DNA Alignment Software

Jerry Learn learn at u.washington.edu
Wed Jan 31 14:30:26 EST 1996

In article <310E5ED5.7385 at physci.ucla.edu>, ecastro at physci.ucla.edu wrote:

>Sequencher (gene codes) commercial, really good and fast, you can do 
>dozens of sequences at a time.  I forget how much it costs....sorry

Sequencher is definitely not free software.  As I recall it was $1800 US.

Although I'm a big fan of Sequencher, I can not recommend it's use for
everyday sequence alignment -- it works wonderfully for aligning data from
a sequencing project and assembling them into contigs.  If you want to
align finished sequences, I think that it has limitations that might have
a severe affect on one's results.  

Instead, I would recommend using ClustalW for aligning finished sequence
data.  It is available via anonymous ftp from:
<ftp://ftp.bio.indiana.edu/molbio/align/> or

I'm not sure how well clustal works for pairwise alignments, but I
recommend it for multiple alignments.
Jerry Learn

Research Associate

Dept. of Microbiology             | Learn at u.washington.edu
University of Washington          | Phone: (206) 616-4286
Box 357740                        |   FAX: (206) 616-1575
Seattle, WA  98195-7740  USA      |     or (206) 543-8297 

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