Statistical tests of models of DNA substitution

Cited by (736)

Items 501–600 of 736

1. Data exploration in phylogenetic inference: scientific, heuristic, or neither
   Taran Grant · 2003 · Cladistics
2. Rampant host switching and multiple female body colour transitions in Philotrypesis (Hymenoptera: Chalcidoidea: Agaonidae)
   Z. -F. Jiang, Da‐Wei Huang, Linlin Chen, Wenquan Zhen, Y G Fu, Zhengqiang Peng · 2006 · Journal of Evolutionary Biology
3. Factors Affecting the Errors in the Estimation of Evolutionary Distances Between Sequences
   David C. Hoyle, Paul G. Higgs · 2003 · Molecular Biology and Evolution
4. Mitochondrial DNA Clocks and the Phylogeny of Danaus Butterflies
   Gugs Lushai, David A. S. Smith, Dave Goulson, J. A. Allen, Norman Maclean · 2003 · International Journal of Tropical Insect Science
5. MISFITS: Evaluating the Goodness of Fit between a Phylogenetic Model and an Alignment
   Minh Anh Nguyen, Steffen Klaere, Arndt von Haeseler · 2010 · Molecular Biology and Evolution
6. An Empirical Test for Branch-Specific Positive Selection
   Gabrielle C. Nickel, David L. Tefft, Karrie C. Goglin, Mark D. Adams · 2008 · Genetics
7. Evolutionary history of the genus Sus inferred from cytochrome b sequences
   Stefano Mona, Ettore Randi, Mila Tommaseo-Ponzetta · 2007 · Molecular Phylogenetics and Evolution
8. Statistical Tests between Competing Hypotheses of Hox Cluster Evolution
   Robert Lanfear, Lindell D. Bromham · 2008 · Systematic Biology
9. A Codon Model for Associating Phenotypic Traits with Altered Selective Patterns of Sequence Evolution
   Keren Halabi, Eli Levy Karin, Laurent Guéguen, Itay Mayrose · 2020 · Systematic Biology
10. Measuring Fit of Sequence Data to Phylogenetic Model: Gain of Power Using Marginal Tests
    Peter J. Waddell, Rissa Ota, David Penny · 2009 · Journal of Molecular Evolution
11. EPISODIC CHROMOSOMAL EVOLUTION IN PLANIPAPILLUS (ONYCHOPHORA: PERIPATOPSIDAE): A PHYLOGENETIC APPROACH TO EVOLUTIONARY DYNAMICS AND SPECIATION
    Matthew V. Rockman, David M. Rowell · 2002 · Evolution
12. Modeling Mitochondrial Protein Evolution Using Structural Information
    Píetro Lió, Nick Goldman · 2002 · Journal of Molecular Evolution
13. Molecular clock-like evolution of human immunodeficiency virus type 1
    Yi Liu, David C. Nickle, Daniel Shriner, Mark A. Jensen, Gerald H. Learn, John E. Mittler, James I. Mullins · 2004 · Virology
14. ImOSM: Intermittent Evolution and Robustness of Phylogenetic Methods
    Minh Anh Nguyen, Tanja Gesell, Arndt von Haeseler · 2011 · Molecular Biology and Evolution
15. The complete mitochondrial genome and phylogenetic analysis of forest musk deer (Moschus berezovskii)
    Hongyuan Peng, Shichang Liu, Bo Zeng, Fangdong Zou, Xiuyue Zhang, Bisong Yue · 2009 · Journal of Natural History
16. Ancestral Gene Reconstruction and Synthesis of Ancient Rhodopsins in the Laboratory
    Belinda S. W. Chang · 2003 · Integrative and Comparative Biology
17. Taxonomic Status and Genetic Variation of Korean Endemic Plants, Eranthis byunsanensis and Eranthis pungdoensis (Ranunculaceae) based on nrDNA ITS and cpDNA Sequences
    Chang Shook Lee, Sung Hee Yeau, Nam Sook Lee · 2012 · Journal of Plant Biology
18. Measuring the Fit of Sequence Data to Phylogenetic Model: Allowing for Missing Data
    Peter J. Waddell · 2004 · Molecular Biology and Evolution
19. Population genetics of Penstemon albomarginatus (Plantaginaceae), a rare Mojave Desert species of conservation concern
    Andrea D. Wolfe, Timothy NeCamp, Susan Fassnacht, Paul D. Blischak, Laura Salter Kubatko · 2016 · Conservation Genetics
20. Molecular systematic relationships and evidence for a recent origin of the thermal spring endemic snails Physella johnsoni and Physella wrighti (Pulmonata: Physidae)
