MUltiple sequence Alignment Software

Peter Rice pmr at
Mon Oct 2 04:26:32 EST 1995

In article <44hklg$81p at> ez041797 at (Jean-Manuel Henry) 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. 

Th eproblem with "pairing lines" is that it is only easy to draw them
between two sequences.

For multiple sequences, the matching residues are usually indicated by
drawing boxes around all the matching residues.

Two programs, PRETTYPLOT and PRETTYBOX, in the EGCG "extended GCG" package
do this, and read pileup's MSF files as input.

EGCG is available from

More information about EGCG is on my home page

Peter Rice                           | Informatics Division
E-mail: pmr at             | The Sanger Centre
Tel: (44) 1223 494967                | Hinxton Hall, Hinxton,
Fax: (44) 1223 494919                | Cambs, CB10 1RQ
URL:   | England

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