ModelFinder: fast model selection for accurate phylogenetic estimates

Kalyaanamoorthy, Subha, Minh, Bui Quang, Wong, Thomas K F, von Haeseler, Arndt, Jermiin, Lars S·2017·Nature Methods

Cited by (1,026)

Items 301–400 of 1,026

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    Emily J. Warschefsky, Eric von Wettberg · 2019 · New Phytologist
  2. Ectosymbiotic bacteria at the origin of magnetoreception in a marine protist
    Caroline L. Monteil, David Vallenet, Nicolas Menguy, Karim Benzerara, Valérie Barbe, Stéphanie Fouteau, Corinne Cruaud, Magali Floriani, Éric Viollier, Géraldine Adryanczyk‐Perrier et al. · 2019 · Nature Microbiology
  3. Phylogenomic analysis and revised classification of atypoid mygalomorph spiders (Araneae, Mygalomorphae), with notes on arachnid ultraconserved element loci
    Marshal C. Hedin, Shahan Derkarabetian, Adan Alfaro, Martín Javier Ramírez, Jason E. Bond · 2019 · PeerJ
  4. A phylogenomic analysis of Nepenthes (Nepenthaceae)
    Bruce Murphy, Félix Forest, Timothy G. Barraclough, James Rosindell, Sidonie Bellot, Robyn S. Cowan, Michal R. Golos, Matthew Jebb, Martin Cheek · 2019 · Molecular Phylogenetics and Evolution
  5. A Repertory of Rearrangements and the Loss of an Inverted Repeat Region in Passiflora Chloroplast Genomes
    Luiz Augusto Cauz‐Santos, Zirlane Portugal da Costa, Caroline Callot, Stéphane Cauet, Maria Imaculada Zucchi, Hélène Bergès, Cássio van den Berg, Maria Lúcia Carneiro Vieira · 2020 · Genome Biology and Evolution
  6. Genetic evidence for the origin ofAedes aegypti, the yellow fever mosquito, in the southwestern Indian Ocean
    John Soghigian, Andrea Gloria‐Soria, Vincent Robert, Gilbert Le Goff, Anna‐Bella Failloux, Jeffrey R. Powell · 2020 · Molecular Ecology
  7. Radiation of nitrogen‐metabolizing enzymes across the tree of life tracks environmental transitions in Earth history
    Parsons, Chris, Stüeken, Eva E., Rosen, Caleb J., Mateos, Katherine, Anderson, Rika E. · 2021 · Geobiology
  8. Systematic prediction of genes functionally associated with bacterial retrons and classification of the encoded tripartite systems
    Mario Rodríguez Mestre, Alejandro González-Delgado, Luis I. Gutierrez-Rus, Francisco Martínez‐Abarca, Nicolás Toro · 2020 · Nucleic Acids Research
  9. Comparative and phylogenetic analyses of six Kenya Polystachya (Orchidaceae) species based on the complete chloroplast genome sequences
    Hui Jiang, Jing Tian, Jiaxin Yang, Xiang Dong, Zhixiang Zhong, Geoffrey Mwachala, Caifei Zhang, Guang‐Wan Hu, Qingfeng Wang · 2022 · BMC Plant Biology
  10. Taxonomic Sampling and Rare Genomic Changes Overcome Long-Branch Attraction in the Phylogenetic Placement of Pseudoscorpions
    Andrew Z. Ontano, Guilherme Gainett, Shlomi Aharon, Jesús A. Ballesteros, Ligia R. Benavides, Kevin F Corbett, Efrat Gavish‐Regev, Mark Stephen Harvey, Scott A. Monsma, Carlos E. Santibáñez‐López et al. · 2021 · Molecular Biology and Evolution
  11. Characterization of a novel type of carbonic anhydrase that acts without metal cofactors
    Yoshihisa Hirakawa, Miki Senda, Kodai Fukuda, Hong Yang Yu, Masaki Ishida, M. Taira, Kazushi Kinbara, Toshiya Senda · 2021 · BMC Biology
  12. HybPhaser: A workflow for the detection and phasing of hybrids in target capture data sets
    Lars Nauheimer, Nicholas Weigner, Elizabeth Joyce, Darren M. Crayn, Charles M. Clarke, Katharina Nargar · 2021 · Applications in Plant Sciences
  13. Complete chloroplast genome sequence of Fagopyrum dibotrys: genome features, comparative analysis and phylogenetic relationships
    Xumei Wang, Tao Zhou, Guoqing Bai, Yuemei Zhao · 2018 · Scientific Reports
  14. The evolution of functional complexity within the β-amylase gene family in land plants