    Elpidio A. Remigio, Dwayne A. W. Lepitzki, Jacqueline S. Lee, Paul D. N. Hebert · 2001 · Canadian Journal of Zoology
21. When Being "Most Likely" Is Not Enough: Examining the Performance of Three Uses of the Parametric Bootstrap in Phylogenetics
    Marcos A. Antezana · 2003 · Journal of Molecular Evolution
22. Evolutionary Similarity Among Genes
    Marc A. Suchard, Robert E. Weiss, Janet S. Sinsheimer, Karin S. Dorman, Megha Patel, Edward R.B. McCabe · 2003 · Journal of the American Statistical Association
23. Adaptive Molecular Evolution
    Ziheng Yang · 2003 · Wiley eBooks
24. Retraction Note: TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics
    Gangolf Jobb, Arndt von Haeseler, Korbinian Strimmer · 2015 · BMC Evolutionary Biology · Retracted
25. Drivers of avian genomic change revealed by evolutionary rate decomposition
    David Alejandro Duchêne, Al-Aabid Chowdhury, Jingyi Yang, Maider Iglesias‐Carrasco, Josefin Stiller, Shaohong Feng, Samir Bhatt, Marcus Thomas P. Gilbert, Guojie Zhang, Joseph A. Tobias et al. · 2025 · Nature
26. 10. Robust Inferences from Ambiguous Alignments
    Benjamin D. Redelings, Marc A. Suchard · 2019 · University of California Press eBooks
27. Population Genetics Based Phylogenetics Under Stabilizing Selection for an Optimal Amino Acid Sequence: A Nested Modeling Approach
    Jeremy M. Beaulieu, Brian C. O’Meara, Russell Zaretzki, Cedric Landerer, Juanjuan Chai, Michael A. Gilchrist · 2018 · Molecular Biology and Evolution
28. The Evolutionary History of the Transposable Element Penelope in the Drosophila virilis Group of Species
    Ramiro Morales‐Hojas, Cristina P. Vieira, Jorge Vieira · 2006 · Journal of Molecular Evolution
29. Narrow species concepts in the Frullania dilatata–appalachiana–eboracensis complex (Porellales, Jungermanniopsida): evidence from nuclear and chloroplast DNA markers
    Andrea Bombosch, A. Wieneke, Ariane Busch, R. Jonas, Jörn Hentschel, Hans‐Peter Kreier, Blanka Shaw, A. Jonathan Shaw, Jochen Heinrichs · 2010 · Plant Systematics and Evolution
30. PHYLOGENETIC SYSTEMATICS OF THE AUSTRALIAN FAIRY SHRIMP GENUS BRANCHINELLA BASED ON MITOCHONDRIAL DNA SEQUENCES
    Elpidio A. Remigio, Paul D. N. Hebert, Brian V. Timms · 2003 · Journal of Crustacean Biology
31. Testing the directionality of evolution: the case of chydorid crustaceans
    Sarah J. Adamowicz, Veronika Sacherová · 2006 · Journal of Evolutionary Biology
32. Examining rates and patterns of nucleotide substitution in plants
    Spencer V. Muse · 2000 · Springer eBooks
33. Testing adequacy for DNA substitution models
    Wei Chen, Toby Kenney, Joseph P. Bielawski, Hong Gu · 2019 · BMC Bioinformatics
34. Generic delimitation and biogeography of Maianthemum and Smilacina (Ruscaceae sensu lato): preliminary results based on partial 3′ matK gene and trnK 3′ intron sequences of cpDNA
    Seung‐Chul Kim, N. S. Lee · 2007 · Plant Systematics and Evolution
35. Hypothesis tests for phylogenetic quartets, with applications to coalescent-based species tree inference
    Jeff Gaither, Laura Salter Kubatko · 2016 · Journal of Theoretical Biology
36. Phylogenetic Analyses
    Punto Bawono, Jaap Heringa · 2014 · Elsevier eBooks
37. Phylogenetic relationships among species of Leotia (Leotiales) based on ITS and RPB2 sequences
    Zhihong Zhong, Donald H. Pfister · 2004 · Mycological Progress
38. Modeling DNA Base Substitution in Large Genomic Regions from Two Organisms
    Von Bing Yap, Terence Paul Speed · 2004 · Journal of Molecular Evolution
39. Phylogenetic relationships of the rare Korean monotypic endemic genus Pentactina Nakai in the tribe Spiraeeae (Rosaceae) based on molecular data
    Chung-Hee Lee, Suk‐Pyo Hong · 2011 · Plant Systematics and Evolution
40. Phylogenetic Inference Using Molecular Data
