Published August 22, 2024 | Version v3.0.0
Software Open

TREvoSim v3.0.0

Creators

  • 1. ROR icon University of Manchester
  • 2. ROR icon Natural History Museum
  • 3. ROR icon Imperial College London
  • 4. ROR icon University of Reading
  • 5. Oxford University Museum of Natural History
  • 6. ROR icon University of Birmingham
  • 7. ROR icon University of Bristol
  • 8. Scripps Institution of Oceanography
  • 9. St. Edmund Hall, University of Oxford
  • 10. ROR icon University of Oxford
  • 11. ROR icon Université de Lille

Description

This release is a new major version (v3.0.0) of TREvoSim. The first release and the underlying model was described in detail in the following paper:

Keating, J.N., Sansom, R.S., Sutton, M.D., Knight, C.G. & Garwood, R.J. 2020. Morphological phylogenetics evaluated using novel evolutionary simulations. Systematic Biology 69(5): 897-912. doi:10.1093/sysbio/syaa012

Version 2.0.0 and associated changes were introduced in the paper:

Mongiardino Koch, N., Garwood, R.J. & Parry, L.A. 2021. Fossils improve phylogenetic analyses of morphological characters. Proceedings of the Royal Society B: 288(1950):20210044. doi: 10.1098/rspb.2021.0044

Version 3.0.0 and all new additions are described in detail in a paper in the Journal of Open Source Software, associated with this release:

Garwood, R.J., Spencer, A.R.T., Bates, C.T.M., Callender-Crowe, L.M, Dunn, F.S., Halliday, T.J.D., Keating, J.N., Mongiardino Koch, N., Parry, L.A., Sansom, R.S., Smith, T.J., Sutton, M.D. & Vanteghem, T. 2024. TREvoSim v3: An individual based simulation for generating trees and character data. JOSS.

The code is archived on zenodo.org: https://doi.org/10.5281/zenodo.13358420.

Documentation:

Change log:

The changes in v3.0.0 are described and discussed fully in the associated paper. In brief, these include:

  • New character options
  • New default simulation parameters
  • Ecosystem engineering functionality
  • An expanding playing field mode
  • New logging capabilities
  • The option to match fitness peaks across environments
  • A no selection mode
  • Mixing of organisms between playing fields
  • Perturbations (periods of accelerated environmental change)
  • The ability to run the simulation for a user-defined number of iterations, as opposed to for set number of species
  • Abstraction of the fitness algorithm from the genome via many-to-one mapping (stochastic layer)
  • A test suite integrated into the software build

Binaries

The following binaries are available for download (installation instructions are present in the documentation):

MacOS

TREvoSim_v3.0.0_Installer_MacOS.dmg image containing the TREvoSim and TREvoSimTest applications and a drag n' drop installer.

Windows x64-bit

TREvoSim_v3.0.0_Installer_Winx64.exe containing the TREvoSim and TREvoSimTest applications.

Files

palaeoware/trevosim-v3.0.0.zip

Files (13.3 MB)

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md5:f4d68425f890a3e49b29ee3d58467a4f
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Additional details

Related works

Is supplement to
Software: https://github.com/palaeoware/trevosim/tree/v3.0.0 (URL)

Software

Repository URL
https://github.com/palaeoware/trevosim/
Programming language
C++, R, reStructuredText, HTML
Development Status
Active