GECOT, the Graph-based Ecological Connectivity Optimization Tool, is an open-source C++ tool designed to tackle systematic conservation (or restoration) planning problems. Given a graph representation of the landscape for each target species, a list of actions for improving the graphs elements and a budget, GECOT allows to select a group of actions whose cost is below the budget and whose impacts on the Landscapes maximizes the ecological connectivity, measured with the Probability of Connectivity indicator (PC).

Installation

For Windows, download and run the last released installer.

For Linux, download and extract the precompiled binaries of the last release.

Otherwise, here is a Docker container for building and testing GECOT.

Usage

$ gecot_optimize --help
GECOT — Graph-based Ecological Connectivity Optimization Tool
Version: 1.0 (built on Oct 26 2026)

Usage:
  gecot_optimize --help
  gecot_optimize --list-algorithms
  gecot_optimize <algorithm> --list-params
  gecot_optimize <algorithm> <instance> <budget> [<parameters> ...]


POSITIONALS:
  algorithm TEXT              Algorithm to use
  instance TEXT               Instance JSON file
  budget FLOAT                Budget value

OPTIONS:
  -h,     --help              Display this help message
  -A,     --list-algorithms   List the available algorithms
  -P,     --list-params       List the parameters of the chosen algorithm
  -a,     --algorithm TEXT    Algorithm to use
  -i,     --instance TEXT     Instance JSON file
  -B,     --budget FLOAT      Budget value
  -o,     --output-json TEXT  Output solution data in JSON file
          --output-csv TEXT   Output solution value in CSV file
  -v,     --verbose           Enable logging of algorithms trace
  -q,     --quiet             Silence all logging except errors
          --max-threads UINT:POSITIVE
                              Limits the number of threads used

Citation

Please cite 'GECOT' when using it in publications using:

Hamonic, F., Vaxès, Y., Couëtoux, B., & Albert, C. H. (2025). GECOT: Graph-based ecological connectivity optimization tool. Methods in Ecology and Evolution, 00, 1–9. https://doi.org/10.1111/2041-210X.70055

Additionally, releases are automatically published to Zenodo (https://doi.org/10.5281/zenodo.15295914)

Acknowledgments

This work has been funded by Region Sud and Natural Solutions (PhD thesis of François Hamonic), and by the ERC project SCALED, grant n°949812 (postdoctoral position).