    Ferran Palero, Keith A. Crandall · 2009 · Crustacean issues
41. Phylogeny of Bruniaceae Based on matK and ITS Sequence Data
    Marcus Quint, Regine Claßen‐Bockhoff · 2006 · International Journal of Plant Sciences
42. Bayesian Inference of Phylogenetics Revisited: Developments and Concerns
    Christopher P. Randle, Mark E. Mort, Daniel J. Crawford · 2005 · Taxon
43. TESTING PHYLOGENETIC HYPOTHESES WITH STRATIGRAPHY AND MORPHOLOGY—A COMMENT ON SMITH (2000)
    Peter J. Wagner · 2002 · Journal of Paleontology
44. The evolutionary history of mammoth wasps (Hymenoptera: Scoliidae)
    Ziad Khouri, Jéssica P. Gillung, Lynn S. Kimsey · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
45. Standard Codon Substitution Models Overestimate Purifying Selection for Non-Stationary Data
    Benjamin D. Kaehler, Von Bing Yap, Gavin A. Huttley · 2017 · Genome Biology and Evolution
46. Assessing topological congruence among concatenation-based phylogenomic approaches in empirical datasets
    Ambrosio Torres, Pablo A. Goloboff, Santiago Andrés Catalano · 2021 · Molecular Phylogenetics and Evolution
47. Robustness of Phylogenetic Inference to Model Misspecification Caused by Pairwise Epistasis
    Andrew F. Magee, Sarah K. Hilton, William S. DeWitt · 2021 · Molecular Biology and Evolution
48. Nuclear and cpDNA Sequences Demonstrate Spontaneous Hybridization Between Goodyera schlechtendaliana Rchb. f. and G. velutina Maxim. (Orchidaceae) in Jeju Island, Korea
    Chang Shook Lee · 2012 · Systematic Botany
49. RNA secondary structure, an important bioinformatics tool to enhance multiple sequence alignment: a case study (Sordariomycetes, Fungi)
    Martina Réblová, Kamila Réblová · 2012 · Mycological Progress
50. Selection of evolutionary models for phylogenetic hypothesis testing using parametric methods
    Brent C. Emerson, Kamal M. Ibrahim, G. M. Hewitt · 2001 · Journal of Evolutionary Biology
51. Approximating Model Probabilities in Bayesian Information Criterion and Decision-Theoretic Approaches to Model Selection in Phylogenetics
    J. Evans, Jack M. Sullivan · 2010 · Molecular Biology and Evolution
52. Identifying model violations under the multispecies coalescent model using P2C2M.SNAPP
    Drew J. Duckett, Tara A. Pelletier, Bryan C. Carstens · 2020 · PeerJ
53. Statistical Modeling of the Monthly Palmer Drought Severity Index
    Debbie J. Dupuis · 2010 · Journal of Hydrologic Engineering
54. Molecular confirmation of the hybrid origin of the critically endangered western Mediterranean endemic Sonchus pustulatus (Asteraceae: Sonchinae)
    Seung‐Chul Kim, Jose Antonio Mejias, Pesach Lubinsky · 2008 · Journal of Plant Research
55. The measurement of test severity, significance tests for resolution, and a unified philosophy of phylogenetic inference
    Kevin de Queiroz · 2004 · Zoologica Scripta
56. Phylogeny of Halgerda (Mollusca : Gastropoda) based on combined analysis of mitochondrial CO1 and morphology
    Shireen J. Fahey · 2003 · Invertebrate Systematics
57. Whole genome/proteome based phylogeny reconstruction for prokaryotes using higher order Markov model and chaos game representation
    Weifeng Yang, Zu‐Guo Yu, Vo Anh · 2015 · Molecular Phylogenetics and Evolution
58. A preliminary phylogenetic analysis of Luidia (Paxillosida: Luidiidae) from Chinese waters with cytochrome oxidase subunit I (COI) sequences
    Ning Xiao, Ruiyu Liu, Shuai Yuan, Zhongli Sha · 2013 · Journal of Ocean University of China
59. Conservation genetics of the endangered Shenandoah salamander (Plethodon shenandoah, Plethodontidae)
    Daniel W. Carpenter, Robin E. Jung, Jack W. Sites · 2001 · Animal Conservation
60. Genetic analysis of the VP4/VP2 coding region in human rhinovirus species C in patients with acute respiratory infection in Japan
