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New Sequence Alignment Software Available

James Thomas jht at u.washington.edu
Fri Feb 8 17:08:20 EST 2002

Fellow Worm Workers,

I write to announce the availability of new sequence alignment and phylogenetic
tree building software that I have written. It is called Bonsai and 
it is available by
download for free from the following site:

(in case you forget this,
it is also linked from the C. elegans WWW Web Server under "Software")

If you have ever used Clustal (any version) and been frustrated by 
its limitations
and the lack of good documentation and explanation of the results, you should
give Bonsai a try. The underlying alignment methods are very similar to Clustal
(possibly slightly improved) but the user interface is greatly 
improved, the doc-
umentation is much more extensive (and growing), and the access to 
the underlying
alignment information (scores etc) is much better. Clustal also does 
a very poor
job with phylogenetic tree construction, which is handled correctly in Bonsai.
Bonsai also includes a number of capabilities that are unavailable in 
Clustal and
other software, including easy graphical tree arrangement, simulated sequence
evolution, and dot matrix display of pairwise alignments. However, 
Bonsai currently 
analyzes only protein sequence, not DNA.

I am in a testing phase for the program and I am trying to achieve a 
limited release
to get feedback on accuracy and bugs before attempting to distribute 
the program
more widely. The program is highly functional in its current form and 
I believe will be
well worth your while to use now compared to competing programs. I 
also am keen to
get feedback from users, and you can expect improved versions of 
Bonsai over the
next year or so. They will remain free and I also expect 
documentation support to
improve. I will change the core user interface as little as possible 
so that things you
get used to now will be similar in the future. Please send feedback to me at
<mailto:jht at u.washington.edu>jht at u.washington.edu and try to provide 
sufficient specific information for me to
fix bugs or modify features effectively.

Best - Jim Thomas

James H. Thomas
Department of Genome Sciences (pka Dept. of Genetics)
University of Washington

PS The program is written in Java and should run on any computer platform that
supports a recent Java Runtime Environment (JDK1.3 for those who know about
these things). This includes Mac OSX, Windows 98 and later, and most any
Unix platform, including Linux. If you use Windows there is a download version
that includes the entire Java Runtime Environment so you will be able to run it
for sure. I have tested Bonsai on Mac OSX and it is a bit pokey but 
runs smoothly.
I know of at least one user who is running it under Linux and apart 
from some of
the usual Java font and minor interface quirks it runs fine.

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