Recent Releases of TREvoSim v3
TREvoSim v3 - TREvoSim v3.0.0
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: 10.5281/zenodo.3619355.
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
- TREvoSimv3.0.0Installer_MacOS.dmg image containing the TREvoSim and TREvoSimTest applications and a drag n' drop installer.
Windows x64-bit
- TREvoSimv3.0.0Installer_Winx64.exe containing the TREvoSim and TREvoSimTest applications.
Scientific Software - Peer-reviewed
- C++
Published by RussellGarwood over 1 year ago
TREvoSim v3 - TREvoSim v3.0.0-rc.1
This is the release candidate for a new major version (v3.0.0) of TREvoSim, for review in the Journal of Open Source Software. 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 being submitted to the journal of open source software, that is associated with this release candidate:
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: 
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
Release information:
Windows
A zip containing all required binaries can be downloaded from the assets below. To run TREvoSim extract all files/directories from the .zip into a single folder. The software can then be launched by double clicking TREvoSim.exe in the root of this directory. All the required libraries have been included.
Mac
A .dmg to install TREovSim can be downloaded from the assets below. To install the software, double click on this file and follow the instructions. You may be required to the approve the software in security and privacy settings before it will launch.
Linux
Any Linux users willing to test a Linux build should contact palaeoware@gmail.com, or follow the instructions in the documentation to build their own version of the software.
Scientific Software - Peer-reviewed
- C++
Published by RussellGarwood almost 2 years ago
TREvoSim v3 - TREvoSim v2.0.0
This is the release of a new version (v2.0.0) 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 accompanies the preprint below:
Mongiardino Koch, N., Garwood, R.J. & Parry, L.A. Preprint. Fossils improve phylogenetic analyses of morphological characters. bioRxiv. doi: 10.1101/2020.12.03.410068v1
The code is archived on zenodo.org: 
Documentation:
Change log:
The changes in v2.0.0 are described and discussed fully in the associated paper. In brief, these allow TREvoSim v2.0.0 trees and data to achieve benchmarks calculated from twelve total evidence analyses, as well as respresenting ongoing development of the package. Changes are: - Addition of multiple playing fields option. Playing fields can have independent or identical environments. - The option to overwrite a random individual when a juveniles is returned to the playing field (instead of the least fit one). - User control of the fitness target in the fitness algorithm (see Keating et al. 2020). - A fitness histogram functionality to assess the fitness landscape in the simulation. - User control of the strength of selection (see Mongiardino Koch et al. 2021 for discussion). - Multiple environments per playing field. Organism fitness is assessed against each environment, and the fitness of an organism is defined by the environment they are best suited to. - The code has been refactored (the biggest change being to the underlying data structures/classes), and the simulation now uses Qt QRandomGenerator tools rather than incorporating random data. - A user-accessible test suite has been added.
Release information:
Windows
A zip containing all required binaries can be downloaded from the assets below. Alternatively an installer is provided. See notes below:
Note 1: The .zip archive contains an executable TREvoSim_2.0.0.exe. The .zip can be extracted and the program run by double clicking this.exe file in the ./bin folder. All the required libraries have been included and are found in the ./bin folder.
Mac
A zip containing TREovSim can be downloaded from the assets below. To install the software, drag and drop the required .app folder(s) into the Applications folder. You may be required to the approve the software in security and privacy settings before it will launch.
Linux
Any Linux users willing to test a Linux build should contact palaeoware@gmail.com.
Scientific Software - Peer-reviewed
- C++
Published by RussellGarwood almost 5 years ago
TREvoSim v3 - TREvoSim v1.0.0
This is the first public release of the TREvoSim software. This release and the underlying model has been described in detail in the following paper:
Keating, J.N., Sansom, R.S., Sutton, M.D., Knight, C.G., and Garwood, R.J. 2020. Morphological phylogenetics evaluated using novel evolutionary simulations. Systematic Biology.
The code is archived on zenodo.org: 
Documentation:
Change log:
Initial public release.
Release information:
Windows
A zip containing all required binaries can be downloaded from the assets below. Alternatively an installer is provided. See notes below:
Note 1: The .zip archive contains an executable TREvoSim.exe. The .zip can be extracted and the program run by double clicking this.exe file in the ./bin folder. All the required libraries have been included and are found in the ./bin folder.
Mac
A zip containing TREovSim can be downloaded from the assets below. To install the software, drag and drop the required .app folder(s) into the Applications folder. You may be required to the approve the software in security and privacy settings before it will launch.
Linux
Any Linux users willing to test a Linux build should contact palaeoware@gmail.com.
Scientific Software - Peer-reviewed
- C++
Published by RussellGarwood almost 6 years ago