    Naoko Kiyota, Izumi Kushibuchi, Miho Kobayashi, Hiroyuki Tsukagoshi, Akihide Ryo, Koichi Nishimura, Asumi Hirata‐Saito, Seiya Harada, Mika Arakawa, Kunihisa Kozawa et al. · 2013 · Journal of Medical Microbiology
61. Systematics and evolution of Tarasa Philippi (Malvaceae): an enigmatic Andean polyploid genus
    Jennifer A. Tate · 2002 · The University of Texas at Austin Digital Collections
62. Neutral and adaptive protein evolution
    Ziheng Yang · 2006 · Oxford University Press eBooks
63. Evolution of DNA or Amino Acid Sequences with Dependent Sites
    Arndt von Haeseler, Michael Schöniger · 1998 · Journal of Computational Biology
64. Accuracy and Power of the Likelihood Ratio Test for Comparing Evolutionary Rates Among Genes
    Jan Erik Aagaard, Patrick C. Phillips · 2005 · Journal of Molecular Evolution
65. Phylogeny based discovery of regulatory elements
    Jason Gertz, Justin C. Fay, Barak A. Cohen · 2006 · BMC Bioinformatics
66. Choosing among Alternative Trees of Multigene Families
    Andrew P. Martin · 2000 · Molecular Phylogenetics and Evolution
67. Adaptive Molecular Evolution
    Ziheng Yang · 2019
68. Molecular systematics of the parasitic genus Conopholis (Orobanchaceae) inferred from plastid and nuclear sequences
    Anuar G. Rodrigues, Alison E. L. Colwell, Saša Stefanović · 2011 · American Journal of Botany
69. Accurate Estimation of Gene Evolutionary Rates Using XRATE, with an Application to Transmembrane Proteins
    Andreas Heger, Chris Paul Ponting, Ian H Holmes · 2009 · Molecular Biology and Evolution
70. Genetic and Morphological Analyses Demonstrate That Schizolecis guntheri (Siluriformes: Loricariidae) Is Likely to Be a Species Complex
    Camila S. Souza, Guilherme José da Costa Silva, Fábio Fernandes Roxo, Fausto Foresti, Cláudio Oliveira · 2018 · Frontiers in Genetics
71. Testing population genetic structure using parametric bootstrapping and MIGRATE-N
    Bryan C. Carstens, Armand Bankhead, P. Joyce, Jack M. Sullivan · 2005 · Genetica
72. Phylogenetic relationships among species of Setaria (Paniceae; Panicoideae; Poaceae) in Korea: insights from nuclear (ITS and kn1) and chloroplast DNA sequence data
    Seonhee Kim, Chang-Seok Kim, Jeongran Lee, In-Yong Lee, Youngjae Chung, Myong‐Suk Cho, Seung‐Chul Kim · 2014 · Plant Systematics and Evolution
73. LineageSpecificSeqgen: generating sequence data with lineage-specific variation in the proportion of variable sites
    Liat Shavit Grievink, David Penny, Mike D Hendy, Barbara R. Holland · 2008 · BMC Evolutionary Biology
74. Evolution of the leukotoxin promoter in genus Mannheimia
    Jesper Larsen, Anders Gorm Pedersen, Robert L. Davies, Peter Kuhnert, Joachim Frey, Henrik Kidmose Christensen, Magne Bisgaard, John Elmerdahl Olsen · 2009 · BMC Evolutionary Biology
75. Avian Evolution During the Pleistocene in North America
    Robert M. Zink, John Klicka · 2000 · Springer eBooks
76. Phylogenetic relationship of the green alga Nanochlorum eukaryotum deduced from its chloroplast rRNA sequences
    Madelyn R. Schreiner, M. Geisert, M. Oed, Josef Arendes, U. G�ngerich, Hans J. Breter, K. St�ber, D. Weinblume · 1995 · Journal of Molecular Evolution
77. An Algorithm for Calculating the Probability of Classes of Data Patterns on a Genealogy
    Jordan M. Koch, Mark T. Holder · 2012 · PLoS Currents
78. Computing Substitution Matrices for Genomic Comparative Analysis
    Minh Duc Cao, Trevor I. Dix, Lloyd Allison · 2009 · Lecture notes in computer science
79. Phylogeography of the Narrow Endemic, Helenium virginicum (Asteraceae), Based upon ITS Sequence Comparisons
    Maryanne C. Simurda, David C. Marshall, John S. Knox · 2005 · Systematic Botany
80. SpartaABC: a web server to simulate sequences with indel parameters inferred using an approximate Bayesian computation algorithm
