Klamath Center for

Conservation Research


The Connectivity Analysis Toolkit


The Connectivity Analysis Toolkit (CAT) combines several new connectivity analysis and linkage mapping methods in an accessible user interface. The CAT software especially facilitates calculation of 'centrality' metrics. Centrality metrics evaluate paths between all possible pairwise combinations of sites on a landscape to rank the contribution of each site to facilitating ecological flows across the network of sites. Computational advances now allow application of centrality metrics to landscapes represented as continuous gradients of habitat quality. This avoids the binary classification of landscapes into patch and matrix required by patch-based analyses of connectivity. It also allows one to avoid the focus on delineating paths between individual pairs of core areas characteristic of most corridor- or linkage-mapping methods of connectivity analysis. However, you can use the CAT for such patch-to-patch linkage mapping as well.

This software is freely available. You may submit your name and email below (optional) if you want to be notified of the release of future versions of the software.

NOTE: The CAT's function for generating hexagon (hxn) files from ASCII files seems to no longer be working properly on some Windows systems. The workaround is download the most recent version of Hexsim from www.hexsim.net and use that software to generate .hxn files, which can then be used as input into the CAT graph generation functions.

If you plan to install the Toolkit on a 64-bit Microsoft Windows operating system, download this version:


If you prefer to download a zipfile rather than a self-executable installer, the CAT is also available in this format.

CAT zipfile for 64-bit Windows:


For users of the Toolkit on 32-bit Microsoft Windows operating systems: I have stopped updating 32-bit binaries due to low demand, but you can download CAT version 1.3.1 for 32-bit systems:


and as a zipfile:


A paper describing the methodology is now published in the journal Conservation Biology (journal website).

To learn about the software without downloading it, see the manual (pdf format).

Or see the online documentation.


Version 1.0 August 10, 2010
Initial release

Version 1.1 October 14, 2010
Major enhancement:  Implementation of time-series min-cost flow.
Several minor bugfixes: e.g., GUI now passes correct alpha value to PageRank.

Version 1.12 October 18, 2010
Bugfix release: Fixed configuration issue between the python libraries py2exe and elementtree that caused python-based functions (betweenness centrality, etc.) to fail with ImportError message.

Version 1.2 October 22, 2011
• Approximate shortest-path betweenness centrality allows faster computation of this metric
• Approximate current flow betweenness centrality allows faster computation of this metric; function also
uses sparse matrices for lower RAM requirements
• Network flow functions updated to LEMON version 1.2.2
• Updates to manual and tutorial dataset
(These are major updates which speed computation in some cases by an order of magnitude.)

Version 1.2.1 April 2, 2012
• Updated python and python packages, including NetworkX to version 1.6.
• Current flow betweenness centrality subset also now uses sparse matrices for lower RAM requirements. (Note that there is no approximate function for current flow betweenness centrality subset, so it is still slow for large datasets).

Version 1.3 July 12, 2013
•Updated python and python packages, including NetworkX to version 1.8dev.
•Updated Hexsim-based functions to Hexsim version 2.5.1, which improves conversion of .asc input file  to hxn file.
•Added support for locales (e.g., areas in Europe) that use a comma instead of a period as decimal separator.

Version 1.3.1 August 19, 2013
•Updated LEMON to version 1.3.
•Turned off arc mixing in network flow functions to resolve potential division by zero error.
•Updated NetworkX to version 1.8.1.
•Updated Hexsim-based functions to Hexsim version 2.5.3.

Version 1.3.2 August 1, 2014
•Updated NetworkX to version 1.9.
•Updated Hexsim-based functions to Hexsim version 3.0.4.

Planned future enhancements: Better support for multi-threaded implementation of of network flow due to release of LEMON 1.3.

For support questions, visit the support forum on Google Groups:

Google Groups
Connectivity Analysis Toolkit

Visit this group