    Matthias Thalmann, Mario Coiro, Tiago Meier, Thomas Wicker, Samuel C. Zeeman, Diana Santelia · 2019 · BMC Evolutionary Biology
  15. Towards a plant model for enigmatic U‐to‐C RNA editing: the organelle genomes, transcriptomes, editomes and candidate RNA editing factors in the hornwort Anthoceros agrestis
    Philipp Gerke, Péter Szövényi, Anna Neubauer, Henning Lenz, Bernard Gutmann, Rose McDowell, Ian Small, Mareike Schallenberg‐Rüdinger, Volker Knoop · 2019 · New Phytologist
  16. Virus-like transposons cross the species barrier and drive the evolution of genetic incompatibilities
    Widen, Sonya A., Bes, Israel Campo, Koreshova, Alevtina, Pliota, Pinelopi, Krogull, Daniel, Burga, Alejandro · 2023 · Science
  17. Resolving the relationships of clams and cockles: dense transcriptome sampling drastically improves the bivalve tree of life
    Sarah Lemer, Rüdiger Bieler, Gonzalo Giribet · 2019 · Proceedings of the Royal Society B Biological Sciences
  18. Novel partiti-like viruses are conditional mutualistic symbionts in their normal lepidopteran host, African armyworm, but parasitic in a novel host, Fall armyworm
    Pengjun Xu, Liyu Yang, Xianming Yang, Tong Li, Robert I. Graham, Kongming Wu, Kenneth L. Wilson · 2020 · PLoS Pathogens
  19. Newly identified sex chromosomes in the Sphagnum (peat moss) genome alter carbon sequestration and ecosystem dynamics
    Adam L. Healey, Bryan Thomas Piatkowski, John T. Lovell, Avinash Sreedasyam, Sarah B. Carey, Sujan Mamidi, Shengqiang Shu, Christopher Plott, Jerry W. Jenkins, Travis J. Lawrence et al. · 2023 · Nature Plants
  20. Advances in the reconstruction of the spider tree of life: A roadmap for spider systematics and comparative studies
    Siddharth Kulkarni, Hannah Marie Wood, Gustavo Hormiga · 2023 · Cladistics
  21. Phylogenetic analysis of Antarctic notothenioids illuminates the utility of RADseq for resolving Cenozoic adaptive radiations
    Thomas J. Near, Daniel J. MacGuigan, Elyse Parker, Carl D. Struthers, CHRIS D. JONES, Alex Dornburg · 2018 · Molecular Phylogenetics and Evolution
  22. Evolution in the Genus Rhinella: A Total Evidence Phylogenetic Analysis of Neotropical True Toads (Anura: Bufonidae)
    Martín O. Pereyra, Boris L. Blotto, Diego Baldo, Juan C. Chaparro, Santiago R. Ron, Agustín J. Elias‐Costa, Patricia P. Iglesias, Pablo Javier Venegas, Maria Tereza C. Thomé, Jhon Jairo Ospina‐Sarria et al. · 2021 · Bulletin of the American Museum of Natural History
  23. Diversity and evolution of the vertebrate chemoreceptor gene repertoire
    Maxime Policarpo, Maude W. Baldwin, Didier Casañe, Walter Salzburger · 2024 · Nature Communications
  24. The Ly6/uPAR protein Bouncer is necessary and sufficient for species-specific fertilization
    Sarah Herberg, Krista R. Gert, Alexander Schleiffer, Andrea Pauli · 2018 · Science
  25. Uncoupled activation and cyclization in catmint reductive terpenoid biosynthesis
    Benjamin R. Lichman, Mohamed Omar Kamileen, Gabriel R. Titchiner, Gerhard Saalbach, Clare E. M. Stevenson, David M. Lawson, Sarah Ellen O'Connor · 2018 · Nature Chemical Biology
  26. Broad phylogenetic analysis of cation/proton antiporters reveals transport determinants
    Gal Masrati, Manish Dwivedi, Abraham Rimon, Yael Gluck-Margolin, Amit Kessel, Haim Ashkenazy, Itay Mayrose, Etana Padan, Nir Ben‐Tal · 2018 · Nature Communications
  27. A comprehensive molecular phylogeny of Geometridae (Lepidoptera) with a focus on enigmatic small subfamilies
    Leidys Murillo‐Ramos, Gunnar Brehm, Pasi Sihvonen, Axel Hausmann, Sille Holm, Hamid Reza Ghanavi, Erki Õunap, Andro Truuverk, Hermann S. Staude, Egbert Friedrich et al. · 2019 · PeerJ