    H. Ashkenazy, Eli Levy Karin, Zach Mertens, R. Cartwright, T. Pupko · 2017 · Nucleic Acids Res.
81. A Cytochrome-b Perspective on Passerina Bunting Relationships
    John Klicka, Adam J. Fry, Robert M. Zink, Christopher W. Thompson · 2001 · The Auk
82. Archiving Molecular Phylogenetic Alignments as NEXUS Files
    Bernard L. Cohen, Jonathan A. Sheps, Mark Wilkinson · 1998 · Systematic Biology
83. Looking for Darwin in Genomic Sequences: Validity and Success Depends on the Relationship Between Model and Data
    Christopher T. Jones, Edward Susko, Joseph P. Bielawski · 2019 · Methods in molecular biology
84. New Phylogenetic Models Incorporating Interval-Specific Dispersal Dynamics Improve Inference of Disease Spread
    Jiansi Gao, Michael R May, Bruce H. Rannala, Brian R. Moore · 2022 · Molecular Biology and Evolution
85. Simulating molecular evolution
    Ziheng Yang · 2006 · Oxford University Press eBooks
86. Phylogenetic Analyses: A Toolbox Expanding towards Bayesian Methods
    Stéphane Aris‐Brosou, Xuhua Xia · 2008 · International Journal of Plant Genomics
87. Maximum Likelihood
    Hirohisa Kishino, M. Hasegawa · 2001 · Encyclopedia of Genetics
88. Inferring language dispersal patterns with velocity field estimation
    Sizhe Yang, Xiaoru Sun, Jin Li, Menghan Zhang · 2024 · Nature Communications
89. The Expected Behaviors of Posterior Predictive Tests and Their Unexpected Interpretation
    Luiza Guimarães Fabreti, Lyndon M. Coghill, Robert C. Thomson, Sebastian Höhna, Jeremy M. Brown · 2024 · Molecular Biology and Evolution
90. The Rise of Statistical Phylogenetics
    Barbara R. Holland · 2013 · Australian & New Zealand Journal of Statistics
91. A falsificationist perspective on the usage of process frequencies in phylogenetics
    Lars Vogt · 2007 · Zoologica Scripta
92. Widespread interspecific phylogenetic tree incongruence between mosquito-borne and insect-specific flaviviruses at hotspots originally identified in Zika virus
    Michael W. Gaunt, John H.‐O. Pettersson, Goro Kuno, Bill Gaunt, Xavier Nicolas de Lamballerie, Ernest Andrew Gould · 2022 · Virus Evolution
93. Comparing the Likelihood Functions of Phylogenetic Trees
    Avner Bar‐Hen, Hirohisa Kishino · 2000 · Annals of the Institute of Statistical Mathematics
94. Robustness of Coalescent Estimators to Between-Lineage Mutation Rate Variation
    Mary K. Kuhner · 2006 · Molecular Biology and Evolution
95. Structure-based methods for the phylogenetic analysis of ribosomal RNA molecules
    Joseph J. Gillespie · 2005
96. The Prevalence and Impact of Model Violations in Phylogenetics Analysis
    Suha Naser-Khdour, Bui Quang Minh, Wenqi Zhang, Eric A. Stone, Robert Lanfear · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
97. Models of nucleotide substitution
    Ziheng Yang · 2014 · Oxford University Press eBooks
98. Phylogenetics of HIV
    David Posada, Keith A. Crandall, David M. Hillis · 2002 · Springer eBooks
99. Assessing the Uncertainty in Phylogenetic Inference
    Hidetoshi Shimodaira, Masami Hasegawa · 2005 · Springer eBooks
100. Inferred Phylogeny in Keckiella (Scrophulariaceae) based on Noncoding Chloroplast and nuclear ribosomal DNA Sequences
     C. Edward Freeman, John Scott Harrison, John P. Janovec, Ron Scogin · 2009 · BioOne Complete (BioOne)