The Wise2 package is entirely open source licensed for use by both
commerical and academic sites. This means that anyone can modify and
redistribute the source code without restriction. However, the use of
the source code as part of a larger, and potentially proprietory
package depends on which portions of the source code you wish to use.
Each directory has a seperate LICENSE or GNULICENSE file which you
should read, but the gist is given below.

The base (base libaries), dynlibsrc (underlying bioinformatics
libaries) and dyc (dynamite compiler) are distributed under a BSD
style license. This means that there is no restriction transfered to
other source code when these pieces of source code are linked with
other (potentially closed source) software libraries or code. These
portions therefore are freely redistributable and freely useable: only
an acknowledgement of the authorship needs to be declared.


The HMMer2 libaries (Sean Eddy's HMM package) and the models directory
(The algorithms for the Wise2 package, and final executable programs)
are both distributed under a Gnu General Public License (GPL). This
means that the entire package as it is distributed with these portions
in is also licensed under GPL, due to the 'infectious' nature of the
GPL.

If people wish to use one of the BSD styled licensed pieces of code,
the best route is to contact me directly so that I can make a clean
distribution with no GPL'd code.


The aim for this rather complicated licensing scheme is to provide
people with the freedom to use the underlying libraries and
technology as they see fit with very little restrictions, but to
ensure that the scientific work that I (and in case of HMMER, Sean
Eddy) provide is not explioted by someone else. By having the
important algorithmical parts of the package protected under GPL,
we ensure that any additional modifications or packages built
on top of our work have to be freely redistributed. However, I must
emphasise that the underlying bioinformatics libaries (base, dynlibsrc)
and the dynamite compiler can be used in any manner at all, as long
as authorship is acknowledged.


For more information, please contact Ewan Birney <birney@ebi.ac.uk>
but I don't like getting into protracted legal arguments. I believe
that this file and Licenses should be enough for any organisation to
figure out how they can use the software.