I use and really like SeqApp. Here is reference to a help sheet I wrote:
http://www.biol.sfu.ca/staff/dc/seqapp.html
SeqApp is a freeware Macintosh program written by Don Gilbert and
available by anonymous ftp (Fetch) or gopher from ftp.bio.indiana.edu.
SeqApp is a powerful program- it is used for storing and aligning data,
and outputting formatted files for PHYLIP, PAUP, and other analysis
programs as well as for printing hard copies of alignments. It also will
compare regions of homology between two sequences (with DottyPlot) and
send sequence to BLAST for similarity searches of all sequences in
GenBank.
However, it has several bugs or unincorporated features. Exploring new
areas of the menu can lead to a program or system crash- thus always have
backup copies of your files, and always save your file regularly while
working and before doing anything new. These dire warnings are intended to
keep your expectations low so you will be pleasantly surprised when use
the program- they are not intended to discourage use of the program. I
rarely have any problems
with SeqApp.
gopher://ftp.bio.indiana.edu:70/11/IUBio-Software+Data/molbio/seqapp
