Statistical tests of models of DNA substitution

Cited by (736)

Items 401–500 of 736

1. Molecular Evidence Resolving the Systematic Position of Hectorella (Portulacaceae)
   Wendy L. Applequist, Warren L. Wagner, Elizabeth A. Zimmer, Molly Nepokroeff · 2006 · Systematic Botany
2. Testing the phylogeny of swordtail fishes using split decomposition and spectral analysis
   Peter J. Lockhart, David Penny, Axel Meyer · 1995 · Journal of Molecular Evolution
3. Adaptive morphological shifts to novel habitats in marine sculpin fishes
   Matthew L. Knope, Jeffrey A. Scales · 2013 · Journal of Evolutionary Biology
4. P3: Phylogenetic Posterior Prediction in RevBayes
   Sebastian Höhna, Lyndon M. Coghill, Genevieve G. Mount, Robert C. Thomson, Jeremy M. Brown · 2017 · Molecular Biology and Evolution
5. CORRELATED EVOLUTIONARY DIVERGENCE OF EGG SIZE AND A MITOCHONDRIAL PROTEIN ACROSS THE ISTHMUS OF PANAMA
   Peter B. Marko, Amy L. Moran · 2002 · Evolution
6. Insertions and Deletions: Computational Methods, Evolutionary Dynamics, and Biological Applications
   Benjamin D. Redelings, Ian Holmes, Gerton A. Lunter, Tal Pupko, Maria O. Anisimova · 2024 · Molecular Biology and Evolution
7. Comparative phylogeography of endemic cyprinids in the south‐west Iberian Peninsula: evidence for a new ichthyogeographic area
   Natacha Mesquita, C. Cunha, Gary Robert Carvalho, Maria M. Coelho · 2007 · Journal of Fish Biology
8. Phylogenetics of Planipapillus, Lawn-Headed Onychophorans of the Australian Alps, Based on Nuclear and Mitochondrial Gene Sequences
   Matthew V. Rockman, David M. Rowell, Noel N. Tait · 2001 · Molecular Phylogenetics and Evolution
9. Phylogenetics by likelihood: Evolutionary modeling as a tool for understanding the genome
   Carolin Kosiol, Lee Bofkin, Simon Whelan · 2005 · Journal of Biomedical Informatics
10. Treeness triangles: visualizing the loss of phylogenetic signal.
    W. White, S. Hills, R. Gaddam, Barbara R. Holland, D. Penny · 2007 · Molecular biology and evolution
11. Analysis of the Evolutionary Relationships of HIV-1 and SIVcpz Sequences Using Bayesian Inference: Implications for the Origin of HIV-1
    Dimitrios N. Paraskevis · 2003 · Molecular Biology and Evolution
12. Diglyphus isaea (Hymenoptera: Eulophidae): a probable complex of cryptic species that forms an important biological control agent of agromyzid leaf miners
    Zhongli Sha, Chao‐Dong Zhu, Robert W. Murphy, Da‐Wei Huang · 2006 · Journal of Zoological Systematics & Evolutionary Research
13. A coalescent framework for comparing alternative models of population structure with genetic data: evolution of Celebes toads
    Ben J. Evans, Jimmy A. McGuire, Rafe M. Brown, Noviar Andayani, Jatna Supriatna · 2008 · Biology Letters
14. Molecular phylogeny of the Cobitoidea (Teleostei: Cypriniformes) revisited: position of enigmatic loach Ellopostoma resolved with six nuclear genes
    Wei‐Jen Chen, Vachira Lheknim, Richard L. Mayden · 2009 · Journal of Fish Biology
15. Chloroplast DNA Sequences Confirm the Placement of the Enigmatic Oceanopapaver within Corchorus (Grewioideae: Malvaceae s.l., Formerly Tiliaceae)
    Barbara Ann Whitlock, Kenneth G. Karol, William S. Alverson · 2003 · International Journal of Plant Sciences
16. Differential Expression of Duplicated Opsin Genes in Two EyeTypes of Ostracod Crustaceans
    Todd H. Oakley, Daniel R. Huber · 2004 · Journal of Molecular Evolution
17. ANALYSIS OF PREDATOR MOVEMENT IN PRAIRIE LANDSCAPES WITH CONTRASTING GRASSLAND COMPOSITION
    Michael L. Phillips, William R. Clark, Sarah M. Nusser, Marsha A. Sovada, Raymond J. Greenwood · 2004 · Journal of Mammalogy
18. Confidence Intervals for the Divergence Time of Two Clades
    Mike Steel, Alan Cooper, David Penny · 1996 · Systematic Biology
