Statistical tests of models of DNA substitution

Cited by (736)

Items 601–700 of 736

1. Forage Response to Swine Effluent: A Cox Nonnested Test of Alternative Functional Forms Using a Fast Double Bootstrap
   Seong C. Park, B. Wade Brorsen, Arthur Louis Stoecker, Jeffory A. Hattey · 2012 · Journal of Agricultural and Applied Economics
2. Multiple maxima of likelihood in phylogenetic trees
   Benny Chor, Michael D. Hendy, Barbara R. Holland, David Penny · 2000 · Research in Computational Molecular Biology
3. OF PIKAS AND PARASITES: HISTORICAL BIOGEOGRAPHY OF AN ALPINE HOST-PARASITE ASSEMBLAGE
   Kurt E. Galbreath · 2008 · eCommons (Cornell University)
4. DISTREE: A tool for estimating genetic distances between aligned DNA sequences
   Johannes Schäfer, Michael Schöniger · 1997 · Computer applications in the biosciences
5. Avoiding ascertainment bias in the maximum likelihood inference of phylogenies based on truncated data
   Asif U. Tamuri, Nick Goldman · 2017 · bioRxiv (Cold Spring Harbor Laboratory)
6. Detecting and visualising the impact of heterogeneous evolutionary processes on phylogenetic estimates
   Lars Sommer Jermiin, David R. Lovell, Bernhard Y. Misof, Peter Gordon Foster, John Robinson · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
7. WitChi: Efficient Detection and Pruning of Compositional Bias in Phylogenomic Alignments Using Empirical Chi-Squared Testing
   Stephan Köstlbacher, Kassiani Panagiotou, Daniel Tamarit, Thijs J. G. Ettema · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
8. ChromEvol v.3: modeling rate heterogeneity in chromosome number evolution
   Anat Shafir, Keren Halabi, Ella Baumer, Itay Mayrose · 2024 · New Phytologist
9. Likelihood-Based Tests of Species Tree Hypotheses
   Richard H. Jr. Adams, Michael DeGiorgio · 2023 · Molecular Biology and Evolution
10. A MODEL FOR PHYLOGENETIC INFERENCE USING STRUCTURAL AND CHEMICAL COVARIATES
    Simon Tavaré, Dean C. Adams, Olivier D. Fedrigo, Gavin J. P. Naylor · 2000 · Pacific Symposium on Biocomputing (PSB)
11. Relative model selection of evolutionary substitution models can be sensitive to multiple sequence alignment uncertainty
    Stephanie J. Spielman, Molly L. Miraglia · 2021 · BMC Ecology and Evolution
12. Power of the likelihood ratio test for models of DNA base substitution
    Gabriela Bettella Cybis, Sílvia R. C. Lopes, Hildete Prisco Pinheiro · 2011 · Journal of Applied Statistics
13. Quantifying the impact of an inference model in Bayesian phylogenetics
    Richèl J.C. Bilderbeek, Giovanni Laudanno, Rampal S. Etienne · 2020 · Methods in Ecology and Evolution
14. Regional Context in the Alignment of Biological Sequence Pairs
    Raymond Sammut, Gavin A. Huttley · 2010 · Journal of Molecular Evolution
15. Maximum likelihood methods
    Ziheng Yang · 2006 · Oxford University Press eBooks
16. Biogeography and phylogenetics of the planktonic foraminifera
    Heidi A. Seears · 2011 · Nottingham ePrints (University of Nottingham)
