Circular and linear DNA diagrams provide a powerful tool for illustrating the features of a genome in their full genomic context. CGView (Stothard and Wishart,2005) is a circular genome viewer that produces PNG, JPEG or scalable vector graphics (SVG) format. It is primarily designed to be part of a pipeline and not an interactive and editable viewer. GenomeDiagram (Pritchard et al., 2006) is a Python module, which can also be used to generate diagrams. GenomePlot (Gibson and Smith, 2003), GenoMap (Sato and Ehira, 2003) and Microbial Genome Viewer (MGV; Kerkhoven et al., 2004), are GUI based but do not provide the ability to directly read in files in the common sequence formats or a filtering tool to define tracks.
Circos (http://mkweb.bcgsc.ca/circos/) is web-based genome comparison visualizer that is configured from flat files. It can be configured for comparisons within a genome or between multiple genomes. There are also commercial packages available that draw circular and linear plots.