1.0000
K2PI	37	-2106.7221	4462.1816	0.0000	1.0000
K2PIG	38	-2107.5138	4470.4874	0.0000	1.0000
F81G	39	-2105.3619	4472.9065	0.0000	1.0000
K2P	36	-2116.6016	4475.2180	0.0000	1.0000
F81I	39	-2106.6381	4475.4588	0.0000	1.0000
SYMG	41	-2101.3223	4478.2725	0.0000	1.0000
F81	38	-2111.4844	4478.4288	0.0000	1.0000
F81IG	40	-2105.0949	4479.0949	0.0000	1.0000
SYMI	41	-2102.2528	4480.1334	0.0000	1.0000
SYMIG	42	-2102.6074	4487.5654	0.0000	1.0000
JC69G	36	-2123.6116	4489.2378	0.0000	1.0000
JC69I	36	-2124.3519	4490.7185	0.0000	1.0000
SYM	40	-2111.5191	4491.9434	0.0000	1.0000
JC69IG	37	-2123.5019	4495.7412	0.0000	1.0000
JC69	35	-2134.0948	4503.4816	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/chr7_5163.phylip = 1 - 831;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_5163.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/chr7_5163.phylip = 1 - 831;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_5163.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/chr7_5163.phylip = 1 - 831;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_5163.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

