Unix vs Linux - the movie.

Joe Felsenstein joe at evolution.genetics.washington.edu
Fri Jul 28 12:14:03 EST 2000

In article <8lrpki$9rv$1 at ezili.sis.pasteur.fr>,
Stephane Bortzmeyer <bortzmeyer at pasteur.fr> wrote:
>...  but there is still the issue of programs
>like Phylip or Clustalw, where you have source but not freedom (one
>more reason not to use the "open source" term). 

Stephane and I have been back and forth over his use of "freedom" enough
times in e-mail that I think neither will change the other's mind.  But
I do want to point out that the particular form of slavery that is
promoted in the PHYLIP license is one where you not only can see the
source code, you can use it whether you are doing commercial, academic,
or personal work, you can modify it, *and* you can redistribute it
all you want -- unless you are going to sell it or sell access to it.
Then our University (and me) have to get some royalties.

>In practice, I think that the peer review is less efficient when you
>cannot make changes and distribute them: you cannot test your ideas so
>widely. And people are less likely to work on a program if they cannot
>distribute and use the changes.

Which is probably why so many people use PHYLIP ... they can do all these

>I would say that freedom is not binary. There is space between free
>and "completely unfree".

True.  And I prefer to restrict your freedom to waltz off and make lots of
money from my code, without paying us a penny.

But as long as you don't do that, feel "free" to modify PHYLIP and
distribute the modifications.  For example, the Institut Pasteur uses a
modified version of PHYLIP on its web-server service, to correct a limitation
that could result in infinite loops when reading data.  They asked my
permission, but actually they didn't need to ask it.  This is only one of
many modified versions of PHYLIP code in distribution.

I am not saying that all bioinformatics code should be distributed under
conditions such as we use.  It just suits us, and I think it is open enough
for most purposes.

Joe Felsenstein         joe at genetics.washington.edu     (IP No.
 Dept. of Genetics, Univ. of Washington, Box 357360, Seattle, WA 98195-7360 USA

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