Have a look at: www.virology.ca
OK, they're not all new... but may be to a lot of this audience.
Over the last 5 yrs my group has been building a database + analysis
system to work with large viral genomes. We now have databases for 13
virus families (not all large viruses).
Most of the tools also work with bacterial genomes.
The tools include: database, genome browser, dotplotter, genome
annotator, MSA editor, BLAST management system.
For some overviews, see the News link at www.virology.ca to a series of
PDFs that describe the tools.
We use the tools integrated with the database, but most also work as
stand-alones. They are written in Java and are platform independent.
University of Victoria