Seaview
http://pbil.univ-lyon1.fr/software/seaview.html
SeaView is a graphical multiple sequence alignment editor that is able to read and write various alignment formats (NEXUS, MSF, CLUSTAL, FASTA, PHYLIP, MASE). It allows to manually edit the alignment, and also to run DOT-PLOT or CLUSTALW programs to locally improve the alignment.
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