17. Caracterização e filogenia moleculares de Acanthamoeba.
    João M. P. Alves · 2001 · Digital Library of Theses and Dissertations (Universidade de São Paulo)
18. An Evolving View of Species Tree Inference
    Laura Salter Kubatko · 2026 · Systematic Biology
19. Phylogeny reconstruction: overview
    Ziheng Yang · 2006 · Oxford University Press eBooks
20. Assessment of Absolute Substitution Model Fit Accommodating Time-Reversible and Non-Time-Reversible Evolutionary Processes
    Vadim V. Goremykin · 2022 · Systematic Biology
21. Phylogeny of Leafhopper Subgenus Errhomus (Erronus) (Hemiptera: Cicadellidae) Based on Mitochondrial DNA Sequences
    Diana G. Johnson, Bryan C. Carstens, Walter S. Sheppard, Richard S. Zack · 2005 · Annals of the Entomological Society of America
22. Analysis and Allocation of Cancer-Related Genes Using Vague DNA Sequence Data
    Muhammad Aslam, Mohammed Albassam · 2022 · Frontiers in Genetics
23. Estimating the Deviation from a Molecular Clock
    Luay K. Nakhleh, Usman Roshan, Lisa Vawter, Tandy J. Warnow · 2002 · Lecture notes in computer science
24. Phylogenetic Hypothesis Testing
    Iker Irisarri, Rafael Zardoya · 2013 · Encyclopedia of Life Sciences
25. Selection of Phylogenetic Models of Molecular Evolution
    David Posada · 2012 · Encyclopedia of Life Sciences
26. Biases in Amino Acid Replacement Matrices and Alignment Scores Due to Rate Heterogeneity
    COLLEEN KELLY, Gary A. Churchill · 1996 · Journal of Computational Biology
27. Analysis of complex HIV-1 intersubtype recombinants using a Bayesian scanning method
    Dimitrios N. Paraskevis, Koen Deforche, Ana Barroso Abecasis, Ricardo Jorge Camacho, Anne‐Mieke Vandamme · 2005 · Infection Genetics and Evolution
28. Phylogeny Estimation Using Likelihood‐Based Methods
    John P. Huelsenbeck · 2019 · Wiley eBooks
29. The Multispecies Coalescent Model Outperforms Concatenation across Diverse Phylogenomic Data Sets
    Xiaodong Jian, Scott V. Edwards, Liang Liu · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
30. A test statistic to quantify treelikeness in phylogenetics
    Caitlin Cherryh, Bùi Quang Minh, Robert Lanfear · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
31. A mutation-selection model of protein evolution under persistent positive selection
    Asif U. Tamuri, Mario dos Reis · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
32. References
    2011 · Elsevier eBooks
33. Neutral and adaptive protein evolution
    Ziheng Yang · 2014 · Oxford University Press eBooks
34. Simulation of Chordate Intron Evolution Using Randomly Generated and Mutated Base Sequences
    Guang-Dong Wang, Yong Wang, Zhen Zeng, Jun‐Ming Mao, Qin-Liu He, Qin Yao, Keping Chen · 2020 · Evolutionary Bioinformatics
35. Dealing with model uncertainty in reconstructing ancestral proteins in the laboratory: examples from archosaur visual pigments and coralfluorescent proteins
    Belinda S. W. Chang, Mikhail V. Matz, Steven F. Field, Johannes Müller, Ilke van Hazel · 2007 · Oxford University Press eBooks
36. IS YOUR PHYLOGENY INFORMATIVE? MEASURING THE POWER OF COMPARATIVE METHODS
    Carl Boettiger, Graham Coop, Peter L. Ralph · 2012 · Evolution
37. Simulating molecular evolution
    Ziheng Yang · 2014 · Oxford University Press eBooks
38. A Novel Test for Absolute Fit of Evolutionary Models Provides a Means to Correctly Identify the Substitution Model and the Model Tree
    Vadim V. Goremykin · 2019 · Genome Biology and Evolution
39. Modeling evolution of protein coding DNA sequences
    Sergei L. Kosakovsky Pond · 2003 · UA Campus Repository (The University of Arizona)
40. Introduction to Applications of the Likelihood Function in Molecular Evolution
    Jutta Buschbom, Arndt von Haeseler · 2005 · Statistics in the health sciences
41. Detecting the Presence and Location of Selection in Proteins
    Tim Massingham · 2008 · Methods in molecular biology
42. piBUSS: a parallel BEAST/BEAGLE utility for sequence simulation under complex evolutionary scenarios
    Filip Bielejec, Philippe Lemey, Luiz Max Carvalho, Guy Baele, Andrew Rambaut, Marc A. Suchard · 2013 · arXiv (Cornell University)
43. Relative model fit does not predict topological accuracy in single-gene protein phylogenetics
    Stephanie J. Spielman · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
