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GIS tools and remote sensing products have opened the possibility to model the impacts of matrix permeability on a broad range of ecological phenomena. LORACS (Landscape ORganization and Connectivity Survey) is JAVA software containing a GUI interface and an API for easy extensibility. The user inputs maps with the relative costs to move within each pixel and the location of source and target patches. The software outputs Multiple Shortest Paths and Conditional Minimum Transit Cost maps. One key feature is the derivation of uncertainty estimates around path length, cost, and spatial distribution. We use data from the Brazilian Atlantic Forest to illustrate how LORACS can be used to translate assumptions about habitat quality into landscape connectivity patterns.