Estimating the pattern of nucleotide substitution

Yang, Ziheng·1994·Journal of Molecular Evolution

Cited by (1,001)

Items 901–1,000 of 1,001

  1. Complete mitochondrial genome of red goral ( Naemorhedus baileyi ) and a complete estimate of the phylogenetic relationships in Caprinae
    Rui Shi, Yujiao Sun, Liwei Teng, Zhensheng Liu · 2015 · Mitochondrial DNA Part A
  2. Predicting the Evolution of two Genes in the Yeast Saccharomyces Cerevisiae
    Jacques Mohcine Bahi, Christophe Guyeux, Antoine Perasso · 2012 · Procedia Computer Science
  3. Variation in the Neisseria meningitidis FadL-like protein: an evolutionary model for a relatively low-abundance surface antigen
    Daniel Yero, Caroline Vipond, Yanet Climent, Gretel Sardiñas, Ian M. Feavers, Rolando Pajón · 2010 · Microbiology
  4. A Robust ANOVA Approach to Estimating a Phylogeny from Multiple Genes
    Ximing Xu, Katherine A. Dunn, Chris Field · 2015 · Molecular Biology and Evolution
  5. Phylogeographical Pattern in the Southern African Grass Tenaxia disticha (Poaceae)
    Hans Peter Linder, Franziska Perl, Yanis Bouchenak‐Khelladi, Nigel Paul Barker · 2014 · Systematic Botany
  6. An Evolution Model for Sequence Length Based on Residue Insertion–Deletion Independent of Substitution: An Application to the GC Content in Bacterial Genomes
    Sophie Lèbre, Christian J. Michel · 2012 · Bulletin of Mathematical Biology
  7. Calculating Higher-Order Moments of Phylogenetic Stochastic Mapping Summaries in Linear Time
    Amrit Dhar, Vladimir N. Minin · 2017 · Journal of Computational Biology
  8. Scaling Up the Phylogenetic Detection of Lateral Gene Transfer Events
    Cheong Xin Chan, Robert Gerald Beiko, Mark A. Ragan · 2016 · Methods in molecular biology
  9. The Influence of the Selection at the Amino Acid Level on Synonymous Codon Usage from the Viewpoint of Alternative Genetic Codes
    Konrad Pawlak, Paweł Błażej, Dorota Mackiewicz, Paweł Mackiewicz · 2023 · International Journal of Molecular Sciences
  10. Genome evolution by transformation, expansion and contraction (GETEC)
    Emmanuel Benard, Sophie Lèbre, Christian J. Michel · 2015 · Biosystems
  11. Distribution of distances between topologies and its effect on detection of phylogenetic recombination
    Leonardo de Oliveira Martins, Hirohisa Kishino · 2009 · Annals of the Institute of Statistical Mathematics
  12. Spatial and temporal variations in species diversity of fish assemblages near a sewage treatment plant in northern Taiwan
    Hungyen Chen, Ching‐Yi Chen, Kwang‐Tsao Shao, Gwo‐Ching Gong · 2019 · Fisheries Science
  13. Morphological and molecular evidence supports the first occurrence of two fishes, Siganus sutor (Valenciennes, 1835) and Seriolina nigrofasciata (Rüppell, 1829) (Actinopterygii: Perciformes), from marine waters of Odisha coast, Bay of Bengal, India
    Tapan Kumar Barik, Surya Narayan Swain, Bijayalaxmi Sahu, Bibarani Tripathy, Usha Rani Acharya · 2020 · Acta Oceanologica Sinica
  14. Computational Analysis of CoV-2, Severe Acute Respiratory Syndrome CoV & Middle East Respiratory Syndrome Genome using MEGA
    Vipan Kumar Sohpal · 2020 · Genomics & Informatics
  15. A Test of Amino Acid Reversibility
    Nick G.C. Smith, Adam Eyre‐Walker · 2001 · Journal of Molecular Evolution
  16. The speciation history of Heliconius : inferences from multilocus DNA sequence data
