TREvoSim v3: An individual based simulation forgenerating trees and character data
Here we present TREvoSim v3.0.0: an agent-/individual-based model written in C++, in which digital organisms evolve, creating phylogenetic character data and trees.Trees inferred from empirical data always carry uncertainty, but TREvoSim can create a known tree alongside associated character data, allowing -for example -assessment of phylogenetic inference methods (Keating et al., 2020;Mongiardino Koch et al., 2021, 2023).The v3.0.0 release adds a range of features to allow greater flexibility in simulating phylogenetic trees and character data (more logging options, finer control over character character and simulation parameters), and to facilitate the study of broader evolutionary topics (e.g.ecosystem engineering, adaptive landscapes, selection).
Authors
- Nicolás Mongiardino Koch (ORCID: https://orcid.org/0000-0001-6317-5869)
- Charles Bates (ORCID: https://orcid.org/0009-0000-8444-6322)
- Thomas J. D. Halliday (ORCID: https://orcid.org/0000-0002-4077-732X)
- Mark D. Sutton (ORCID: https://orcid.org/0000-0002-7137-7572)
- Joseph N. Keating (ORCID: https://orcid.org/0000-0002-2667-7795)
- Luke A. Parry (ORCID: https://orcid.org/0000-0002-3910-0346)
- Russell J. Garwood (ORCID: https://orcid.org/0000-0002-2803-9471)
- Frances S. Dunn (ORCID: https://orcid.org/0000-0001-7080-5283)
- Thomas J. Smith (ORCID: https://orcid.org/0000-0002-2083-7452)
- Robert S. Sansom (ORCID: https://orcid.org/0000-0003-1926-2556)
- Leah M. Callender-Crowe (ORCID: https://orcid.org/0000-0002-5870-1964)
- Alan R.T. Spencer (ORCID: https://orcid.org/0000-0001-6590-405X)
- Thomas Vanteghem (ORCID: https://orcid.org/0009-0003-3513-8448)
Publication Details
- Journal
- The Journal of Open Source Software
- Published
- 2024-09-12
- DOI
- https://doi.org/10.21105/joss.06722
- Citations
- 1
- Primary Topic
- Insect and Arachnid Ecology and Behavior
- Type
- article
- Field-Weighted Citation Impact
- 0.55
Funders
- Alexander von Humboldt-Stiftung
- Leverhulme Trust
- Sight Research UK
- Biotechnology and Biological Sciences Research Council
- Natural Environment Research Council