MuGeN is a software package for the visual exploration of multiple annotated genome portions. It is capable of simultaneously displaying genome portions loaded from various sources both local and remote and mix these with analysis result plots. It can also be used to generate images of these displays in a wide range of formats (PNG, PostScript, IMAP, XFig). Analysis results conform to an XML DTD, allowing easy integration of third-party analysis packages. Most of the display parameters can be customized, either interactively or through a preferences file.