    Margarita Beltrán · 2005 · OpenGrey (Institut de l'Information Scientifique et Technique)
  17. Phylogeny Estimation Using Likelihood‐Based Methods
    John P. Huelsenbeck · 2019 · Wiley eBooks
  18. A new molecular evolution model for limited insertion independent of substitution
    Sophie Lèbre, Christian J. Michel · 2013 · Mathematical Biosciences
  19. Measuring Phylogenetic Information of Incomplete Sequence Data
    Tae‐Kun Seo, Olivier Gascuel, Jeffrey L. Thorne · 2021 · Systematic Biology
  20. Neutral and adaptive protein evolution
    Ziheng Yang · 2014 · Oxford University Press eBooks
  21. Morphometric and Molecular Characterization of Anastrepha Species in the spatulata Group (Diptera, Tephritidae)
    Zuzinaide Vidal Bomfim, K M Lima, Janisete Gomes Silva, Marco Antônio Costa, Roberto Antonio Zucchi · 2014 · Annals of the Entomological Society of America
  22. Computational Evaluation of the Strict Master and Random Template Models of Endogenous Retrovirus Evolution
    Fabrícia Ferreira do Nascimento, Allen G. Rodrigo · 2016 · PLoS ONE
  23. Ophiostoma sugadairense , a new species in the Ophiostoma piceae complex associated with bark beetles infesting Japanese larch in Japan
    Jin Li, Hayato Masuya, Izumi Okane, Yuichi Yamaoka · 2017 · Mycoscience
  24. Representations of Search Spaces in the Problem of Mutational Pressure Optimization According to Protein-Coding Sequences
    Paweł Błażej, Małgorzata Wnętrzak, Małgorzata Grabińska, Paweł Mackiewicz · 2017 · Journal of Computational Biology
  25. Simulating molecular evolution
    Ziheng Yang · 2014 · Oxford University Press eBooks
  26. Forcing reversibility in the no-strand-bias substitution model allows for the theoretical and practical identifiability of its 5 parameters from pairwise DNA sequence comparisons
    Osvaldo Zagordi, Jean R. Lobry · 2005 · Gene
  27. Migratory ecology of skipjack tuna Katsuwonus pelamis caught off Kyushu Island, Japan —a potential size screening effect of the Kuroshio
    Hideyuki Yamashita, Takashi Yanagimoto, Kay Sakuma, TAKUTO KIMURA, Kohei Kurosaka, Miki Ogura · 2018 · NIPPON SUISAN GAKKAISHI
  28. Fossombronia isaloensis Cargill & D.A.Callaghan, a new liverwort from sandstone massifs in southern Madagascar
    D. Christine Cargill, Des A. Callaghan, Laura L. Forrest, Catherine Reeb · 2020 · Journal of Bryology
  29. Seeing the woodhoopoe for the trees: should we abandon Namibia's Violet Woodhoopoe Phoeniculus damarensis as a species?
    Robert E. Simmons, Morné A. Du Plessis, Terry A J Hedderson · 2005 · Ibis
  30. The reversible stationary markov process for estimating the pattern of nucleotide substitution: A response to Ziheng Yang
    Cecilia Saccone, Cecilia Lanave, Graziano Pesole, Giuliano Preparata · 1995 · Journal of Molecular Evolution
  31. An Approximate Maximum Likelihood Approach, Applied to Phylogenetic Trees
    Henrik Jönsson, Bo Söderberg · 2003 · Journal of Computational Biology
  32. Ergodicity of some dynamics of DNA sequences
    Mikael Falconnet, Nina Gantert, Ellen Saada · 2019 · arXiv (Cornell University)
  33. An alignment-free generalization to indels of Felsenstein's phylogenetic pruning algorithm
    Oscar Westesson, Gerton A. Lunter, Benedict Paten, Ian Holmes · 2011 · arXiv (Cornell University)
  34. Potential role of Mercury pollutants in the success of Methicillin-Resistant Staphylococcus aureus USA300 in Latin America
