| References |
|
|
Abascal F,
Zardoya R and
Posada D
(2005)
ProtTest: selection of best‐fit models of protein evolution.
Bioinformatics
21:
2104–2105.
|
|
|
Abdo Z,
Minin VN,
Joyce P and
Sullivan J
(2005)
Accounting for uncertainty in the tree topology has little effect on the decision‐theoretic approach to model selection in phylogeny estimation.
Molecular Biology and Evolution
22:
691–703.
|
|
|
book
Akaike H
(1973)
"Information theory and an extension of the maximum likelihood principle".
In: Petrov BN and
Csaki F (eds)
Second International Symposium on Information Theory,
pp. 267–281.
Budapest: Akademiai Kiado.
|
|
|
Arbiza L,
Patricio M,
Dopazo H and
Posada D
(2011)
Genome‐wide heterogeneity of nucleotide substitution model fit.
Genome Biology and Evolution
3:
896–908.
|
|
|
Box GEP
(1976)
Science and statistics.
Journal of the American Statistical Association
71:
791–799.
|
|
|
Buckley TR and
Cunningham CW
(2002)
The effects of nucleotide substitution model assumptions on estimates of nonparametric bootstrap support.
Molecular Biology and Evolution
19:
394–405.
|
|
|
book
Cannarozzi GM and
Schneider A (eds)
(2012)
Codon Evolution: Mechanisms and Models.
Oxford, UK: Oxford University Press.
|
|
|
Darriba D,
Taboada GL,
Doallo R and
Posada D
(2011)
ProtTest 3: fast selection of best‐fit models of protein evolution.
Bioinformatics
27:
1164–1165.
|
|
|
book
Edwards AWF
(1972)
Likelihood.
Cambridge, UK: Cambridge University Press.
|
|
|
Fan Y,
Wu R,
Chen M‐H,
Kuo L and
Lewis PO
(2011)
Choosing among partition models in Bayesian phylogenetics.
Molecular Biology and Evolution
28:
523–532.
|
|
|
Felsenstein J
(1981)
Evolutionary trees from DNA sequences: a maximum likelihood approach.
Journal of Molecular Evolution
17:
368–376.
|
|
|
Frati F,
Simon C,
Sullivan J and
Swofford DL
(1997)
Evolution of the mitochondrial cytochrome oxidase II gene in Collembola.
Journal of Molecular Evolution
44:
145–158.
|
|
|
Goldman N
(1993)
Statistical tests of models of DNA substitution.
Journal of Molecular Evolution
36:
182–198.
|
|
|
Hasegawa M,
Kishino K and
Yano T
(1985)
Dating the human‐ape splitting by a molecular clock of mitochondrial DNA.
Journal of Molecular Evolution
22:
160–174.
|
|
|
Huelsenbeck JP and
Crandall KA
(1997)
Phylogeny estimation and hypothesis testing using maximum likelihood.
Annual Review of Ecology and Systematics
28:
437–466.
|
|
|
Huelsenbeck JP,
Larget B and
Alfaro ME
(2004)
Bayesian phylogenetic model selection using reversible jump Markov Chain Monte Carlo.
Molecular Biology and Evolution
21:
1123–1133.
|
|
|
book
Jukes TH and
Cantor CR
(1969)
"Evolution of protein molecules".
In: Munro HM (ed.)
Mammalian Protein Metabolism.
pp. 21–132.
New York: Academic Press.
|
|
|
Keane TM,
Creevey CJ,
Pentony MM,
Naughton TJ and
Mclnerney JO
(2006)
Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified.
BMC Evolutionary Biology
6:
29.
|
|
|
Kedzierska AM,
Drton M,
Guigó R and
Casanellas M
(2012)
SPIn: model selection for phylogenetic mixtures via linear invariants.
Molecular Biology and Evolution
29:
929–937.
|
|
|
Kelsey CR,
Crandall KA and
Voevodin AF
(1999)
Different models, different trees: the geographic origin of PTLV‐I.
Molecular Phylogenetics and Evolution
13:
336–347.
|
|
|
book
Kendall M and
Stuart A
(1979)
The Advanced Theory of Statistics.
London: Charles Griffin.
|
|
|
Kosakovsky Pond SL and
Frost SD
(2005)
Datamonkey: rapid detection of selective pressure on individual sites of codon alignments.
Bioinformatics
21:
2531–2533.
|
|
|
Kosakovsky Pond SL,
Frost SD and
Muse SV
(2005)
HYPHY: hypothesis testing using phylogenies.
Bioinformatics
21:
676–679.
|
|
|
Lemmon AR and
Moriarty EC
(2004)
The importance of proper model assumption in Bayesian phylogenetics.
Systematic Biology
53:
265–277.
|
|
|
Luo A,
Qiao H and
Zhang Y
(2010)
Performance of criteria for selecting evolutionary models in phylogenetics: a comprehensive study based on simulated datasets.
BMC Evolutionary Biology
10:
242.
|
|
|
Minin V,
Abdo Z,
Joyce P and
Sullivan J
(2003)
Performance‐based selection of likelihood models for phylogeny estimation.
