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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. Example: C/PMxProjects/Manuals&Guides

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.

PMxLite: PMx made simpler.

  • Included Supplementary Software
    PMxLite is included with the PMx installation package (Version 1.6.2.20200613 or newer).

    PMxceptional is included (Version 1.8.0.20231218 or newer).

  • Welcome to PMxLite
    An introduction to PMxLite, a version where some of PMx’s advanced features and options have been removed for a more streamlined user experience. PMxLite is automatically included when you download PMx.

  • 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 Customizing PMx
    Detailed instructions for changing which features are visible to the user in PMx (recommended for advanced users only).

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

  • Training Available from SCTI Partners

    A list of links to training resources developed by SCTI partners.

  • Group Management Package
    A package for managing pedigrees of group-living organisms and exporting the group history data to PMx, developed by Belén Jiménez-Mena, Kristine Schad Eebes, and Bob Lacy.

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 help@scti.tools

Vortex

  • Ballou, J.D., K. Traylor-Holzer, A. Turner, A.F. Malo, D. Powell, J. Maldonado, and L. Eggert. 2008. Simulation model for contraceptive management of the Assateague Island feral horse population using individual-based data. Wildlife Research 35: 502-512.

  • Pacioni, C. and Mayer, F. 2017. vortexR: an R package for post Vortex simulation analysis. Methods in Ecology and Evolution 8:1477-1481.

  • Pacioni, C., Williams, M., Lacy, R.C., Spencer, P.B.S. and Wayne, A.F. 2017. Predators and genetic fitness: key threatening factors for the conservation of bettong species. Pacific Concervation Biology 23:200-212.
  • Harrisson KA, Pavlova A, Da Silva AG, Rose R, Bull JK, Lancaster ML, Murray N, Quin B, Menkhorst P, Magrath MJL, and Sunnucks P (2016) Scope for genetic rescue of an endangered subspecies though re-establishing natural gene flow with another subspecies. Molecular Ecology 25:1242-1258

  • Pavlova A, Beheregaray LB, Coleman R, Gilligan D, Harrisson KA, Ingram BA, Kearns J, Lamb AM, Lintermans M, Lyon J, Nguyen TTT, Sasaki M, Tonkin Z, Yen JDL, and Sunnucks P (2017) Severe consequences of habitat fragmentation on genetic diversity of an endangered Australian freshwater fish: A call for assisted gene flow. Evolutionary Applications 10:531-550

  • Zilko JP, Harley D, Pavlova A, and Sunnucks P (2021) Applying population viability analysis to inform genetic rescue that preserves locally unique genetic variation in a critically endangered mammal. Diversity 13:382

  • Stojanovic, D., T. Neeman, R. Lacy, K.A. Farquharson, C.J. Hogg, and R. Heinsohn. 2022. Effects of non-random juvenile mortality on small, inbred populations. Biological Conservation 268:109504. doi: 10.1016/j.biocon.2022.109504.

  • Manlik, O., R.C. Lacy, W.B. Sherwin, H. Finn, N.R. Loneragan, and S.J. Allen. 2022. A stochastic model for estimating sustainable limits to wildlife mortality in a changing world. Conservation Biology. doi:10.1111/cobi.13897

  • Heinsohn, R., R. Lacy, A. Elphinstone, D. Ingwersen, B.J. Pitcher, M. Roderick, E. Schmelitschek, M. Van Sluys, D. Stojanovic, J. Tripovich, and R. Crates. 2022. Population viability in data deficient nomadic species: what it will take to save regent honeyeaters from extinction. Biological Conservation 266:109430. doi: 10.1016/j.biocon.2021.109430

  • Lacy, R.C., R.S. Wells, M.D. Scott, J.B. Allen, A.A. Barleycorn, K.W. Urian, and S. Hofmann. Assessing the viability of the Sarasota Bay community of bottlenose dolphins. Frontiers in Marine Science 8:788086. doi: 10.3389/fmars.2021.788086.

  • Williams, R., R.C. Lacy, E. Ashe, A. Hall, S. Plourde, I.H. McQuinn, and V. Lesage. 2021. Climate change complicates efforts to ensure survival and recovery of St. Lawrence Estuary beluga. Marine Pollution Bulletin 173:113096. doi.org/10.1016/j.marpolbul.2021.113096

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.
  • Robledo-Ruiz DA, Pavlova A, Clarke RH, Magrath MJL, Quin B, Harrisson KA, Gan HM, Low GW, and Sunnucks P (2022) A novel framework for evaluating in situ breeding management strategies in endangered populations. Molecular Ecology Resources 22:239-253

  • Ballou, J.D., R.C. Lacy, K. Traylor-Holzer, K. Bauman, J.A. Ivy, and C. Asa. 2023. Strategies for establishing and using genome resource banks to protect genetic diversity in conservation breeding programs. Zoo Biology 42:175-184. doi: 10.1002/zoo.21741

  • Gooley, R.M., K.L. Dicks, G.M. Ferrie, R.C. Lacy, J.D. Ballou, T. Callicrate, K.-P. Koepfli, C.W. Edwards, and B. S. Pukazhenthi. 2021. Applying genomics to metapopulation management in North American insurance populations of southern sable antelope (Hippotragus niger niger) and addra gazelle (Nanger dama ruficollis).  Global Ecology and Conservation 33: e01969. doi: 10.1016/j.gecco.2021.e01969.

MetaModel Manager

Outbreak

Educational Materials

Outbreak

Vortex

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
2019 Annual Report