    Claude-Alexandre Gustave, Jean‐Philippe Rasigade, Patrícia Martins-Simões, Florence Couzon, Chloé Bourg, Anne Tristan, Frederic J. Laurent, Thierry Wirth, François Vandenesch · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
  35. The causes and consequences of variation in evolutionary processes acting on DNA sequences
    Lee Bofkin · 2006 · Europe PMC (PubMed Central)
  36. Probabilistic Models for the Study of Protein Evolution
    Jeffrey L. Thorne, N. Goldman · 2003 · Wiley eBooks
  37. Robust Phylogenetics
    Qin Liu, Bùi Quang Minh, Robert Lanfear, Michael Charleston, Shane A. Richards, Barbara R. Holland · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  38. Improving the Scalability of Bayesian Phylodynamic Inference through Efficient MCMC Proposals
    Remco Bouckaert, Paula Weidemüller, Luis R. Esquivel Gomez, Nicola Felix Müller · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  39. High ward-level and within-sample diversity of Klebsiella pneumoniae on a Malawian neonatal unit revealed by single colony whole genome sequencing and post-enrichment metagenomics
    Oliver Pearse, Allan M. Zuza, Rebecca Lester, Helen Mangochi, Patricia Siyabu, Edith Tewesa, Thomas Edwards, Nicholas R Thomson, Nicholas Feasey, Kondwani Kawaza et al. · 2025 · medRxiv
  40. piqtree: a python package for seamless phylogenetic inference with IQ-TREE
    R A McArthur, Thomas K. F. Wong, Yapeng Lang, Richard Andrew Morris, Katherine Caley, Vijini Mallawaarachchi, Bùi Quang Minh, Gavin A. Huttley · 2026 · Molecular Biology and Evolution
  41. 高度特化等级裂腹鱼类分子系统发育与生物地理学
    德奎 何, 毅峰 陈 · 2007 · Chinese Science Bulletin (Chinese Version)
  42. Models of amino acid and codon substitution
    Ziheng Yang · 2014 · Oxford University Press eBooks
  43. Genetic Diversification of Crimean‐Congo Hemorrhagic Fever Virus Lineage Europe 1
    Yàn Li · 2025 · Annals of the New York Academy of Sciences
  44. Phylogenetic analysis and machine learning identify signatures of selection and predict deleterious mutations in common bean (Phaseolus vulgaris L.)
    Henry A. Cordoba-Novoa, Edward S. Buckler, M. Cinta Romay, Ana Berthel, L Johnson, Parthiba M. Balasubramanian, Valerio Hoyos‐Villegas · 2026 · BMC Biology
  45. Multiple conversion between the genes encoding bacterial class-I release factors
    Sohta A. Ishikawa, Ryoma Kamikawa, Yuji Inagaki · 2015 · Scientific Reports
  46. Models of amino acid and codon substitution
    Ziheng Yang · 2006 · Oxford University Press eBooks
  47. Coalescent theory and species trees
    Ziheng Yang · 2014 · Oxford University Press eBooks
  48. Bases-dependent Rapid Phylogenetic Clustering (Bd-RPC) enables precise and efficient phylogenetic estimation in viruses
    Bin Ma, Huimin Gong, Qianshuai Xu, Yuan Gao, Aohan Guan, Haoyu Wang, Kexin Hua, Rui Luo, Hui Jin · 2024 · Virus Evolution
  49. Plasmid conjugation drives within–patient plasmid diversity
    Fan Grayson, Leo Loman, Toby Nonnenmacher, Diane Pople, Jack Pollard, Bharat Patel, David Williams, Luke S. Hounsome, Katie L. Hopkins, Julie V. Robotham et al. · 2025 · Microbial Genomics
  50. Relaxing the Hypotheses of Symmetry and Time-Reversibility in Genome Evolutionary Models
    Jacques Mohcine Bahi, Christophe Guyeux, Antoine Perasso · 2014 · British Journal of Mathematics & Computer Science
