Max V Myakishev wrote:
>> I am looking for the tool to perform
> pairwise alignment of 200,000 and 20,000 bp sequences.
>> Preferable computer platforms: WWW > PC > Mac > UNIX.
>> I already tried many programs and most of them
> are limited by the input sequence size 32000.
>> Max V Myakishev, Ph.D.
> Email: max at scientist.com
If you want a dot-matrix style similarity comparison, D3HOM and D4HOM
in the Unix version of FSAP allow sequences of up to 750,000bp
(or greater if you recompile). Have a look at
(Note: the DOS versions of these programs do NOT allow
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