Multiple DNA sequence alignment

Brian Foley brianf at
Fri Jan 21 08:43:00 EST 1994

Brian Foley (brianf at wrote:
: 	Do you not have the UWGCG programs available on a mainframe
: at your campus?  Just use your Mac as a terminal to the mainframe and
: use PILEUP program from UWGCG.  It beats anything I've seen on the Mac
: itself.

	I'd like to add that the spreadsheet macros published in
BioTechniques, Vol 15, No 6, Pages 1084-1089 by Margo Haygood
title = "Spreadsheet Macros for Coloring Sequence Alignments" are
pretty nice.  They do not do the alignment itself, but do a great
job of highlighting conserved areas of already aligned sequences,
both protein and nucleic acid.

******* From Margo Haygood ****************************

At the time the article went to press, we didn't have the files up on
Internet.  They are now and here are the instructions:

Obtaining the Excel macros (in the mac style of compressed file) for
coloring sequences:

By Gopher:

Connect to the server navigate to the directory
SIO-Department/MBRD/haygood and thenjust double click on the file to
retrieve it.

By anonymous ftp:

ftp to, login as anonymous with email address as the password.
The files are in the directory Haygood.

        The file color_macro.sea.hqx is a BinHex 4.0 file of a
self-extracting archie containing the Excel macros, a readme and
a set of test files.

For difficulties obtaining the files from, contact John
Studarus at jstudaru at sdcc5.UCSD.EDU

For questions about the operation of the macros contact Margo Haygood at
mhaygood at

For PC users:

We have put up a PC accessible file (a self-extracting .exe file, it is in
the same location). At the moment, the macro file it creates need to be
renamed as color.xlm.  The .xlm extension allows Excel to recognize it
immediately as a macro file.  The next one we put up will do that

Excel for Windows has a bug that causes the colors to display less nicely
on a PC than they do on the mac (the actual file is unaffected because if
you transfer back to the mac the file displays fine).  I don't know if it
affects output.  If anyone comes up with a fix, let me know. On the up
side, the macros run much faster on a PC.  Even for mac users, for really
large files it can be worth it do to the coloring on a PC and transfer back
to the mac.

*  Brian Foley               *     If we knew what we were doing   *
*  Molecular Genetics Dept.  *     it wouldn't be called research  *
*  University of Vermont     *                                     *

More information about the Methods mailing list