  28. Contrasting Gene Decay in Subterranean Vertebrates: Insights from Cavefishes and Fossorial Mammals
    Maxime Policarpo, Julien Fumey, Philippe Lafargeas, Delphine Naquin, Claude Thermes, Magali Naville, Corentin Dechaud, Jean‐Nicolas Volff, Cédric Cabau, Christophe Klopp et al. · 2020 · Molecular Biology and Evolution
  29. Expanded Diversity and Phylogeny of mer Genes Broadens Mercury Resistance Paradigms and Reveals an Origin for MerA Among Thermophilic Archaea
    Christos A. Christakis, T. Barkay, E. Boyd · 2021 · Frontiers in Microbiology
  30. Isolation of a methyl-reducing methanogen outside the Euryarchaeota
    Kejia Wu, Lei Zhou, Guillaume Tahon, Laiyan Liu, Li Jiang, Jianchao Zhang, Fengfeng Zheng, Chengpeng Deng, Wenhao Han, Liping Bai et al. · 2024 · Nature
  31. Integrative approach using Yersinia pestis genomes to revisit the historical landscape of plague during the Medieval Period
    Amine Namouchi, Meriam Guellil, Oliver Kersten, Stephanie Hänsch, Claudio Ottoni, Boris V. Schmid, Elsa Pacciani, Luisa Quaglia, Marco Vermunt, Egil Lindhart Bauer et al. · 2018 · Proceedings of the National Academy of Sciences
  32. Chloroplast Genome Sequence of Artemisia scoparia: Comparative Analyses and Screening of Mutational Hotspots
    Shabina Iram, Muhammad Qasim Hayat, Muhammad Nouman Tahir, Alvina Gul, Abdullah Abdullah, Ibrar Ahmed · 2019 · Plants
  33. A phylogenomics approach to characterizing sensory neuron membrane proteins (SNMPs) in Lepidoptera
    Huijie Zhang, Wei Xu, Quan-mei Chen, Le-Na Sun, Alisha R. Anderson, Qingyou Xia, Alexie Papanicolaou · 2020 · Insect Biochemistry and Molecular Biology
  34. Novel RNA viruses associated with Plasmodium vivax in human malaria and Leucocytozoon parasites in avian disease
    Justine Charon, Matthew J. Grigg, John‐Sebastian Eden, Kim A. Piera, Hafsa Rana, Timothy William, Karrie A. Rose, Miles P. Davenport, Nicholas M. Anstey, Edward Charles Holmes · 2019 · PLoS Pathogens
  35. A nitrogenase-like enzyme system catalyzes methionine, ethylene, and methane biogenesis
    Justin A. North, Adrienne B. Narrowe, Weili Xiong, Kathryn M. Byerly, Guanqi Zhao, Sarah J. Young, Srividya Murali, John A. Wildenthal, William R. Cannon, Kelly C. Wrighton et al. · 2020 · Science
  36. Discovery and characterization of a novel family of prokaryotic nanocompartments involved in sulfur metabolism
    Robert J. Nichols, Benjamin J. LaFrance, Naiya R. Phillips, Devon R. Radford, Luke M. Oltrogge, Luis E. Valentin-Alvarado, Amanda J. Bischoff, Eva Nogales, David F. Savage · 2021 · eLife
  37. Detection and Typing of Plasmids in Acinetobacter baumannii Using rep Genes Encoding Replication Initiation Proteins
    Margaret M. C. Lam, Jonathan Koong, Kathryn E. Holt, Ruth M. Hall, Mohammad Hamidian · 2022 · Microbiology Spectrum
  38. Guanidinium export is the primal function of SMR family transporters
    Ali A. Kermani, Christian B. Macdonald, Roja Gundepudi, Randy B Stockbridge · 2018 · Proceedings of the National Academy of Sciences
  39. Characterization of the complete chloroplast genome sequence of Dalbergia species and its phylogenetic implications
    Yun Chun Song, Yongjiang Zhang, Jin Xu, Weimin Li, Mingfu Li · 2019 · Scientific Reports
  40. Integrative taxonomy, biogeography and conservation of freshwater mussels (Unionidae) in Russia
    Иван Николаевич Болотов, Alexander Vasilevich Kondakov, Ekaterina S. Konopleva, Ilya V. Vikhrev, Olga V. Aksenova, Andrey S. Aksenov, Yulia V. Bespalaya, Alexey V. Borovskoy, Данилов Петр Петрович, Геннадий Александрович Дворянкин et al. · 2020 · Scientific Reports
  41. SepF is the FtsZ anchor in archaea, with features of an ancestral cell division system