19. Drift and Directional Selection Are the Evolutionary Forces Driving Gene Expression Divergence in Eye and Brain Tissue of Heliconius Butterflies
    Ana Catalán, Adriana D. Briscoe, Sebastian Höhna · 2019 · Genetics
20. Inferring the Deep Past from Molecular Data
    Tom A. Williams, Dominik Schrempf, Gergely J. Szöllősi, Cymon J. Cox, Peter Gordon Foster, T. Martin Embley · 2021 · Genome Biology and Evolution
21. Phylogeny and biogeography of Morinaceae (Dipsacales) based on nuclear and chloroplast DNA sequences
    C BELL · 2003 · Organisms Diversity & Evolution
22. Detailed genetic analysis of hemagglutinin-neuraminidase glycoprotein gene in human parainfluenza virus type 1 isolates from patients with acute respiratory infection between 2002 and 2009 in Yamagata prefecture, Japan
    Katsumi Mizuta, Mika Saitoh, Miho Kobayashi, Hiroyuki Tsukagoshi, Yoko Aoki, Tatsuya Ikeda, Chieko Abiko, Noriko Katsushima, Tsutomu Itagaki, Masahiro Noda et al. · 2011 · Virology Journal
23. Duplications and functional divergence of ADP-glucose pyrophosphorylase genes in plants
    Nikolaos Georgelis, Edward Louis Braun, L. Curtis Hannah · 2008 · BMC Evolutionary Biology
24. Experimental design in caecilian systematics: phylogenetic information of mitochondrial genomes and nuclear rag1.
    Diego San Mauro, D. Gower, T. Massingham, M. Wilkinson, R. Zardoya, J. Cotton · 2009 · Systematic Biology
25. Identifying stochastic oscillations in single-cell live imaging time series using Gaussian processes
    Nick E. Phillips, Cerys S Manning, Nancy Papalopulu, Magnus Rattray · 2017 · PLoS Computational Biology
26. Nucleotide sequence of rbcL and phylogenetic relationships of Setchellanthus caeruleus (Setchellanthaceae)
    Kenneth G. Karol, James Eric Rodman, Elena Conti, Kenneth J. Sytsma · 1999 · Taxon
27. How Well Does Your Phylogenetic Model Fit Your Data?
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28. Model selection in statistical historical biogeography of Neotropical insects—The Exophthalmus genus complex (Curculionidae: Entiminae)
    Guanyang Zhang, Usmaan Basharat, Nicholas Joseph Matzke, Nico M. Franz · 2016 · Molecular Phylogenetics and Evolution
29. A CYTOCHROME-b PERSPECTIVE ON PASSERINA BUNTING RELATIONSHIPS
    John Klicka, Adam J. Fry, Robert M. Zink, Christopher W. Thompson · 2001 · The Auk
30. Accounting for coalescent stochasticity in testing phylogeographical hypotheses: modelling Pleistocene population structure in the Idaho giant salamander Dicamptodon aterrimus
    B. C. C Arstens, J. D. D Egenhardt, A. L. S Tevenson · 2005
31. Applications of Ancestral Protein Reconstruction in Understanding Protein Function: GFP-Like Proteins
    Belinda S. W. Chang, Juan Antonio Ugalde, Mikhail V. Matz · 2005 · Methods in enzymology on CD-ROM/Methods in enzymology
32. Enigmatic phylogeny of skuas: an alternative hypothesis
    Michael J. Braun, Robb Thomas Brumfield · 1998 · Proceedings of the Royal Society B Biological Sciences
33. Duplication of floral regulatory genes in the Lamiales
    Jan E. Aagaard, Richard G. Olmstead, John H. Willis, Patrick C. Phillips · 2005 · American Journal of Botany
34. Molecular Evolution and Phylogeny of the Drosophila saltans Species Group Inferred from the Xdh Gene
    Francisco Rodrı́guez-Trelles, Rosa Tarrı́o, Francisco J. Ayala · 1999 · Molecular Phylogenetics and Evolution
35. Maximum-Likelihood Methods for Phylogeny Estimation
    Jack M. Sullivan · 2005 · Methods in enzymology on CD-ROM/Methods in enzymology
36. The paradox of seduction by irrelevant details: How irrelevant information helps and hinders self-regulated learning
    Traci Sitzmann, Stefanie K Johnson · 2014 · Learning and Individual Differences
