[Bioperl-l] free software to estimate dS and dN in pairwise comparisons

Carnë Draug carandraug+dev at gmail.com
Wed Jan 11 14:43:33 UTC 2017

On 11 January 2017 at 01:30, Fields, Christopher J
<cjfields at illinois.edu> wrote:
> On 10 January 2017 at 23:05, Horacio Montenegro <h.montenegro at gmail.com> wrote:
>>      ok, I understand now. Anyway, here is a snippet from pamlDOC.pdf
>> from PAML 4.9c, reiterating PAML is distributed under GNU GPL license:
>> [...]
>>     The author may have changed his mind, but as far as I can see it
>> is still GPLed.
> I normally would agree, but for anyone working in the commercial domain the licensing is technically and (more importantly) legally ambiguous IMO, and any legal counsel would advise not using the code until that license is clarified one way or another.  This is also the reason Debian won’t release a PAML package it until the language in the README.txt is changed to clarify the license.
> Note (in that thread) this has been going on over a year; the intent is obvious that this should be GPL’d.

There are other issues even if you use it for academic purposes.
I want to write free software for others and make it easily available
but the dependency on PAML prevents that.

  * free software dependent on it inherits that lack of freedom.

  * non-free software is not packaged by Linux distribution (or is
    packaged into the non-free repositories which are disabled by


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