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I'd like to calculate least cost paths between fragments using a cost raster I created based on habitat suitability values.

I saw that most people use Linkage Mapper, but I don't have access to ArcGIS. I also saw the gdistance function, but it is based on a DEM and I'd rather use my cost layer.

Is there an open source alternative to Linkage Mapper? Or can it be used without ArcGIS?

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QGIS (open source) has a new plugin called Least-Cost-Paths Network (open source, GNU GPL v3) (https://github.com/xrubio/LCPNetwork) that will take a set of origin and destination points and calculate the optimal least cost path across a cost surface using Djikstra.

GRASS GIS has r.cost (https://grass.osgeo.org/grass74/manuals/r.cost.html) and other tools that might meet your needs.

Linkage Mapper appears to require ArcGIS 10.0 but works with 9.3 through to 10.4 (https://sites.google.com/a/circuitscape.org/circuitscape/linkagemapper)

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