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Tipdatingbeast: An r package to assist the implementation of phylogenetic tip-dating tests using beast

Rieux Adrien, Khatchikian Camilo E.. 2017. Tipdatingbeast: An r package to assist the implementation of phylogenetic tip-dating tests using beast. Molecular Ecology Resources, 17 (4) : pp. 608-613.

Journal article ; Article de recherche ; Article de revue à facteur d'impact
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Rieux-2017-TIPDATINGBEAST_ an R package to ass.pdf

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Url - jeu de données : https://cran.r-project.org/package=TipDatingBeast / Url - jeu de données : https://doi.org/10.5061/dryad.43q71

Quartile : Outlier, Sujet : ECOLOGY / Quartile : Q1, Sujet : EVOLUTIONARY BIOLOGY / Quartile : Q1, Sujet : BIOCHEMISTRY & MOLECULAR BIOLOGY

Additional Information : Accès aux jeux de données : The TIPDATINGBEAST package is freely available from https://cran.r-project.org/web/packages/TipDatingBeast/index.html. The influenza data set used in the manuscript can be found in the ‘Virus Practical.zip’ file available from http://beast.bio.ed.ac.uk/tutorials. Example log files generated by BEAST that can be directly used to test the analyses and plot functions are available from the Dryad depository (doi: 10.5061/dryad.43q71)

Abstract : Molecular tip dating of phylogenetic trees is a growing discipline that uses DNA sequences sampled at different points in time to coestimate the timing of evolutionary events with rates of molecular evolution. In this context, beast, a program for Bayesian analysis of molecular sequences, is the most widely used phylogenetic tool. Here, we introduce tipdatingbeast, an r package built to assist the implementation of various phylogenetic tip-dating tests using beast. tipdatingbeast currently contains two main functions. The first one allows preparing date-randomization analyses, which assess the temporal signal of a data set. The second function allows performing leave-one-out analyses, which test for the consistency between independent calibration sequences and allow pinpointing those leading to potential bias. We apply those functions to an empirical data set and supply practical guidance for results interpretation.

Classification Agris : U10 - Computer science, mathematics and statistics
000 - Other themes

Champ stratégique Cirad : Hors axes (2014-2018)

Agence(s) de financement européenne(s) : European Research Council, European Regional Development Fund

Projet(s) de financement européen(s) : Building an Integrated Genetic Infectious Disease Epidemiology Approach

Auteurs et affiliations

  • Rieux Adrien, CIRAD-BIOS-UMR PVBMT (REU)
  • Khatchikian Camilo E., University of Pennsylvania (USA)

Source : Cirad-Agritrop (https://agritrop.cirad.fr/585759/)

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