37. Molecular phylogeny of European and African Barbus and their West Asian relatives in the Cyprininae (Teleostei: Cypriniformes) and orogenesis of the Qinghai-Tibetan Plateau
    Jing Wang, Xiaoyun Wu, Ziming Chen, Zhaoping Yue, Wei Ma, Shanyuan Chen, Heng Xiao, Robert W. Murphy, Ya‐Ping Zhang, RuiGuang Zan et al. · 2013 · Chinese Science Bulletin
38. Inferring the Root of Isoëtes: Exploring Alternatives in the Absence of an Acceptable Outgroup
    Eric Schuettpelz, Sara B. Hoot · 2006 · Systematic Botany
39. [23] Combined DNA and protein alignment
    Jotun Hein, Jens Støvlbæk · 1996 · Methods in enzymology on CD-ROM/Methods in enzymology
40. Phylogenetic relationships of the Japanese minnows, Pseudorasbora (Cyprinidae), as inferred from mitochondrial 16S rRNA gene sequences
    Katsutoshi Watanabe, Kei’ichiroh Iguchi, Kazumi Hosoya, Mutsumi Nishida · 2000 · Ichthyological Research
41. A new phylogenetic protocol: dealing with model misspecification and confirmation bias in molecular phylogenetics
    Lars Sommer Jermiin, Renee A. Catullo, Barbara R. Holland · 2020 · NAR Genomics and Bioinformatics
42. Generality of the Structurally Constrained Protein Evolution model: assessment on representatives of the four main fold classes
    Gustavo D. Parisi, Julián Echave · 2004 · Gene
43. Identification and characterization of RING-finger ubiquitin ligase UBR7 in mammalian spermatozoa
    Shawn W. Zimmerman, Young‐Joo Yi, Miriam Sutovsky, Fred W. van Leeuwen, Gavin C. Conant, Peter Šutovský · 2014 · Cell and Tissue Research
44. Philosophy and Phylogenetic Inference: A Comparison of Likelihood and Parsimony Methods in the Context of Karl Popper's Writings on Corroboration
    Mark Edward Siddall · 2001 · Cladistics
45. Elucidating the Population Histories and Transmission Dynamics of Papillomaviruses Using Phylogenetic Trees
    Chi-Keong Ong, Sean Nee, Andrew Rambaut, Hans‐Ulrich Bernard, Paul Harvey · 1997 · Journal of Molecular Evolution
46. Dynamically Heterogenous Partitions and Phylogenetic Inference: An Evaluation of Analytical Strategies with Cytochrome b and ND6 Gene Sequences in Cranes
    Carey Krajewski, Matthew G. Fain, Larry Buckley, David G. King · 1999 · Molecular Phylogenetics and Evolution
47. PAML (Phylogenetic Analysis by Maximum Likelihood)
    Michael P. Cummings · 2004 · Wiley eBooks
48. Molecular Phylogenetic Reconstruction
    Michael Weiß, Markus Göker · 2011 · Elsevier eBooks
49. Testing Synchrony in Historical Biogeography: The Case of New World Primates and Hystricognathi Rodents
    Letícia Loss de Oliveira, Barbara O. Aguiar, Carlos Guerra Schrago · 2012 · Evolutionary Bioinformatics
50. Power Analysis of Tests for Loss of Selective Constraint in Cave Crayfish and Nonphotosynthetic Plant Lineages
    Jim Leebens‐Mack, Claude W. dePamphilis · 2002 · Molecular Biology and Evolution
51. Posterior Mapping and Posterior Predictive Distributions
    Jonathan P. Bollback · 2005 · Statistics in the health sciences
52. A New Method for Characterizing Replacement Rate Variation in Molecular Sequences: Application of the Fourier and Wavelet Models to Drosophila and Mammalian Proteins
    Pavel S Morozov, T. Ya. Sitnikova, Gary A. Churchill, Francisco J. Ayala, Andrey Rzhetsky · 2000 · Genetics
53. Small Mammal Investigation in Spotted Fever Focus with DNA-Barcoding and Taxonomic Implications on Rodents Species from Hainan of China
    Liang Lu, Douglas Chesters, Wen Zhang, Guichang Li, Ying Ma, Huailei Ma, Xiuping Song, Haixia Wu, Fengxia Meng, Chao‐Dong Zhu et al. · 2012 · PLoS ONE
54. πBUSS: 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 · 2014 · BMC Bioinformatics
55. Phylogeographic incongruence of codistributed amphibian species based on small differences in geographic distribution
