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Software & Manuals

For full descriptions of each software package, please use the dropdown Software menu at the top of this website.

Please note that the manual (and sometimes technical documentation or sample data) is automatically included with the software download and can be found in one of two places:

  1. The directory where you installed the software on your machine, usually within C/Program Files (x86).
  2. The directory where you installed the project file for the software, usually with C.

For case studies and introductory material, please see the Educational Materials Section of this page.

Vortex is an individual-based stochastic simulation program.

  • Included Supplementary Software

    Executable files for Vortex Adaptive Manager, Eddy (the educational ‘lite’ version of Vortex), and MMMacro Entry can be found in Species Conservation Toolkit Initiative/Vortex10 in the directory where you installed the software on your machine, usually in Program files (x86).

  • Vortex Deterministic Life Table Tool

    An excel sheet that allows you to look at the deterministic calculations for a set of Vortex input values.

PMx provides genetic and demographic population management tools.

  • A Guide to Using the Selection Tab
    Detailed instructions for using the selection tab released in PMx version 1.5.8 and newer.

  • A Guide to PMx Life Table Calculations
    Documentation for how life tables are calculated in PMx.

  • Group Management Package
    A package for managing pedigrees of group-living organisms and then exporting the group history data to PMx is now available! This package was developed by Belén Jiménez-Mena and is available at its official Github site. Click ‘Group Management Package’ above to go to GitHub.

  • PartInbr for Partial Inbreeding Coefficients

    This program calculates inbreeding coefficients, partial inbreeding coefficients with respect to each founder and proportion of the genome contributed by each founder. The program is run as a Windows application, with a simple user interface to prompt for input and output file names. This download includes the source code (in C#; feel free to use and modify it for your own uses), sample input files, the executable, and a document with further description and instructions.

    A paper that uses the partial inbreeding coefficients to analyze the distribution of genetic load among founders is:

    Lacy, R.C, G. Alaks, and A. Walsh. 1996. Hierarchical analysis of inbreeding depression in Peromyscus polionotus. Evolution 50:2187-2200. 

MMM facilitates linking and running models interactively.

Outbreak is an individual-based stochastic simulation of disease dynamics.

Spatial models individual movements.

Publications

If you use SCTI tools in your research and would like to share your publication on our website, please contact us at contribute@scti.tools

Vortex

PMx

  • Jamieson, I.G., and R.C. Lacy. 2012. Managing genetic issues in reintroduction biology. Pages 441-475 in: J.G. Ewen, D.P. Armstrong, K.A. Parker, & P.J. Seddon, eds. Reintroduction Biology: Integrating Science and Management. Wiley-Blackwell, Oxford, UK.

MetaModel Manager

Outbreak

Educational Materials

For a highly useful textbook that provides a lot of the background for how and when to use Vortex, PMx, and other tools for guiding the management of populations, see:

Frankham, R., J.D. Ballou, K. Ralls, M.D.B. Eldridge, M.R. Dudash, C.B. Fenster, R.C. Lacy, and P. Sunnucks. 2017. Genetic Management of Fragmented Animal and Plant Populations. Oxford University Press, Oxford UK.

Promotional Materials

SCTI Brochure
2018 Annual Report