Empirical problems of the hierarchical likelihood ratio test for model selection.

No abstract is available for this paper.

• Publication year

  2004

• Venue

  Systematic Biology

• Publication date

  2004-12-01

• Fields of study

  Biology, Mathematics, Medicine

• Identifiers
  DOI 10.1080/10635150490888868PMID 15764562
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

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  2003influential reference
• Using MODELTEST and PAUP* to Select a Model of Nucleotide Substitution

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  2003influential reference
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• The position of arthropods in the animal kingdom: a search for a reliable outgroup for internal arthropod phylogeny.

  1998cited by this paper
• MODELTEST: testing the model of DNA substitution

  1998influential reference
• Molecular evidence for multiple origins of Insectivora and for a new order of endemic African insectivore mammals.

  1998cited by this paper
• Phylogeny of frogs of the Physalaemus pustulosus species group, with an examination of data incongruence.

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  1998cited by this paper
• Applied Regression Analysis: Draper/Applied Regression Analysis

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• Molecular systematics of the Canidae.

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• Angiosperm Phylogeny Inferred from 18S Ribosomal DNA Sequences

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• Evolution of the Mitochondrial Cytochrome Oxidase II Gene in Collembola

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  1997cited by this paper
• TESTING HYPOTHESES OF CHAETOGNATH ORIGINS: LONG BRANCHES REVEALED BY 18S RIBOSOMAL DNA

  1996cited by this paper
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  1996cited by this paper
• Inconsistency of evolutionary tree topology reconstruction methods when substitution rates vary across characters.

  1996cited by this paper
• Success of maximum likelihood phylogeny inference in the four-taxon case.

  1995cited by this paper
• MAXIMUM LIKELIHOOD TREES FROM DNA SEQUENCES: A PECULIAR STATISTICAL ESTIMATION PROBLEM

  1995cited by this paper
• A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates.

  1994cited by this paper
• Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods

  1994cited by this paper
• fastDNAmL: a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood

  1994cited by this paper
• Estimation of evolutionary distances between nucleotide sequences

  1994cited by this paper
• Model selection in the estimation of the number of nucleotide substitutions.

  1994cited by this paper
• Relative efficiencies of the maximum-likelihood, neighbor-joining, and maximum-parsimony methods when substitution rate varies with site.

  1994cited by this paper
• Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees.

  1993influential reference
• Statistical tests of models of DNA substitution

  1993cited by this paper
• Subset Selection in Regression

  1992cited by this paper
• Subset Selection in Regression

  1991cited by this paper
• The general stochastic model of nucleotide substitution.

  1990influential reference
• Tetrapod phylogeny inferred from 18S and 28S ribosomal RNA sequences and a review of the evidence for amniote relationships.

  1990cited by this paper
• Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in hominoidea

  1989influential reference
• Sélection of subsets of regression variables

  1984cited by this paper
• Documentation of Effectiveness of Psychosocial Interventions: Discussion of Dr. Miller’s Paper

  1984cited by this paper
• Estimation of evolutionary distances between homologous nucleotide sequences.

  1981cited by this paper
• A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences

  1980cited by this paper
• Evolution of Protein Molecules

  1979cited by this paper
• The Choice of Variables in Observational Studies

  1974cited by this paper
• Maximum Likelihood and Minimum-Steps Methods for Estimating Evolutionary Trees from Data on Discrete Characters

  1973cited by this paper
• Why Stepdown Procedures in Variable Selection

  1970cited by this paper
• CHAPTER 24 – Evolution of Protein Molecules

  1969cited by this paper
• Applied Regression Analysis.

  1967cited by this paper
• On the identification of the significant independent variables in linear models

  1967cited by this paper
• Mammalian protein metabolism

  1964cited by this paper
• Mathematical Methods for Digital Computers

  1960cited by this paper

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