    N Pende, Adrià Sogues, Daniela Megrian, Anna Sartori-Rupp, Patrick England, Hayk Palabikyan, Simon K.‐M. R. Rittmann, Martín Graña, Anne Marie Wehenkel, Pedro M. Alzari et al. · 2021 · Nature Communications
  42. Phylogenomic Analysis of the Phylum Nematoda: Conflicts and Congruences With Morphology, 18S rRNA, and Mitogenomes
    Mohammed Ismail Ahmed, Nickellaus G. Roberts, Funmilola Adediran, Ashleigh B. Smythe, Kevin M. Kocot, Oleksandr V. Holovachov · 2022 · Frontiers in Ecology and Evolution
  43. Ecogenomics sheds light on diverse lifestyle strategies in freshwater CPR
    M. Chiriac, Paul-Adrian Bulzu, A. Andrei, Y. Okazaki, S. Nakano, M. Haber, V. Kavagutti, Paul Layoun, R. Ghai, M. Salcher · 2021 · Microbiome
  44. Solanum americanum genome-assisted discovery of immune receptors that detect potato late blight pathogen effectors
    Xiao Lin, Yuxin Jia, Robert Heal, Maxim Prokchorchik, Maria Sindalovskaya, Andrea Carolina Olave-Achury, Moffat Makechemu, Sebastian Fairhead, Azka Noureen, Jung Heo et al. · 2023 · Nature Genetics
  45. Stepwise emergence of the neuronal gene expression program in early animal evolution
    Sebastián R. Najle, Xavier Grau‐Bové, Anamaria Elek, Cristina Navarrete, Damiano Cianferoni, Cristina Chiva, Didac Cañas-Armenteros, Arrate Mallabiabarrena, Kai Kamm, Eduard Sabidó et al. · 2023 · Cell
  46. Rhizobia–diatom symbiosis fixes missing nitrogen in the ocean
    Bernhard Tschitschko, Mertcan Esti, Miriam Philippi, Abiel T. Kidane, Sten Littmann, Katharina Kitzinger, Daan R. Speth, Shengjie Li, Alexandra Claudia Kraberg, Daniela Tienken et al. · 2024 · Nature
  47. Pseudogenization and Resurrection of a Speciation Gene.
    K. Esfeld, Andrea E. Berardi, Michel Moser, E. Bossolini, L. Freitas, C. Kuhlemeier · 2018 · Current Biology
  48. Comparative genomics of Aeromonas veronii: Identification of a pathotype impacting aquaculture globally
    Hasan Cihad Tekedar, Salih Kumru, Jochen Blom, Andy Perkins, Matt J. Griffin, Hossam Abdelhamed, Attila Karsi, Mark L. Lawrence · 2019 · PLoS ONE
  49. Description and initial characterization of metatranscriptomic nidovirus-like genomes from the proposed new family Abyssoviridae, and from a sister group to the Coronavirinae, the proposed genus Alphaletovirus
    Khulud Bukhari, Geraldine Mulley, Anastasia A. Gulyaeva, Lanying Zhao, Guocheng Shu, Jianping Jiang, Benjamin W. Neuman · 2018 · Virology
  50. The application of high-throughput sequencing technology to analysis of amoA phylogeny and environmental niche specialisation of terrestrial bacterial ammonia-oxidisers
    Axel Aigle, James I. Prosser, Cécile Gubry‐Rangin · 2019 · Environmental Microbiome
  51. Membrane Lipid Composition of the Moderately Thermophilic Ammonia-Oxidizing Archaeon “ Candidatus Nitrosotenuis uzonensis” at Different Growth Temperatures
    Nicole J. Bale, Márton Palatinszky, W. Irene C. Rijpstra, Craig William Herbold, Michael Wagner, Jaap S. Sinninghe Damsté · 2019 · Applied and Environmental Microbiology
  52. Culicidae evolutionary history focusing on the Culicinae subfamily based on mitochondrial phylogenomics
    Alexandre Freitas da Silva, Laís Ceschini Machado, Márcia Bicudo de Paula, Carla Júlia da Silva Pessoa Vieira, Roberta Vieira de Morais Bronzoni, Maria Alice Varjal de Melo Santos, Gabriel Luz Wallau · 2020 · Scientific Reports
  53. Extensive introgression and mosaic genomes of Mediterranean endemic lizards
    Weizhao Yang, Nathalie Feiner, Catarina Pinho, Geoffrey M. While, Antigoni Kaliontzopoulou, David James Harris, Daniele Salvi, Tobias Uller · 2021 · Nature Communications
  54. Genome-scale sequencing and analysis of human, wolf, and bison DNA from 25,000-year-old sediment
