If you're looking for a tool to align and edit nucleotide and protein sequences, our Base-By-Base has a variety of extra features that could be useful. Available at: www.virology.ca
We're pretty much at version3 these days. It focuses on comparisons and visualization of alignments, and can display GenBank CDS regions as well as user-added comments.
We're embarking on some system maintenance, so there might be times when the site is down.
Hillary, W., S.H. Lin, and C. Upton. 2011.
Base-By-Base version 2: single nucleotide-level analysis of whole viral genome alignments, BMC Microbial Informatics and Experimentation, 1:2
William Hillary, Song-Han Lin and Chris Upton*
Brodie, R., A.J. Smith, R.L. Roper, V. Tcherepanov, and C. Upton. 2004.
Base-By-Base: Single nucleotide-level analysis of whole viral genome alignments, BMC Bioinformatics, 5, 96.