Joe Thornton's notes on DNA sequence manipulation programs

May 3, 1999
To: Darcy Kelley
Fm: Joe Thornton
Re: Sequence analysis software

Dear Darcy:

In response to your request for information on sequence analysis software, here is a brief note on what I use, its strengths and weaknesses, and a recommendation for some programs I feel the department should obtain. This is not intended as an exhaustive evaluation; although I do quite a bit of analysis of DNA and protein sequences, this list is circumscribed by my personal experience.

While there are other sequence alignment programs, I consider this a generally valid and trustworthy algorithm, because it uses sophisticated multiple-sequence alignment methods guided by a phylogenetic tree, which the program itself evaluates from the sequences.

Sequencher is available for Mac; a Windows version was supposedly scheduled for release last year, but I don’t know if it came out or not. It will run on a network and can be purchased for any given number of simultaneous users (that means as many as x persons can be using the program at one time, but there is no limit on the number of potential users, so long as they are connected to the network). It is not cheap -- around $1500 per user. In my view, however, it is clearly worth it.

Sequencher is published by Gene Codes,, phone 734-769-7249.