    Pere Gelabert, Susanna Sawyer, Anders Bergström, Ashot Margaryan, Thomas C. Collin, Tengiz Meshveliani, Anna Belfer‐Cohen, David Lordkipanidze, Nino Jakeli, Zinovi Matskevich et al. · 2021 · Current Biology
  55. Phylogenomics and species delimitation of the economically important Black Basses (Micropterus)
    Daemin Kim, Andrew T. Taylor, Thomas J. Near · 2022 · Scientific Reports
  56. Comparative genomics reveals the distinct evolutionary trajectories of the robust and complex coral lineages
    Hua Ying, Ira Cooke, Susanne Sprungala, Weiwen Wang, David C. Hayward, Yurong Tang, Gavin A. Huttley, Eldon E. Ball, Sylvain Forêt, David John Miller · 2018 · Genome biology
  57. In silico analysis of fungal small RNA accumulation reveals putative plant mRNA targets in the symbiosis between an arbuscular mycorrhizal fungus and its host plant
    Alessandro Silvestri, Valentina Fiorilli, Laura Miozzi, Gian Paolo Accotto, Massimo Turina, Luisa Lanfranco · 2019 · BMC Genomics
  58. Whole Genome Shotgun Phylogenomics Resolves the Pattern and Timing of Swallowtail Butterfly Evolution
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  59. Complete Chloroplast Genomes of Anthurium huixtlense and Pothos scandens (Pothoideae, Araceae): Unique Inverted Repeat Expansion and Contraction Affect Rate of Evolution
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  60. Environmental gradients reveal stress hubs pre-dating plant terrestrialization
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  61. An integrative approach to discovering cryptic species within the Bemisia tabaci whitefly species complex
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  62. A phylogenomic resolution of the sea urchin tree of life
    Nicolás Mongiardino Koch, Simon E. Coppard, Harilaos A Lessios, Derek E. G. Briggs, Rich Mooi, Greg W. Rouse · 2018 · BMC Evolutionary Biology
  63. Using Core Genome Alignments To Assign Bacterial Species
    Matthew C. Chung, James B. Munro, Hervé Tettelin, Julie C. Dunning Hotopp · 2018 · mSystems
  64. Intracellular amorphous Ca-carbonate and magnetite biomineralization by a magnetotactic bacterium affiliated to the Alphaproteobacteria
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  65. No Assembly Required: Using BTyper3 to Assess the Congruency of a Proposed Taxonomic Framework for the Bacillus cereus Group With Historical Typing Methods
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  66. Adding leaves to the Lepidoptera tree: capturing hundreds of nuclear genes from old museum specimens
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  67. Genomic Signatures Supporting the Symbiosis and Formation of Chitinous Tube in the Deep-Sea Tubeworm Paraescarpia echinospica
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  74. Chromosome-level assembly of the horseshoe crab genome provides insights into its genome evolution
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  81. Quantifying population-specific growth in benthic bacterial communities under low oxygen using H218O
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  83. Variation Among Biosynthetic Gene Clusters, Secondary Metabolite Profiles, and Cards of Virulence Across Aspergillus Species
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  84. Methanogenic archaea in peatlands
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  86. Transmission of Severe Acute Respiratory Syndrome Coronavirus 2 during Border Quarantine and Air Travel, New Zealand (Aotearoa)
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  94. The rise of diversity in metabolic platforms across the Candidate Phyla Radiation
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