  51. Models of nucleotide substitution
    Ziheng Yang · 2006 · Oxford University Press eBooks
  52. Diversifying evolution of endo-beta-1,4-glucanase in termites (Isoptera).
    Qinggang Xu, Yue Zhou, Jun Li, Huayou Chen, Jian Lü, Keping Chen, Jianchu Mo, Zhu Muyuan, Chiyu Zhang · 2010 · Sociobiology
  53. The application of cophylogenic tools to gene sets
    Bernard R. Baum, Douglas A. Johnson · 2010 · Taxon
  54. Survey of molecular phylogenetics
    Martina Talianová · 2007 · Plant Soil and Environment
  55. A New Species of the Sand-burrowing Dogielinotidae, Haustorioides furotai, from Tokyo Bay, Japan (Crustacea: Amphipoda)
    Hiroshi Ogawa, Yoshitake Takada, Kay Sakuma · 2021 · Species Diversity
  56. Environmental factors affect the evolution of linguistic subgroups in Borneo
    Alexander D. Smith, Taraka Rama · 2022 · Diachronica
  57. Evolutionary Distances
    Naruya Saitou · 2018 · Computational biology
  58. Bayesian methods
    Ziheng Yang · 2006 · Oxford University Press eBooks
  59. Reconstructing Phylogenies Using Branch-Variable Substitution Models and Unaligned Biomolecular Sequences: A Performance Study and New Resampling Method
    Rei Doko, Kevin J. Liu · 2023 · ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB)
  60. TAXON DELINEATION IN GELECHIOID MOTHS: FROM PHYLOGENETICS TO DNA BARCODING
    Mari Kekkonen · 2014 · Työväentutkimus Vuosikirja
  61. Stochastic Modeling of Biological Sequence Evolution
    Keyuan Xu · 2005 · DSpace@MIT (Massachusetts Institute of Technology)
  62. Filogenia Molecular e Biogeografia das Espécies e Subespécies do Gênero Ramphastos (Piciformes: Ramphastidae)
    José Salvatore Leister Patané · 2007 · Digital Library of Theses and Dissertations (Universidade de São Paulo)
  63. The Effect of Cultural Values on Caregiving by Generation
    Yun-Jeong Kim, Hyun‐Jung Kang · 2015 · Indian Journal of Science and Technology
  64. Estimating evolutionary rate of local protein binding surfaces: a Bayesian Monte Carlo approach
    Yan Yuan Tseng, Jie Liang · 2005 · Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)
  65. Molecular Evolution, Models of
    Joseph P. Bielawski · 2016 · Elsevier eBooks
  66. Computational Modeling of Drug Resistance: Structural and Evolutionary Models
    Maryah Safi · 2014 · TSpace (University of Toronto)
  67. Null Codon-Based Models of Synonymous and Nonsynonymous Substitution From a Phylogenetic Perspective.
    David A. McClellan · 1999
  68. Ratite molecular evolution, phylogeny and biogeography inferred from complete mitochondrial genomes
    Oliver Haddrath · 2000 · Library and Archives Canada (Government of Canada)
  69. Predicting the Evolution of Gene $ura3$ in the Yeast Saccharomyces Cerevisiae
    Jacques Mohcine Bahi, Christophe Guyeux, Antoine Perasso · 2017 · arXiv (Cornell University)
  70. Phylogeny inference under the general Markov model using MST-backbone
    Prabhav Kalaghatgi · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
  71. Shedding light on the underlying characteristics of genomes using Kronecker model families of codon evolution
    Maryam Zaheri, Nicolas Salamin · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
  72. Virus Evolution
    Yukiko Suzuki, A. Wyndham, T. Gojobori · 2003 · Wiley eBooks
  73. Maximum likelihood methods
    Ziheng Yang · 2014 · Oxford University Press eBooks
  74. Molecular Dating of Evolutionary Events
    David Alejandro Duchêne, Lindell D. Bromham · 2015 · Encyclopedia of earth sciences series/Encyclopedia of earth sciences
  75. The Impact of Multiple Sequence Alignment Error on Phylogenetic Estimation under Variable-Across-Phylogeny Substitution Models
    Rei Doko, Kevin J. Liu · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  76. A phylogenetic analysis of the Accipitridae (class Aves).
