SeaView is a graphical multiple sequence alignment editor developed by Manolo Gouy. SeaView is able to read and write various alignment formats (NEXUS, MSF, CLUSTAL, FASTA, PHYLIP, MASE). It allows one to manually edit the alignment, and also to run DOT-PLOT or MSA programs to locally improve the alignment.
The original reference for SeaView is Galtier et al. (1996).
You can download versions of SeaView for Macintosh, Windows or Linux from the SeaView web site.