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dc.contributor.author
Hagen, Oskar
dc.contributor.author
Stadler, Tanja
dc.date.accessioned
2018-04-04T11:42:37Z
dc.date.available
2018-03-22T04:14:55Z
dc.date.available
2018-04-04T11:42:37Z
dc.date.issued
2018-03
dc.identifier.issn
2041-210X
dc.identifier.issn
2041-2096
dc.identifier.other
10.1111/2041-210X.12917
en_US
dc.identifier.uri
http://hdl.handle.net/20.500.11850/251720
dc.identifier.doi
10.3929/ethz-b-000251720
dc.description.abstract
1. Understanding macroevolutionary processes using phylogenetic trees is a challenging and complex process that draws on mathematics, computer science and biology. Given the development of complex mathematical models and the growing computational processing power, simulation tools are becoming increasingly popular. 2. In order to simulate phylogenetic trees, most evolutionary biologists are forced to build their own algorithms or use existing tools built on different platforms and/or as standalone programmes. The absence of a simulation tool accommodating for user‐chosen model specifications limits, amongst others, model testing and pipelining with approximate Bayesian computation methods or other subsequent statistical analysis. 3. We introduce “TreeSimGM,” an r‐package simulation tool for phylogenetic trees under a general Bellman and Harris model. This package allows the user to specify any desired probability distribution for the waiting times until speciation and extinction (e.g. age‐dependent speciation/extinction). Upon speciation, the user can specify whether one descendant species corresponds to the ancestor species inheriting its age or whether both descendant species are new species of age 0. Moreover, it is possible to scale the waiting time to speciation/extinction for newly formed species. Thus, “TreeSimGM” not only allows the user to simulate stochastic phylogenetic trees assuming several popular existing models, such as the Yule model, the constant‐rate birth–death model, and proportional to distinguishable arrangement models, but it also allows the user to formulate new models for exploration. A short explanation of the supported models and a few examples of how to use our package are presented here. 4. As an r‐package, “TreeSimGM” allows flexible and powerful stochastic phylogenetic tree simulations. Moreover, it facilitates the pipelining of outputs or inputs with other functions in r. “TreeSimGM” contributes to the tools available to the r community in the fields of ecology and evolution, is freely available under the GPL‐2 licence and can be downloaded at https://cran.r-project.org/web/packages/TreeSimGM.
en_US
dc.format
application/pdf
en_US
dc.language.iso
en
en_US
dc.publisher
Wiley
en_US
dc.rights.uri
http://creativecommons.org/licenses/by/4.0/
dc.subject
birth–death model
en_US
dc.subject
macroevolution
en_US
dc.subject
phylogeny
en_US
dc.subject
simulation
en_US
dc.title
TreeSimGM: Simulating phylogenetic trees under general Bellman–Harris models with lineage-specific shifts of speciation and extinction in R
en_US
dc.type
Journal Article
dc.rights.license
Creative Commons Attribution 4.0 International
dc.date.published
2017-10-17
ethz.journal.title
Methods in Ecology and Evolution
ethz.journal.volume
9
en_US
ethz.journal.issue
3
en_US
ethz.journal.abbreviated
Methods ecol. evol.
ethz.pages.start
754
en_US
ethz.pages.end
760
en_US
ethz.version.deposit
publishedVersion
en_US
ethz.grant
New phylogenetic methods for inferring complex population dynamics
en_US
ethz.identifier.wos
ethz.identifier.scopus
ethz.publication.place
Oxford
en_US
ethz.publication.status
published
en_US
ethz.leitzahl
ETH Zürich::00002 - ETH Zürich::00012 - Lehre und Forschung
ethz.leitzahl
ETH Zürich::00002 - ETH Zürich::00012 - Lehre und Forschung::00007 - Departemente::02060 - Dep. Biosysteme / Dep. of Biosystems Science and Eng.::09490 - Stadler, Tanja / Stadler, Tanja
ethz.leitzahl
ETH Zürich::00002 - ETH Zürich::00012 - Lehre und Forschung::00007 - Departemente::02350 - Dep. Umweltsystemwissenschaften / Dep. of Environmental Systems Science::02722 - Institut für Terrestrische Oekosysteme / Institute of Terrestrial Ecosystems::09553 - Pellissier, Loïc / Pellissier, Loïc
ethz.leitzahl.certified
ETH Zürich::00002 - ETH Zürich::00012 - Lehre und Forschung::00007 - Departemente::02060 - Dep. Biosysteme / Dep. of Biosystems Science and Eng.::09490 - Stadler, Tanja / Stadler, Tanja
ethz.leitzahl.certified
ETH Zürich::00002 - ETH Zürich::00012 - Lehre und Forschung::00007 - Departemente::02350 - Dep. Umweltsystemwissenschaften / Dep. of Environmental Systems Science::02722 - Institut für Terrestrische Oekosysteme / Institute of Terrestrial Ecosystems::09553 - Pellissier, Loïc / Pellissier, Loïc
ethz.grant.agreementno
335529
ethz.grant.fundername
EC
ethz.grant.funderDoi
10.13039/501100000780
ethz.grant.program
FP7
ethz.date.deposited
2018-03-22T04:14:58Z
ethz.source
SCOPUS
ethz.eth
yes
en_US
ethz.availability
Open access
en_US
ethz.rosetta.installDate
2018-04-04T11:42:44Z
ethz.rosetta.lastUpdated
2019-02-02T16:34:31Z
ethz.rosetta.versionExported
true
ethz.COinS
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