GeneSpy, a User-Friendly and Flexible Genomic Context Visualizer

Bioinformatics. 2019 Jan 15;35(2):329-331. doi: 10.1093/bioinformatics/bty459.


Summary: The exploration and comparison of genome organization is routinely used in the frame of genomic and phylogenomic analyses. As a consequence, in the past few years, various tools allowing visualizing genomic contexts have been developed. However, their use is often hampered by a lack of flexibility, particularly concerning associated databases input formats and figure customization. Here we present GeneSpy, a graphical user interface that allows the visualization and dynamic exploration of eukaryotic and prokaryotic annotated genomes. GeneSpy relies on user-friendly manageable local databases and allows the easy customization and production of figures in a multitude of formats.

Availability and implementation: GeneSpy is freely available at for Linux, Mac OS and Windows under CeCILL license ( It is written in Python 2.7 and depends on Matplotlib, Tkinter and Sqlite libraries.

Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computational Biology
  • Computer Graphics*
  • Databases, Genetic
  • Genome
  • Genomics*
  • Software*
  • User-Computer Interface*