plotcon plots the quality of conservation of a sequence alignment.
Here is a sample session with plotcon:
% plotcon -sformat msf alignment.msf
Mandatory qualifiers (bold if not always prompted):
File containing a sequence alignment.
Number of columns to average alignment quality over. The larger this value is, the smoother the plot will be.
Display as data.
This is the scoring matrix file used when comparing sequences. By default, it is the file EBLOSUM62 (for proteins) or the file EDNAFULL (for nucleic sequences). These files are found in the data directory of the EMBOSS installation.
Output the match data to a file, instead of plotting it.