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

[Mark A. Jensen]

Carnë-
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?
MAJ


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.
>
>
> chris
>
> On 1/10/17, 5:05 PM, "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:
>>
>>© Copyright 1993-2016 by Ziheng Yang
>>The software package is provided "as is" without warranty of any 
>> kind.
>>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: 
>>> https://groups.google.com/d/msg/pamlsoftware/NFu_lNBoAEA/VonOWvh6CgAJ
>>>
>>> BioPerl will always be open and free; Carnë knows this though, he’s 
>>> a bioperl contributor (and I would consider him a core developer).
>>>
>>> chris
>>>
>>> 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 [1]), so not restricted to academic 
>>> use. And
>>>     BioPerl is distributed under a dual-license GNU / Artistic 
>>> License
>>>     (see "license" at [2]).
>>>
>>>     best, Horacio
>>>
>>>     [1] http://abacus.gene.ucl.ac.uk/software/paml.html
>>>     [2] 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 
>>> sequences.
>>>     >
>>>     > 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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