displaying alignments

Michael D. Baron "/G=michael/S=baron/OU=morbillivirus/OU=pirbright/OU=i a h/" at AFRC.ac.uk
Tue Dec 21 09:00:19 EST 1993

Dear Netters,
I am looking for a program which will allow me to display/print the 
alignment I have made of a set of protein sequences. Ideally, it will 
shade, or otherwise highlight, the residues that match a consensus, 
allowing for conservative replacements; it would be nice to 
distinguish highly conserved from less conserved residues.

I HAVE ALREADY TRIED the GCG program Prettybox, but found that there 
are still some bugs in it, in that it makes some pretty strange 
decisions as to what is the consensus, and doesn't respond properly to 
the PLURALITY setting (which *should* allow one to say that one wants 
at least X residues to agree before there is a consensus).This is sad, 
as the program would otherwise seem to be perfect. I have also tried 
BOXSHADE (ftp'd from the EMBL archive), which is also very nice, but 
which insists on there being a consensus residue at every site, which makes 
for a confusing picture. 

I have tried PrettyPlot which works, but does not allow one to 
distinguish between degrees of conservation (residues are either in 
the box or out), and the PrettyPrint option in Don Gilbert's wonderful 
SeqApp, which only highlights identical residues.

If you know of, or even have written, a program which displays 
alignments, I would be grateful to hear from you. No commercial 
software, I'm afraid, as there is no spare cash to buy anything at the 

Thanks in advance,

Michael Baron (BARON at AVRI.AFRC.AC.UK)

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