[Bioperl-l] free software to estimate dS and dN in pairwise comparisons
Mark A. Jensen
maj at fortinbras.us
Wed Jan 11 02:41:34 UTC 2017
About 300 years ago (in 2005), I actually wrote some Perl that does
dS/dN from first principles.
I have it and could put it up on GitHub. I might even be able to figure
out how it works and write a readme, assuming I can translate it from
the cuneiform. Interested?
On 2017-01-10 20:30, Fields, Christopher J wrote:
> 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.
> On 1/10/17, 5:05 PM, "Horacio Montenegro" <h.montenegro at gmail.com>
>> ok, I understand now. Anyway, here is a snippet from pamlDOC.pdf
>>from PAML 4.9c, reiterating PAML is distributed under GNU GPL
>>© Copyright 1993-2016 by Ziheng Yang
>>The software package is provided "as is" without warranty of any
>>In no event shall the author or his employer be held responsible for
>>any damage resulting from the use of this software, including but not
>>limited to the frustration that you may experience in using the
>>package. The program package, including source codes, example data
>>sets, executables, and this documentation, is maintained by Ziheng
>>Yang and distributed under the GNU GPL v3.
>> The author may have changed his mind, but as far as I can see it
>>is still GPLed.
>>On Tue, Jan 10, 2017 at 8:32 PM, Fields, Christopher J
>><cjfields at illinois.edu> wrote:
>>> This is based on the text from the README.txt file with the
>>> distribution, which contradicts the license in the ‘src’ directory:
>>> ‘PAML is distributed free of charge for academic use only’
>>> There are others expressing licensing concerns as well, note this
>>> thread from the Debian folks:
>>> BioPerl will always be open and free; Carnë knows this though, he’s
>>> a bioperl contributor (and I would consider him a core developer).
>>> On 1/10/17, 2:38 PM, "Bioperl-l on behalf of Horacio Montenegro"
>>> <bioperl-l-bounces+cjfields=illinois.edu at mailman.open-bio.org on
>>> behalf of h.montenegro at gmail.com> wrote:
>>> What is free for academic use only? PAML is distributed under
>>> GNU GPL
>>> v3 (see "introduction" at ), so not restricted to academic
>>> use. And
>>> BioPerl is distributed under a dual-license GNU / Artistic
>>> (see "license" at ).
>>> best, Horacio
>>>  http://abacus.gene.ucl.ac.uk/software/paml.html
>>>  http://search.cpan.org/~cjfields/BioPerl-Run-1.007001/
>>> On Tue, Jan 10, 2017 at 6:19 PM, Carnë Draug
>>> <carandraug+dev at gmail.com> wrote:
>>> > I am looking for a piece of free software to estimate
>>> synonymous and
>>> > non-synonymous (dS and dN) distances between aligned
>>> > I have found codeml on Bio::Tools::Run::Phylo::PAML::Codeml
>>> but that
>>> > is not free software (it's for academic use only). Can
>>> anyone suggest
>>> > an alternative?
>>> > Thank you
>>> > Carnë
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