    Craig A. Steele, Andrew T. Storfer · 2006 · Molecular Phylogenetics and Evolution
56. PHYLOGEOGRAPHY AND HISTORY OF GIANT GALÁPAGOS TORTOISES
    Adalgisa Caccone, Gabriele Gentile, James P. Gibbs, Thomas H. Fritts, Howard L. Snell, Jessica Betts, Jeffrey R. Powell · 2002 · Evolution
57. Model adequacy tests for probabilistic models of chromosome‐number evolution
    Anna Rice, Itay Mayrose · 2020 · New Phytologist
58. Roadmap to the study of gene and protein phylogeny and evolution—A practical guide
    Florian Jacques, Paulina Bolívar, Kristian Pietras, Emma U. Hammarlund · 2023 · PLoS ONE
59. Identifying Optimal Models of Evolution
    Lars Sommer Jermiin, Vivek Jayaswal, Faisal M. Ababneh, John Robinson · 2016 · Methods in molecular biology
60. The evolutionary history of krill inferred from nuclear large subunit rDNA sequence analysis
    Simon Jarman · 2001 · Biological Journal of the Linnean Society
61. Mitochondrial Variation in Sharp-Tailed Snakes (Contia tenuis): Evidence of a Cryptic Species
    Chris R. Feldman, Greg S. Spicer · 2002 · Journal of Herpetology
62. X Chromosome Inactivation and Xist Evolution in a Rodent Lacking LINE-1 Activity
    Michael A. Cantrell, Bryan C. Carstens, Holly A. Wichman · 2009 · PLoS ONE
63. Genetic Distance for a General Non-Stationary Markov Substitution Process
    Benjamin D. Kaehler, Von Bing Yap, Rongli Zhang, Gavin A. Huttley · 2014 · Systematic Biology
64. Evaluation of the Amazon River delta as a barrier to gene flow for the regional malaria vector,Anopheles aquasalis(Diptera: Culicidae) in northeastern Brazil
    Temeika L. Fairley, Marinete Marins Póvoa, Jan Evelyn Conn · 2002 · Journal of Medical Entomology
65. A tenth crucial question regarding model use in phylogenetics
    John Gatesy · 2007 · Trends in Ecology & Evolution
66. Felsenstein Phylogenetic Likelihood
    David Posada, Keith A. Crandall · 2021 · Journal of Molecular Evolution
67. Conservation genetics, evolution and distinct population segments of the Mojave fringe-toed lizard, Uma scoparia
    Robert W. Murphy, Tanya L. Trépanier, David J. Morafka · 2006 · Journal of Arid Environments
68. FROM MORE TO FEWER? TESTING AN ALLEGEDLY PERVASIVE TREND IN THE EVOLUTION OF MORPHOLOGICAL STRUCTURE
    Sarah J. Adamowicz, Aandy Purvis · 2006 · Evolution
69. Testing Substitution Models Within a Phylogenetic Tree
    G. Weiss · 2003 · Molecular Biology and Evolution
70. A method for determining the position and size of optimal sequence regions for phylogenetic analysis
    Maria Jesus Martin, Fernando Gónzález‐Candelas, Francisco Sobrino, Joaquı́n Dopazo · 1995 · Journal of Molecular Evolution
71. Posterior predictive checks of coalescent models: P2C2M, an R package
    Michael Gruenstaeudl, Noah M. Reid, Gregory L. Wheeler, Bryan C. Carstens · 2015 · Molecular Ecology Resources
72. Phylogenetics of the common raven complex (Corvus: Corvidae) and the utility of ND4, COI and intron 7 of the β‐fibrinogen gene in avian molecular systematics
    Chris R. Feldman, Kevin E. Omland · 2005 · Zoologica Scripta
73. Sequences of psychrophilic fungi amplified from glacier-preserved ascolichens
    Paula T. DePriest, Natalia V Ivanova, Dianne Fahselt, Vagn Alstrup, Andrea Gargas · 2000 · Canadian Journal of Botany
74. Phylogenetic Tree Reconstruction Accuracy and Model Fit when Proportions of Variable Sites Change across the Tree
    Liat Shavit Grievink, David Penny, Michael D. Hendy, Barbara R. Holland · 2010 · Systematic Biology
75. Testing a Molecular Clock without an Outgroup: Derivations of Induced Priors on Branch-Length Restrictions in a Bayesian Framework
    Marc A. Suchard, Robert E. Weiss, Janet S. Sinsheimer · 2003 · Systematic Biology
