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Re: [RFS] clustalw

On Thu, 6 Mar 2008, Aaron Darling wrote:

The mauveAligner codebase depends on the library refactorization of clustalw 1.83. I believe the new 2.x series of clustal releases was rewritten from scratch. Although I have not checked, I would assume that the internal structure would be quite different to 1.83 and that it would be much more work to refactor 2.x into a library than it would be for me to remove the current dependency on clustalw altogether.

OK, just take whatever option you feel apropriate.  From a licensing
point of view my guess is that you are well advised to remove the
current dependency. (see below)

That said, I investigated the licensing of the clustalw 1.83 codebase from which libClustalW derives. I found this statement at the top of the readme:


Clustal W is freely available to the user community. However, Clustal W is
increasingly being distributed as part of commercial sequence analysis
packages. To help us safeguard future maintenance and development, commercial
distributors of Clustal W must take out a NON-EXCLUSIVE LICENCE. Anyone
wishing to commercially distribute version 1.81 of Clustal W should contact the
authors unless they have previously taken out a licence.


Since I do not distribute libClustalW or Mauve commercially, I believe I am within the scope and spirit of the license.

I think you personally are safe - except that you turned the license into
GPL in the tarball which is downloadable from your web site.  The clean way
would have been that you have added the automake stuff, tagged your work
GPL and leave the original clustalw stuff with the license you are
quoting above.  Just turning the license of the whole tarball is wrong.

If the original clustalw authors feel otherwise, however, they are welcome to contact me. I probably did misstep by not including the license in a file when I refactored it into a library. I've now committed the license to the source code repository.


Sorry, haven't had time to make an official libGenome release yet. I will do it in conjunction with the next official Mauve release. This could take some time (weeks?)

Well, I think I have to wait with packaging Mauve until the clustalw
issue is solved in the downloadable tarball anyway.  So I might decide
to work with SVN for everything or wait until you released a new version.
I think I will maintain some preliminary SVN stuff in private and be
prepared to get proper packages ready shortly after your new release.
It would be great if you could drop a note here on this list once this
has happened.

Kind regards and thanks for your input



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