LQGraph implements methods for optimizing the connectivity of sites administered to protect biodiversity (a conservation area network). The methods are suitable for existing protected areas (for example, national parks) or a proposed network. We model the landscape using graphs. The user provides a quality score for each site in the landscape outside the conservation areas. Based on these scores, LQGraph finds contiguity areas of maximum quality to link the conservation areas. The contiguity areas can be filtered to prioritize those that connect the conservation areas with the minimum number of sites or area. Compared with existing methods for establishing connectivity in a conservation area network, LQGraph can analyze substantially larger networks. LQGraph also identifies sites that efficiently isolate conservation areas, which is useful for halting the spread of pathogens or invasive species. The software provides routines for constructing the required input files and for visualizi...