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

[Mark A. Jensen]

And here it is -- still runs! No BioPerl required, as it turns out.

https://github.com/majensen/dnds

MAJ

On 2017-01-10 21:41, Mark A. Jensen wrote:
> 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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