44. The causes and consequences of variation in evolutionary processes acting on DNA sequences
    Lee Bofkin · 2006 · Europe PMC (PubMed Central)
45. Probabilistic Models for the Study of Protein Evolution
    Jeffrey L. Thorne, N. Goldman · 2003 · Wiley eBooks
46. Models of amino acid and codon substitution
    Ziheng Yang · 2014 · Oxford University Press eBooks
47. Mitochondrial Genome “Evolution” of Arctic Warbler (Phylloscopus borealis sensu lato) Occurs in Its Nuclear Genome
    Liudmila N. Spiridonova, O. P. Valchuk, Ya. А. Red’kin · 2024 · Russian Journal of Genetics
48. Efficient identification of phylogenetically informative alignment sites via sparse learning
    Carlos Guerra Schrago · 2026 · Molecular Phylogenetics and Evolution
49. Estimating the evidence of selection and the reliability of inference in unigenic evolution
    Andrew D. Fernandes, Benjamin P. Kleinstiver, David R. Edgell, Lindi M. Wahl, Gregory Brian Gloor · 2010 · Algorithms for Molecular Biology
50. GeLL: a generalized likelihood library for phylogenetic models
    Daniel Money, Simon Whelan · 2015 · Bioinformatics
51. Models of amino acid and codon substitution
    Ziheng Yang · 2006 · Oxford University Press eBooks
52. Coalescent theory and species trees
    Ziheng Yang · 2014 · Oxford University Press eBooks
53. Models of nucleotide substitution
    Ziheng Yang · 2006 · Oxford University Press eBooks
54. Phylogenetic approaches to identifying fragments of the same gene, with application to the wheat genome
    Ivana Piližota, Clément Marie Train, Adrian Altenhoff, Henning Redestig, Christophe Dessimoz · 2018 · Bioinformatics
55. Rejoinder for discussion on “Horseshoe‐based Bayesian nonparametric estimation of effective population size trajectories”
    James R. Faulkner, Andrew F. Magee, Beth Shapiro, Vladimir N. Minin · 2020 · Biometrics
56. Bayesian methods
    Ziheng Yang · 2006 · Oxford University Press eBooks
57. Functional prediction through phylogenetic inference and structural classification of proteins
    Kimmen V. Sjölander, Chelsea Dvorak Specht · 2005 · Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics
58. Genetic diversity and evolutionary age of parthenogenetic oribatid mites (Acari: Oribatida)
    Michael Heethoff · 2008 · Technischen Universität Darmstadt
59. Speciation, phylogeography, and gene flow in giant salamanders (Dicamptodon)
    Craig A. Steele · 2006 · Research Exchange (Washington State University)
60. ModelTeller: model selection for optimal phylogenetic reconstruction using machine learning
    Shiran Abadi, Oren Avram, Saharon Rosset, Tal Pupko, Itay Mayrose · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
61. PHYLOGENETIC STUDIES ON DIDELPHID MARSUPIALS II. NONMOLECULAR DATA AND NEW IRBP SEQUENCES: SEPARATE AND COMBINED ANALYSES OF DIDELPHINE RELATIONSHIPS WITH DENSER
    Taxon Sampling, Robert S. Voss · 2003
62. Relative model selection of evolutionary substitution models can be sensitive to multiple sequence alignment uncertainty
    Stephanie J. Spielman, Molly L. Miraglia · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
63. Phylogenetic Likelihood
    Leonardo de Oliveira Martins, Diego Mallo, David Posada · 2013 · Encyclopedia of Life Sciences
64. Maximum likelihood methods
    Ziheng Yang · 2014 · Oxford University Press eBooks
65. Inferring the Past: Phylogenetic Trees
    2005 · Springer eBooks
66. AliSim-HPC: parallel sequence simulator for phylogenetics
    Nhan Ly-Trong, Giuseppe M. J. Barca, Bùi Quang Minh · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
67. State Space Misspecification in Morphological Phylogenetics: A Pitfall for Models and Parsimony Alike
    E. J. Huang · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
68. Computational statistics in molecular phylogenetics
    William Fletcher · 2011 · UCL Discovery (University College London)
69. Phylogenetische Entwicklung asiatischer Wasserbüffel anhand Polymorphismen in der mitochondrialen D-loop Region
    Gerold Kierstein · 2001
70. Exploring the boundaries of shallow phylogeny in the YESS group and the dynamics of gene cluster and operon formation in bacterial genomes
    Fergal J. Martin · 2009 · Maynooth University ePrints and eTheses Archive (Maynooth University)
71. Molecular Phylogenetic Analysis