    Robert R. Sheehy · 1995 · UA Campus Repository (The University of Arizona)
  77. Computational statistics in molecular phylogenetics
    William Fletcher · 2011 · UCL Discovery (University College London)
  78. Modeling Site-Specific Mutation Patterns in Pandemic-Scale Phylogenetics
    Samuel Martin, Nhan Ly-Trong, Bùi Quang Minh, Nick Goldman, Nicola De Maio · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  79. The statistical approach to molecular phylogeny: Evidence for a nonhyperthermophilic common ancestor
    Nicolas Galtier · 2007 · Springer eBooks
  80. Probabilistic model-based approach to evolutionary analysis of non-coding sequences
    Jaebum Kim · 2010 · Illinois Digital Environment for Access to Learning and Scholarship (University of Illinois at Urbana-Champaign)
  81. Estimating Human Point Mutation Rates from Codon Substitution Rates
    Kazuharu Misawa · 2012 · InTech eBooks
  82. Amino Acid Substitution Matrices Estimated by Maximum Likelihood
    Leonardo Martins, Paolo Marinho de Andrade Zanotto · 2001 · Proceedings Genome Informatics Workshop/Genome informatics
  83. Des algorithmes bioinformatiques pour la recherche des régions génomiques responsables d'une maladie
    Dunarel Badescu · 2009 · Archipel (Université du Québec à Montréal)
  84. Méthodes de distance pour l'inférence phylogénomique
    Alexis Criscuolo · 2006 · HAL
  85. Evaluating Estimates of Markov Models of Sequence Evolution through Simulation
    Keyuan Xu, George C. Verghese, Peter C. Doerschuk · 2005 · Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)
  86. Random Local Clock and Molecular Evolution Studies on Corydalis (Papaveraceae s. l.)
    Sophia Wan-Pyo Hong · 2012 · International Journal of Biology
  87. Phylogenetic analysis of HIV-1 in Mpumalanga
    P Msimanga · 2013 · SUNScholar (Stellenbosch University)
  88. Phylogenetic Trees Predicted by an Irreversible Markov Process
    Erich Bohl, Ryan Hamilton, Peter Lancaster · 2008 · MIMS EPrints (University of Southampton)
  89. GENETIC DIVERSITY WITHIN THE LLANO POCKET GOPHER, GEOMYS TEXENSIS
    L. Rex McAliley, Philip D. Sudman · 2005 · The Southwestern Naturalist
  90. A computational system for identifyingcis-regulatory elements in closely related genomes
    Lee A. Newberg, Mukkai S. Krishnamoorthy, Thomas M. Smith · 2006
  91. DNA Barcodes for certain endangered Indian Tylophora species
    V. A. Sebastian, R. B. Subramanian, Laura de la Cruz, Vincent Braganza · 2010
  92. GRAMMICA (CONVOLVULACEAE) USING PLASTID AND NUCLEAR DNA SEQUENCES 1
    Saša Stefanović, Maria Kuzmina, Mihai Costea · 2007
  93. INTRODUCTION TO PHYLOGENETICS: A STUDY OF MAXIMUM PARSIMONY AND MAXIMUM LIKELIHOOD METHODS
    Naomi R. Iuhasz · 2010
  94. Operators on Networks
    Delio Mugnolo · 2014 · Understanding complex systems
  95. Needle fungi and tree health of Pinus radiata in Tasmania
    Istiana Prihatini · 2014 · UTAS Research Repository
  96. A NEW TEST TO BUILD CONFIDENCE REGIONS USING BALANCED MINIMUM EVOLUTION
    Wei Dai · 2013 · Library and Archives Canada (Government of Canada)
  97. A likelihood based clustering method for detection of recombination for DNA and Amino Acid sequences
    Li Li · 2016 · DalSpace (Dalhousie University)
  98. Testing Patterns of Nucleotide Substitution Rates at Multiple Genes
    Wenli X. Tao · 2002 · NCSU Libraries Repository (North Carolina State University Libraries)
  99. Molecular Phylogenetics: A Tool for Elucidation of Evolutionary Processes from Biological Data
    Martina Talianová · 2015 · Apple Academic Press eBooks
  100. Comparison of methods and tests on trees
    Ziheng Yang · 2006 · Oxford University Press eBooks