Adaptive dating and fast proposals: Revisiting the phylogenetic relaxed clock model
Author
Abstract
Suggested Citation
DOI: 10.1371/journal.pcbi.1008322
Download full text from publisher
References listed on IDEAS
- Alexei J Drummond & Simon Y W Ho & Matthew J Phillips & Andrew Rambaut, 2006. "Relaxed Phylogenetics and Dating with Confidence," PLOS Biology, Public Library of Science, vol. 4(5), pages 1-1, March.
- Robert G. Moyle & Carl H. Oliveros & Michael J. Andersen & Peter A. Hosner & Brett W. Benz & Joseph D. Manthey & Scott L. Travers & Rafe M. Brown & Brant C. Faircloth, 2016. "Tectonic collision and uplift of Wallacea triggered the global songbird radiation," Nature Communications, Nature, vol. 7(1), pages 1-7, November.
- Gelman A., 2004. "Parameterization and Bayesian Modeling," Journal of the American Statistical Association, American Statistical Association, vol. 99, pages 537-545, January.
- Bob Mau & Michael A. Newton & Bret Larget, 1999. "Bayesian Phylogenetic Inference via Markov Chain Monte Carlo Methods," Biometrics, The International Biometric Society, vol. 55(1), pages 1-12, March.
Citations
Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
Cited by:
- Lauren Jelley & Jordan Douglas & Xiaoyun Ren & David Winter & Andrea McNeill & Sue Huang & Nigel French & David Welch & James Hadfield & Joep Ligt & Jemma L. Geoghegan, 2022. "Genomic epidemiology of Delta SARS-CoV-2 during transition from elimination to suppression in Aotearoa New Zealand," Nature Communications, Nature, vol. 13(1), pages 1-8, December.
- Jordan Douglas & David Winter & Andrea McNeill & Sam Carr & Michael Bunce & Nigel French & James Hadfield & Joep Ligt & David Welch & Jemma L. Geoghegan, 2022. "Tracing the international arrivals of SARS-CoV-2 Omicron variants after Aotearoa New Zealand reopened its border," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
Most related items
These are the items that most often cite the same works as this one and are cited by the same works as this one.- Alexandra Gavryushkina & David Welch & Tanja Stadler & Alexei J Drummond, 2014. "Bayesian Inference of Sampled Ancestor Trees for Epidemiology and Fossil Calibration," PLOS Computational Biology, Public Library of Science, vol. 10(12), pages 1-15, December.
- Olawale Awe O. & Adedayo Adepoju A., 2018. "Modified Recursive Bayesian Algorithm For Estimating Time-Varying Parameters In Dynamic Linear Models," Statistics in Transition New Series, Statistics Poland, vol. 19(2), pages 258-293, June.
- Leonardo Oliveira Martins & Hirohisa Kishino, 2010. "Distribution of distances between topologies and its effect on detection of phylogenetic recombination," Annals of the Institute of Statistical Mathematics, Springer;The Institute of Statistical Mathematics, vol. 62(1), pages 145-159, February.
- Heng Liu & Caizhu Huang & Heng Lian & Xia Cui, 2023. "Hierarchical Spatially Varying Coefficient Process Regression for Modeling Net Anthropogenic Nitrogen Inputs (NANI) from the Watershed of the Yangtze River, China," Sustainability, MDPI, vol. 15(16), pages 1-15, August.
- Joachim Schmidt & Lars Opgenoorth & Steffen Höll & Ralf Bastrop, 2012. "Into the Himalayan Exile: The Phylogeography of the Ground Beetle Ethira clade Supports the Tibetan Origin of Forest-Dwelling Himalayan Species Groups," PLOS ONE, Public Library of Science, vol. 7(9), pages 1-15, September.
- Barry G Hall & Stephen J Salipante, 2007. "Measures of Clade Confidence Do Not Correlate with Accuracy of Phylogenetic Trees," PLOS Computational Biology, Public Library of Science, vol. 3(3), pages 1-9, March.
- Qian, Song S., 2012. "On model coefficient estimation using Markov chain Monte Carlo simulations: A potential problem and the solution," Ecological Modelling, Elsevier, vol. 247(C), pages 302-306.
