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