MUltiple sequence Alignment Software

David N. Levy david_levy at
Mon Oct 2 14:02:42 EST 1995

In article <DFtwxt.Cpt at>
horton at (Robert Horton) writes:

> I have used gcg's "pileup" and "best-fit" to do some sequence alignment. 
> : I am looking for a program (any platform) which is a mix between these two
> : utilities.  "Best-fit" wil draw pairing lines between any two sequences 
> : so that it is relatively easy to identify stretches of homogeneity and 
> : heterogeneity, unfortunately it will only pair two sequences at a time. 
> : "Pile-up" will pair multiple sequences at oncer , but will not indicate 
> : pairing lines (i.e. you must go through the aligned sequences by hand to 
> : find pair or mismatches) . I would like a program that can draw pairing 
> : lines between multiple sequences.  Any ideas would be greatly 
> : appreciated. 

Have you tried the "pretty" command in GCG?  It formats the output to
whatever you wish, for example, you can have the output be a consensus
sequence displayed at the bottom of the alignment with dashes (or any
other symbol) used in the aligment for all matches and the letter of
the single letter code displayed for the mismatches occurring in the
sequence.  The output is very flexible; this is only one option.  The
pretty command is used after an alignment is done with pileup.  

Also, the program "ClustalV" is available at in either Mac or DOS or Unix
format.  This program is similar to pileup plus pretty, but runs
independently on your PC.

David N. Levy, Ph.D.
Division of Molecular Genetics
Dana-Farber Cancer Insitute
Boston, MA 02115
david_levy at

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