- Iliana Bista & Jonathan M. D. Wood & Thomas Desvignes & Shane A. McCarthy & Michael Matschiner & Zemin Ning & Alan Tracey & James Torrance & Ying Sims & William Chow & Michelle Smith & Karen Oliver & , 2023. "Genomics of cold adaptations in the Antarctic notothenioid fish radiation," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
- Haitao Shang & Daniel H. Rothman & Gregory P. Fournier, 2022. "Oxidative metabolisms catalyzed Earth’s oxygenation," Nature Communications, Nature, vol. 13(1), pages 1-9, December.
- Mingyuan Chen & Dakshina De Silva & Aurelie Slechten, 2021. "Director appointments, boardroom networks, and firm environmental performance," Working Papers 332157256, Lancaster University Management School, Economics Department.
- Yankuo Sun & Jiabao Xing & Samuel L. Hong & Nena Bollen & Sijia Xu & Yue Li & Jianhao Zhong & Xiaopeng Gao & Dihua Zhu & Jing Liu & Lang Gong & Lei Zhou & Tongqing An & Mang Shi & Heng Wang & Guy Bael, 2024. "Untangling lineage introductions, persistence and transmission drivers of HP-PRRSV sublineage 8.7," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
- O. Olawale Awe & A. Adedayo Adepoju, 2018. "Modified Recursive Bayesian Algorithm For Estimating Time-Varying Parameters In Dynamic Linear Models," Statistics in Transition New Series, Polish Statistical Association, vol. 19(2), pages 239-258, June.
- Mekala Sundaram & Janna R Willoughby & Nathanael I Lichti & Michael A Steele & Robert K Swihart, 2015. "Segregating the Effects of Seed Traits and Common Ancestry of Hardwood Trees on Eastern Gray Squirrel Foraging Decisions," PLOS ONE, Public Library of Science, vol. 10(6), pages 1-16, June.
- Jonathon D. Gass & Nichola J. Hill & Lambodhar Damodaran & Elena N. Naumova & Felicia B. Nutter & Jonathan A. Runstadler, 2023. "Ecogeographic Drivers of the Spatial Spread of Highly Pathogenic Avian Influenza Outbreaks in Europe and the United States, 2016–Early 2022," IJERPH, MDPI, vol. 20(11), pages 1-17, June.
- Nico Neureiter & Peter Ranacher & Nour Efrat-Kowalsky & Gereon A. Kaiping & Robert Weibel & Paul Widmer & Remco R. Bouckaert, 2022. "Detecting contact in language trees: a Bayesian phylogenetic model with horizontal transfer," Palgrave Communications, Palgrave Macmillan, vol. 9(1), pages 1-14, December.
- Yang, Mingan & Dunson, David B. & Baird, Donna, 2010. "Semiparametric Bayes hierarchical models with mean and variance constraints," Computational Statistics & Data Analysis, Elsevier, vol. 54(9), pages 2172-2186, September.
- Michael D Nowak & Andrew B Smith & Carl Simpson & Derrick J Zwickl, 2013. "A Simple Method for Estimating Informative Node Age Priors for the Fossil Calibration of Molecular Divergence Time Analyses," PLOS ONE, Public Library of Science, vol. 8(6), pages 1-13, June.
- Elena Rivas & Sean R Eddy, 2008. "Probabilistic Phylogenetic Inference with Insertions and Deletions," PLOS Computational Biology, Public Library of Science, vol. 4(9), pages 1-21, September.
- Bethany L Dearlove & Simon D W Frost, 2015. "Measuring Asymmetry in Time-Stamped Phylogenies," PLOS Computational Biology, Public Library of Science, vol. 11(7), pages 1-16, July.
- Hoan X. Dinh & Davinder Singh & Diana Gomez de la Cruz & Goetz Hensel & Jochen Kumlehn & Martin Mascher & Nils Stein & Dragan Perovic & Michael Ayliffe & Matthew J. Moscou & Robert F. Park & Mohammad , 2022. "The barley leaf rust resistance gene Rph3 encodes a predicted membrane protein and is induced upon infection by avirulent pathotypes of Puccinia hordei," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
Corrections
All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:plo:pcbi00:1008322. See general information about how to correct material in RePEc.
If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.
If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .
If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.
For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: ploscompbiol (email available below). General contact details of provider: https://journals.plos.org/ploscompbiol/ .
Please note that corrections may take a couple of weeks to filter through the various RePEc services.