    John P. Huelsenbeck · 2001 · Palaeobiology II
72. Filogènia, filogeografia i estructura poblacional de peixos marins amb diferents capacitats de dispersió
    Josep Carreras-Carbonell · 2006 · LA Referencia (Red Federada de Repositorios Institucionales de Publicaciones Científicas)
73. Estudos de citogenética e de filogenia molecular em roedores da tribo Akodontini
    Karen Ventura · 2009
74. Genealogia, distribuição e história de haplótipos do gene mitocondrial NADH 4 em populações do Aedes (Stegomyia) aegypti (Diptera: Culicidae) no Brasil
    José Eduardo Bracco · 2005
75. Interspecific Relationships and Origins of Taxus and Cephalotaxus
    Da‐Cheng Hao · 2009 · International Conference on Bioinformatics and Biomedical Engineering
76. Regime shifts in ecology and evolution
    Carl Boettiger · 2012 · ProQuest Demo Repository
77. Phylogenetic analysis of HIV-1 in Mpumalanga
    P Msimanga · 2013 · SUNScholar (Stellenbosch University)
78. Estudio de proceso de colonización y radiación adaptativa del género "Pholcus" (Araneae, Pholcidae) en el archipiélago Canario
    Dimitar Dimitrov · 2005 · LA Referencia (Red Federada de Repositorios Institucionales de Publicaciones Científicas)
79. Filogenia molecular e biogeografia: jacus e jacutingas (Cracidae)
    Erwin Tramontini Grau · 2008
80. FUNCTIONAL DIVERGENCE AT THE MOLECULAR LEVEL: ROBUSTNESS, ASYMMETRY, AND CONVERGENCE
    Gavin C. Conant · 2004
81. A CYTOCHROME-b PERSPECTIVE ON PASSERINA
    Bunting Relationships, John Klicka, Adam J. Fry, Robert M. Zink, Christopher W. Thompson · 2001
82. SONCHUS ALLIANCE (ASTERACEAE: SONCHINAE) IN THE MACARONESIAN ISLANDS'
    Chung-Hee Lee, Seung‐Chul Kim, Karen E. Lundy, Arnoldo Santos‐Guerra · 2005
83. ANOLE: PATTERNS OF WITHIN-ISLAND MOLECULAR AND MORPHOLOGICAL DIVERGENCE
    Anita Malhotra, Roger S. Thorpe · 2000
84. Stochastic Search Strategy for Estimation of Maximum Likelihood
    Laura A. Salter, Dennis K. Pearl · 2001
85. Molecular Phylogenetics: A Tool for Elucidation of Evolutionary Processes from Biological Data
    Martina Talianová · 2015 · Apple Academic Press eBooks
86. Comparison of methods and tests on trees
    Ziheng Yang · 2006 · Oxford University Press eBooks
87. Molecular Phylogenies and Virulence Evolution
    Bruce H. Rannala · 2002 · Cambridge University Press eBooks
88. Bayesian computation (MCMC)
    Ziheng Yang · 2014 · Oxford University Press eBooks
89. Comparison of phylogenetic methods and tests on trees
    Ziheng Yang · 2014 · Oxford University Press eBooks
90. Probabilistic Models and Learning
    Timo Koski · 2001 · Computational biology
91. Molecular clock and estimation of species divergence times
    Ziheng Yang · 2006 · Oxford University Press eBooks
92. Molecular Evolution of Dim-light Visual Pigments in Neotropical Geophagine Cichlids
    Shannon P. Refvik · 2012 · TSpace (University of Toronto)
93. Genetic Diversity and Phylogeographic Structure of the Parasitic Plant Genus Conopholis (Orobanchaceae): Implications for Systematics and Post-glacial Colonization of North America
    Anuar G. Rodrigues · 2014 · TSpace (University of Toronto)
94. Methodological Review Phylogenetics by likelihood: Evolutionary modeling as a tool for understanding the genome
    Carolin Kosiol, Lee Bofkin, Simon Whelan · 2005
95. The lac operon in the wild
    Fabienne Jesse · 2017 · Institute of Science and Technology Austria
96. The Exploration of Effect of Model Misspecification and Development of an Adequacy-Test for Substitution Model in Phylogenetics
    Wei Chen · 2012 · Library and Archives Canada (Government of Canada)
97. Model-based approaches to discovering diversity : new implementations, tests of adequacy and an empirical application to central American Diptera
    Noah M. Reid · 2013
98. A phylogenetic approach disentangles interlocus gene conversion tract length and initiation rate
    Xiang Ji, Jeffrey L. Thorne · 2019 · arXiv (Cornell University)
99. Research article MOLECULAR CHARACTERIZATION OF TWO SPECIES OF SPILOSTETHUS (INSECTA: LYAGEIDAE) AND PHYLOGENETIC RECONSTRUCTION USING 16S RIBOSOMAL RNA GENE FRAGMENT
    K. P. Sanjayan, V. Rama · 2013
100. Genomes of Animal Mitochondria have not Evolved According to Common Models of Substitution Probabilities
     James A. Cavender · 2020 · bioRxiv (Cold Spring Harbor Laboratory)