RT Journal
A1 Parks, Donovan H.
A1 Porter, Michael
A1 Churcher, Sylvia
A1 Wang, Suwen
A1 Blouin, Christian
A1 Whalley, Jacqueline
A1 Brooks, Stephen
A1 Beiko, Robert G.
T1 GenGIS: A geospatial information system for genomic data
JF Genome Research 
JO Genome Research 
YR 2009 
FD October 01 
VO 19 
IS 10 
SP 1896 
OP 1904 
DO 10.1101/gr.095612.109 
UL http://genome.cshlp.org/content/19/10/1896.abstract 
AB The increasing availability of genetic sequence data associated with explicit geographic and ecological information is offering new opportunities to study the processes that shape biodiversity. The generation and testing of hypotheses using these data sets requires effective tools for mathematical and visual analysis that can integrate digital maps, ecological data, and large genetic, genomic, or metagenomic data sets. GenGIS is a free and open-source software package that supports the integration of digital map data with genetic sequences and environmental information from multiple sample sites. Essential bioinformatic and statistical tools are integrated into the software, allowing the user a wide range of analysis options for their sequence data. Data visualizations are combined with the cartographic display to yield a clear view of the relationship between geography and genomic diversity, with a particular focus on the hierarchical clustering of sites based on their similarity or phylogenetic proximity. Here we outline the features of GenGIS and demonstrate its application to georeferenced microbial metagenomic, HIV-1, and human mitochondrial DNA data sets.