Статья

BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis

Remco BouckaertCentre of Computational Evolution, University of Auckland, Auckland, New ZealandTimothy G. VaughanETH Zürich, Department of Biosystems Science and Engineering, 4058 Basel, SwitzerlandJoëlle Barido‐SottaniETH Zürich, Department of Biosystems Science and Engineering, 4058 Basel, SwitzerlandSebastián DuchêneDepartment of Biochemistry and Molecular Biology, University of Melbourne, Melbourne, Victoria, AustraliaMathieu Fourmentithree institute, University of Technology Sydney, Sydney, AustraliaAlexandra GavryushkinaDepartment of Biochemistry, University of Otago, Dunedin 9016, New ZealandJoseph HeledGraham JonesDepartment of Biological and Environmental Sciences, University of Gothenburg, Box 461, SE 405 30 Göteborg, SwedenDenise KühnertMax Planck Institute for the Science of Human History, Jena, GermanyNicola De MaioEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridgeshire, UKMichael MatschinerDepartment of Environmental Sciences, University of Basel, 4051 Basel, SwitzerlandFábio K. MendesCentre of Computational Evolution, University of Auckland, Auckland, New ZealandNicola F. MüllerETH Zürich, Department of Biosystems Science and Engineering, 4058 Basel, SwitzerlandHuw A. OgilvieDepartment of Computer Science, Rice University, Houston, TX 77005-1892, USALouis du PlessisDepartment of Zoology, University of Oxford, Oxford, OX1 3PS, UKAlex PopingaCentre of Computational Evolution, University of Auckland, Auckland, New ZealandAndrew RambautInstitute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Edinburgh, EH9 3FL UKDavid A. RasmussenDepartment of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, USAIgor SiveroniDepartment of Infectious Disease Epidemiology, Imperial College London, Norfolk Place, W2 1PG, UKMarc A. SuchardDepartment of Biomathematics, David Geffen School of Medicine, University of California, Los Angeles, CA, USAChieh‐Hsi WuDepartment of Statistics, University of Oxford, OX1 3LB, UKDong XieCentre of Computational Evolution, University of Auckland, Auckland, New ZealandChi ZhangInstitute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, ChinaTanja StadlerETH Zürich, Department of Biosystems Science and Engineering, 4058 Basel, SwitzerlandAlexei J. DrummondCentre of Computational Evolution, University of Auckland, Auckland, New Zealand

2019en

ABI

Аннотация

Elaboration of Bayesian phylogenetic inference methods has continued at pace in recent years with major new advances in nearly all aspects of the joint modelling of evolutionary data. It is increasingly appreciated that some evolutionary questions can only be adequately answered by combining evidence from multiple independent sources of data, including genome sequences, sampling dates, phenotypic data, radiocarbon dates, fossil occurrences, and biogeographic range information among others. Including all relevant data into a single joint model is very challenging both conceptually and computationally. Advanced computational software packages that allow robust development of compatible (sub-)models which can be composed into a full model hierarchy have played a key role in these developments. Developing such software frameworks is increasingly a major scientific activity in its own right, and comes with specific challenges, from practical software design, development and engineering challenges to statistical and conceptual modelling challenges. BEAST 2 is one such computational software platform, and was first announced over 4 years ago. Here we describe a series of major new developments in the BEAST 2 core platform and model hierarchy that have occurred since the first release of the software, culminating in the recent 2.5 release.

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Идентификаторы

DOI: 10.1371/journal.pcbi.1006650

Цитирования и источники

Цитирований: 10Использованных источников: 0

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