MOTIVATION: Analysis of multiple genomes requires sophisticated tools that provide search, visualization, interactivity and data export. Comparative genomics datasets tend to be large and complex, making development of these tools difficult. In addition to scalability, comparative genomics tools must also provide user-friendly interfaces such that the research scientist can explore complex data with minimal technical expertise. RESULTS: We describe a new version of the Sybil software package and its application to the important human pathogen Streptococcus pneumoniae. This new software provides a feature-rich set of comparative genomics tools for inspection of multiple genome structures, mining of orthologous gene families and identification of potential vaccine candidates. AVAILABILITY: The S.pneumoniae resource is online at http://strepneumo-sybil.igs.umaryland.edu. The software, database and website are available for download as a portable virtual machine and from http://sourceforge.net/projects/sybil.
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