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Online tree expansi...
Online tree expansion could help solve the problem of scalability in Bayesian phylogenetics
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- Truszkowski, Jakub (författare)
- Gothenburg University,Göteborgs universitet,Institutionen för biologi och miljövetenskap,Department of Biological and Environmental Sciences,Univ Gothenburg, Dept Biol & Environm Sci, POB 461, SE-40530 Gothenburg, Sweden.;Gothenburg Global Biodivers Ctr, Box 461, S-41319 Gothenburg, Sweden.,Department of Biological and Environmental Sciences , University of Gothenburg, P. O. Box 461, SE.405 30 Gothenburg , Sweden;Gothenburg Global Biodiversity Centre , Box 461, 405 30 Gothenburg , Sweden
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- Perrigo, Allison L. (författare)
- Gothenburg University,Göteborgs universitet,Institutionen för biologi och miljövetenskap,Department of Biological and Environmental Sciences,Univ Gothenburg, Dept Biol & Environm Sci, POB 461, SE-40530 Gothenburg, Sweden.;Gothenburg Global Biodivers Ctr, Box 461, S-41319 Gothenburg, Sweden.,Department of Biological and Environmental Sciences , University of Gothenburg, P. O. Box 461, SE.405 30 Gothenburg , Sweden;Gothenburg Global Biodiversity Centre , Box 461, 405 30 Gothenburg , Sweden
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- Broman, David, 1977- (författare)
- KTH,Programvaruteknik och datorsystem, SCS,Department of Computer Science and Digital Futures, KTH Royal Institute of Technology , SE.100 44 Stockholm , Sweden
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- Ronquist, Fredrik, 1962- (författare)
- Naturhistoriska riksmuseet,Enheten för bioinformatik och genetik,Fredrik Ronquists grupp
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- Antonelli, Alexandre, 1978 (författare)
- Gothenburg University,Göteborgs universitet,Institutionen för biologi och miljövetenskap,Department of Biological and Environmental Sciences,Univ Gothenburg, Dept Biol & Environm Sci, POB 461, SE-40530 Gothenburg, Sweden.;Gothenburg Global Biodivers Ctr, Box 461, S-41319 Gothenburg, Sweden.;Royal Bot Gardens, Richmond TW9 3AE, Surrey, England.;Univ Oxford, Dept Plant Sci, South Parks Rd, Oxford OX1 3RB, England.,Department of Biological and Environmental Sciences , University of Gothenburg, P. O. Box 461, SE.405 30 Gothenburg , Sweden;Gothenburg Global Biodiversity Centre , Box 461, 405 30 Gothenburg , Sweden;Royal Botanic Gardens, Kew, Richmond , Surrey TW9 3AE , UK;Department of Plant Sciences, University of Oxford, South Parks Road , Oxford OX1 3 RB , UK
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(creator_code:org_t)
- Oxford University Press (OUP), 2023
- 2023
- Engelska.
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Ingår i: Systematic Biology. - : Oxford University Press (OUP). - 1063-5157 .- 1076-836X. ; 72:5, s. 1199-1206
- Relaterad länk:
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https://doi.org/10.1...
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https://gup.ub.gu.se...
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https://doi.org/10.1...
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https://urn.kb.se/re...
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https://urn.kb.se/re...
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Abstract
Ämnesord
Stäng
- Bayesian phylogenetics is now facing a critical point. Over the last 20 years, Bayesian methods have reshaped phylogenetic inference and gained widespread popularity due to their high accuracy, the ability to quantify the uncertainty of inferences and the possibility of accommodating multiple aspects of evolutionary processes in the models that are used. Unfortunately, Bayesian methods are computationally expensive, and typical applications involve at most a few hundred sequences. This is problematic in the age of rapidly expanding genomic data and increasing scope of evolutionary analyses, forcing researchers to resort to less accurate but faster methods, such as maximum parsimony and maximum likelihood. Does this spell doom for Bayesian methods? Not necessarily. Here, we discuss some recently proposed approaches that could help scale up Bayesian analyses of evolutionary problems considerably. We focus on two particular aspects: online phylogenetics, where new data sequences are added to existing analyses, and alternatives to Markov chain Monte Carlo (MCMC) for scalable Bayesian inference. We identify 5 specific challenges and discuss how they might be overcome. We believe that online phylogenetic approaches and Sequential Monte Carlo hold great promise and could potentially speed up tree inference by orders of magnitude. We call for collaborative efforts to speed up the development of methods for real-time tree expansion through online phylogenetics.
Ämnesord
- NATURVETENSKAP -- Matematik -- Sannolikhetsteori och statistik (hsv//swe)
- NATURAL SCIENCES -- Mathematics -- Probability Theory and Statistics (hsv//eng)
- NATURVETENSKAP -- Biologi -- Bioinformatik och systembiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Bioinformatics and Systems Biology (hsv//eng)
- NATURVETENSKAP -- Biologi -- Evolutionsbiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Evolutionary Biology (hsv//eng)
Nyckelord
- Bayesian inference
- MCMC
- phylogeny
- sequential Monte Carlo
- placement
- inference
- performance
- mixtures
- Evolutionary Biology
- Bayesian inference
- Diversity of life
Publikations- och innehållstyp
- ref (ämneskategori)
- art (ämneskategori)
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