'Pretty box' or alike software?

Michael D. Baron michael.baron at bbsrc.ac.uk
Mon Jun 3 12:38:15 EST 1996

Gilles VACHON wrote:
> Hi all,
> I am trying to make nice alignments of two protein sequences for the first t=
> ime.
> I realize we don't have a software to make boxes etc...
> Someone told me Pretty box is useful to do the job.
> Is it available ot is there a similar program to nicely align seuences?

Gilles, do you want to *align* the two sequences,or display an existing 
alignment? If the former, PRETTYBOX, PRETTYPLOT, BOXSHADE, ALSCRIPT etc. 
will not help, as they all display preexisting multiple alignments. You 
need a program to compute the optimum alignment of the two sequences. I 
use the GCG programs GAP or BESTFIT for this, I haven't used any non-GCG 
If you just want to display, PRETTYPLOT and PRETTYBOX are part of the 
EGCG package, I think. The others are available from various FTP sites, 
look at recent messages in this group.
best of luck,
Michael D. Baron
michael.baron at bbsrc.ac.uk

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