Linux vs Unix for doing bioinformatics

Joe Felsenstein joe at evolution.genetics.washington.edu
Thu Mar 2 02:24:34 EST 2000

In article <Rit*4D1lo at news.chiark.greenend.org.uk>,
Tim Cutts  <timc at chiark.greenend.org.uk> wrote:
>In article <89isp9$b9e$1 at ezili.sis.pasteur.fr>,
>Stephane Bortzmeyer <bortzmeyer at pasteur.fr> wrote:
>>The Subject: is incorrect. Linux is an Unix, like a dog is a mammal or
>>an applepie is a pie.
>Although I agree with you in spirit, the pedantic truth is that Linux is
>not Unix; it is a unix-like operating system, but it's not unix.

He cites various FAQs and web pages.  Those were written to ensure that
no lawyer will bother these Linux organizations.

>From a legal viewpoint, Linux isn't Unix.  From a functional viewpoint,
for the purposes most of us use it for, it is Unix.  We find some source
code written to work on Unix, which does something bioinformatic.  We want to
know whether it will work on Linux.  If we try it on Windows98, it
won't work.   If we try it on MacOS, it won't.  If we try it on Linux
it usually will.

For the bioinformatic Unix source code stuff I want to run, it usually works
fine on Linux, and is less likely to run on my Digital Unix system, which
is one that has the approval of the lawyers.   Mostly that's because of
32/64 bit issues, which aren't affected but what some lawyer thinks is Unix.

(Ok, I'm quibbling.  This thread has been interesting and I have
enjoyed the helpful discussion of how well or not Linux systems work for
computational molecular biology.)

>Right, that's enough pedantry.  You can now go back to calling Linux
>unix and I won't care.  :-)

Fair enough.

Joe Felsenstein         joe at genetics.washington.edu
 Dept. of Genetics, Univ. of Washington, Box 357360, Seattle, WA 98195-7360 USA

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