Well, I only got two replies so I guess I have to answer my own question :-)
The query was how to convert the text output of a MACAW alignment into
any standard sequence format so I can use it with (for instance) profilemake,
PAUP, Phylip, PrettyBox, etc.
Thanks to B.L. Cohen and Martti Tolvanen for pointing out the usefulness
of ReadSeq from Don Gilbert, however, readseq chokes on these files (at
least my late 1992 version does, and I don't see anything in the current
README on IUBIO to indicate that the current version can recognize this
format, though I may be missing something).
So I took an old line sorting program I wrote when I was learning C and
modified it to sort in the opposite direction and strip leading names
and trailing numbers so as to generate a Pearson format file.
It's ugly, it's full of unnecessary typedefs (the shell was written when I was
writing C but thinking in Pascal :-) it's inefficient (though it's not too
slow on my quadra), but it's small, uses little memory, and works. If there's
any interest I'll post it to the mailing list (it's about 400 lines, but
Let me know if you want it.
Michael Lonetto // Phone: 415-476-1493 // Email: lonetto at cgl.ucsf.edu
UCSF Depts. of Stomatology and Microbiology, San Francisco, CA 94143-0512