[Bioclusters] BioEdit - Andrew Shewmaker

bioclusters@bioinformatics.org bioclusters@bioinformatics.org
Wed, 25 Feb 2004 15:58:00 -0500

Dear Andrew 

I saw the letter you'd posted (below)on bioinformatics.org looking for a
replacement for BioEdit. I have pretty much the problems you'd described in your
mail. Did you get any useful responses/ replacements ?

with best regards
Srikanth Rajagopalan
Post-Doctoral Associate
Department of Neurology
Yale University School of Medicine
PO Box 208018
333 Cedar Street
New Haven , CT 06510, USA


I'm a cluster admin and I try to help my biologists on their
desktops as well.  I've got a few people who have been
using Bioedit, but it is unmaintained and does not work on
their newer machines running MS Windows XP.  I've searched a
bit and found that others are also having trouble with it,
especially with clustalw.

I'm pointing my biologists at the Staden package and ClustalX
as possible/partial? replacements for Bioedit, but I'm pretty
sure that they aren't a complete replacement.  Here is a list
of the things Bioedit does that they want, and I would
appreciate any help in locating applications that would fit.

cutting and pasting sequences
aligning multiple sequences in the same window (clustalW)
similarity matrix
slide residues
grab and drag
inserting/deleting gaps
nucleotide composition
complement and reverse compliment
restriction map
create concensus sequence
phylogenetic tree
find conserved regions
identity/similarity shading of nucleotides
color manipulation
BLAST over the internet (allows BLASTing of multiple sequences)

Some of these features, such as the integrated BLAST network
client aren't as critical since I've set up a local server.
I'm also setting up Phred/Phrap, Artemis, and ClustalW on the
server, but I know they will continue to want something like
Bioedit on their desktops.  So if anyone has any suggestions
I would appreciate them.

Thank you,


Andrew Shewmaker, Associate Engineer
Phone: 1-208-526-1276
Idaho National Eng. and Environmental Lab.
P.0. Box 1625, M.S. 3605
Idaho Falls, Idaho 83415-3605