For manual alignments I invite you to try my multiple sequence editor
Esee3 which is available via anonymous ftp from:
trog.mbb.sfu.ca (directory pub/esee)
or
alanine.gcg.com (directory pub/msdos)
the files of interest are: esee3zip.exe and xeseezip.exe
Eric Cabot
cabot at gcg.com
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Regards,
Eric L. Cabot
cabot at gcg.com