Systematic Biology
52:
674–683.
|
|
|
Posada D
(2001)
The effect of branch length variation on the selection of models of molecular evolution.
Journal of Molecular Evolution
52:
434–444.
|
|
|
Posada D
(2006)
ModelTest Server: a web‐based tool for the statistical selection of models of nucleotide substitution online.
Nucleic Acids Research
34:
W700–W703.
|
|
|
Posada D
(2008)
jModelTest: phylogenetic model averaging.
Molecular Biology and Evolution
25:
1253–1256.
|
|
|
Posada D and
Buckley TR
(2004)
Model selection and model averaging in phylogenetics: advantages of akaike information criterion and bayesian approaches over likelihood ratio tests.
Systematic Biology
53:
793–808.
|
|
|
Posada D and
Crandall KA
(1998)
MODELTEST: testing the model of DNA substitution.
Bioinformatics
14:
817–818.
|
|
|
Posada D and
Crandall KA
(2001a)
Selecting models of nucleotide substitution: an application to human immunodeficiency virus 1 (HIV‐1).
Molecular Biology and Evolution
18:
897–906.
|
|
|
Posada D and
Crandall KA
(2001b)
Selecting the best‐fit model of nucleotide substitution.
Systematic Biology
50:
580–601.
|
|
|
Posada D and
Crandall KA
(2001c)
Simple (wrong) models for complex trees: a case from retroviridae.
Molecular Biology and Evolution
18:
271–275.
|
|
|
Pupko T,
Huchon D,
Cao Y,
Okada N and
Hasegawa M
(2002)
Combining multiple data sets in a likelihood analysis: which models are the best?
Molecular Biology and Evolution
19:
2294–2307.
|
|
|
Ripplinger J and
Sullivan J
(2008)
Does choice in model selection affect maximum likelihood analysis?
Systematic Biology
57:
76–85.
|
|
|
Rodrigue N,
Lartillot N and
Philippe H
(2008)
Bayesian comparisons of codon substitution models.
Genetics
180:
1579–1591.
|
|
|
Schwarz G
(1978)
Estimating the dimension of a model.
The Annals of Statistics
6:
461–464.
|
|
|
Suchard MA,
Weiss RE and
Sinsheimer JS
(2001)
Bayesian selection of continuous‐time Markov chain evolutionary models.
Molecular Biology and Evolution
18:
1001–1013.
|
|
|
Sullivan J and
Joyce P
(2005)
Model selection in phylogenetics.
Annual Review of Ecology, Evolution and Systematics
36:
445–466.
|
|
|
Sullivan J,
Markert JA and
Kilpatrick CW
(1997)
Phylogeography and molecular systematics of the Peromyscus aztecus species group (Rodentia: Muridae) inferred using parsimony and likelihood.
Systematic Biology
46:
426–440.
|
|
|
Sullivan J and
Swofford DL
(1997)
Are guinea pigs rodents? The importance of adequate models in molecular phylogenies.
Journal of Mammalian Evolution
4:
77–86.
|
|
|
Tamura K
(1994)
Model selection in the estimation of the number of nucleotide substitutions.
Molecular Biology and Evolution
11:
154–157.
|
|
|
book
Tavaré S
(1986)
"Some probabilistic and statistical problems in the analysis of DNA sequences".
In: Miura RM (ed.)
Some Mathematical Questions in Biology – DNA Sequence Analysis.
pp. 57–86.
Providence, RI: American Mathematical Society.
|
|
|
book
Thorne JL and
Goldman N
(2003)
"Probabilistic models for the study of protein evolution".
In: Balding DJ,
Bishop M and
Cannings C (eds)
Handbook of Statistical Genetics.
pp. 209–226.
Chichester, England: Wiley.
|
|
|
Yang Z
(1996)
Among‐site rate variation and its impact on phylogenetic analysis.
Trends in Ecology & Evolution
11:
367–372.
|
|
|
Yang Z,
Goldman N and
Friday A
(1995)
Maximum likelihood trees from DNA sequences: a peculiar statistical estimation problem.
Systematic Biology
44:
384–399.
|
|
|
Zhang J
(1999)
Performance of likelihood ratio tests of evolutionary hypotheses under inadequate substitution models.
Molecular Biology and Evolution
16:
868–875.
|
| Further Reading |
|
|
Johnson JB and
Omland KS
(2003)
Model selection in ecology and evolution.
Trends in Ecology & Evolution
19:
101–108.
|
|
|
Kelchner SA and
Thomas MA
(2007)
Model use in phylogenetics: nine key questions.
Trends in Ecology and Evolution
22:
87–94.
|
|
|
book
Posada D
(2009)
"Selecting models of molecular evolution".
In: Vandamme AM,
Salemi M and
Lemey P (eds)
The Phylogenetic Handbook,
2nd edn.
Cambridge, UK: Cambridge University Press.
|
|
|
book
Posada D (ed.)
(2009)
"Selection of models of DNA evolution with jModelTest".
In: Bioinformatic Analysis of DNA Sequences.
Clifton, NJ, USA: Humana Press.
|