Have you tried ClustalX? I believe it is available for Windows, here
(the .zip file):
Paul Wary wrote:
> There are several sequence alignment programs (e.g. Dialign, Spidey)
> available on the Web, which are accessible through HTML-based forms
> (however, this means I have to go online every time I want to perform
> an alignment). Sometimes excutables for several computer platforms can
> be downloaded but usually they are command-line operated, which is not
> very convenient.
>> Is it possible to set up a local HTML-based form or any other type of
> user-friendly interface using the command-line operated DOS
> executables? I do not know any programming languages but I do know
> some HTML.