76. Advances in understanding the evolution of HIV.
    Keith A. Crandall, Daniel A. Vasco, David Posada, Hiromi Imamichi · 1999 · PubMed
77. Sphaerolejeunea (Lejeuneaceae, Porellales) is a synonym of Lejeunea
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78. Phylogenetic relationships of extant zokors (Myospalacinae) (Rodentia, Spalacidae) inferred from mitochondrial DNA sequences
    Junhu Su, Weihong Ji, Jing Wang, Dianne M. Gleeson, Janwei Zhou, Limin Hua, Yanming Wei · 2013 · Mitochondrial DNA
79. Peri-Tyrrhenian Phylogeography in the Land SnailSolatopupa guidoni(Pulmonata)
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80. The scale of genetic differentiation in the Dunes Sagebrush-Lizard (Sceloporus arenicolus), an endemic habitat specialist
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81. Rapid Evaluation of the Phylogenetic Congruence of Sequence Data Using Likelihood Ratio Tests
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82. Synthetic gene technology: Applications to ancestral gene reconstruction and structure-function studies of receptors
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83. Testing for Equality of Molecular Evolutionary Rates: A Comparison Between a Relative-Rate Test and a Likelihood Ratio Test
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84. Dynamic programming procedure for searching optimal models to estimate substitution rates based on the maximum-likelihood method
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85. A duplication of gcyc predates divergence within tribe Coronanthereae (Gesneriaceae): Phylogenetic analysis and evolution
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86. Maximum Likelihood Analysis of Gene-Based and Structure-Based Process Partitions, Using Mammalian Mitochondrial Genomes
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87. Application of the Likelihood Function in Phylogenetic Analysis
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88. Investigating Signs of Recent Evolution in the Pool of Proviral HIV Type 1 DNA during Years of Successful HAART
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89. Morphological and molecular characterisation of Paranoplocephala buryatiensis n. sp. and P. longivaginata Chechulin & Gulyaev, 1998 (Cestoda: Anoplocephalidae) in voles of the genus Clethrionomys
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90. Phylogenetic Relationships of Cyprinid Fishes in SubgenusNotropisInferred from Nucleotide Sequences of the Mitochondrially Encoded CytochromebGene
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91. Differences in Performance among Test Statistics for Assessing Phylogenomic Model Adequacy
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92. A Mutation–Selection Model of Protein Evolution under Persistent Positive Selection
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93. Conservation genetics and breeding system of Penstemon debilis (Plantaginaceae), a rare beardtongue endemic to oil shale talus in western Colorado, USA
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94. A dated molecular phylogeny of the Proctolabinae (Orthoptera, Acrididae), especially the Lithoscirtae, and the evolution of their adaptive traits and present biogeography
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95. Local and global multivariate analysis of geographical mitochondrial DNA variation in Leuciscus cephalus L. 1758 (Pisces: Cyprinidae) in the Balkan Peninsula
    Jean-Dominique Durand, Bruno Guinand, Yvette Bouvet · 1999 · Biological Journal of the Linnean Society
96. AliSim-HPC: parallel sequence simulator for phylogenetics
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97. Phylogeny and historical demography of economically important rodents of the genus Arvicanthis (Mammalia: Muridae) from the Nile Valley: of mice and men
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98. P2C2M.GMYC: An R package for assessing the utility of the Generalized Mixed Yule Coalescent model
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99. Phylogenetic models and model selection for noncoding DNA
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100. The complete mitochondrial genome of Damora sagana and phylogenetic analyses of the family Nymphalidae
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