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GenGIS is a free and open-source bioinformatics application that allows geographic data to be merged with information about biological sequences collected from the environment. It consists of a 3D graphical user interface in which the user can navigate and explore the data, as well as a Python interface that allows easy scripting of statistical analyses using the Rpy libraries.

The Aneides lugubris of Western California, on of the top hotspots on the planet for species diversity where 33 of 44 salamander species are endemic to the state.

Loading Data

The Salamander data consists of a 2D map (Cali.tiff), location data (Aneides_Locations_Filtered.csv) and a phylogenetic tree (Aneides_Filtered.tre). For basic information on using the GenGIS interface and loading data please see the Banza Katydid Tutorial.

Changing Visual Properties

The location set properties were selected to differentiate the data set my mtDNA clades. The properties of the phylogenetic display were selected to ensure maximum visibility of locations on the map. For further details on setting visual properties see the Banza Katydid or GOS tutorials.

Creating Cartograms

Contact Information

We encourage you to send us suggestions for new features. GenGIS is in active development and we are interested in discussing all potential applications of this software. Suggestions, comments, and bug reports can be sent to Rob Beiko ( If reporting a bug, please provide as much information as possible and, if possible, a simplified version of the data set which causes the bug. This will allow us to quickly resolve the issue.