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.
Alternatively, Windows users can use BioEdit ver. 7.0.9 or Geneious. Keep note that BioEdit cannot read NEXUS formatted files, so the format must be changed to a different type (e.g., FASTA) beforehand. A free 2-week trial version of Geneious Basic is available from the Geneious web site.