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Probably not helpful, but kaks() in the seqinr package of r will do something better than Nei-gojobori, but worse than PAML.</p>
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<div id="x_divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> Bioperl-l <bioperl-l-bounces+darren.obbard=ed.ac.uk@mailman.open-bio.org> on behalf of Roy Chaudhuri <roy.chaudhuri@gmail.com><br>
<b>Sent:</b> Wednesday, January 11, 2017 3:13:01 PM<br>
<b>To:</b> Mark A. Jensen; bioperl-l@mailman.open-bio.org; carandraug+dev@gmail.com<br>
<b>Subject:</b> Re: [Bioperl-l] free software to estimate dS and dN in pairwise comparisons</font>
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<div class="PlainText">Should probably note that the Nei-Gojobori and LWL methods are quite
<br>
old, and do not take account of transition/transversion rate variation <br>
so may produce misleading results. The more sophisticated models <br>
implemented in PAML (codeml and yn00) are probably a better bet if you <br>
can sort out the licence issue.<br>
<br>
Cheers,<br>
Roy.<br>
<br>
On 11/01/2017 04:45, Mark A. Jensen wrote:<br>
> And here it is -- still runs! No BioPerl required, as it turns out.<br>
><br>
> <a href="https://github.com/majensen/dnds">https://github.com/majensen/dnds</a><br>
><br>
> MAJ<br>
><br>
> On 2017-01-10 21:41, Mark A. Jensen wrote:<br>
>> Carnë-<br>
>> About 300 years ago (in 2005), I actually wrote some Perl that does<br>
>> dS/dN from first principles.<br>
>> I have it and could put it up on GitHub. I might even be able to<br>
>> figure out how it works and write a readme, assuming I can translate<br>
>> it from the cuneiform. Interested?<br>
>> MAJ<br>
>><br>
>><br>
>> On 2017-01-10 20:30, Fields, Christopher J wrote:<br>
>>> I normally would agree, but for anyone working in the commercial<br>
>>> domain the licensing is technically and (more importantly) legally<br>
>>> ambiguous IMO, and any legal counsel would advise not using the code<br>
>>> until that license is clarified one way or another. This is also the<br>
>>> reason Debian won’t release a PAML package it until the language in<br>
>>> the README.txt is changed to clarify the license.<br>
>>><br>
>>> Note (in that thread) this has been going on over a year; the intent<br>
>>> is obvious that this should be GPL’d.<br>
>>><br>
>>><br>
>>> chris<br>
>>><br>
>>> On 1/10/17, 5:05 PM, "Horacio Montenegro" <h.montenegro@gmail.com><br>
>>> wrote:<br>
>>><br>
>>>> ok, I understand now. Anyway, here is a snippet from pamlDOC.pdf<br>
>>>> from PAML 4.9c, reiterating PAML is distributed under GNU GPL license:<br>
>>>><br>
>>>> © Copyright 1993-2016 by Ziheng Yang<br>
>>>> The software package is provided "as is" without warranty of any kind.<br>
>>>> In no event shall the author or his employer be held responsible for<br>
>>>> any damage resulting from the use of this software, including but not<br>
>>>> limited to the frustration that you may experience in using the<br>
>>>> package. The program package, including source codes, example data<br>
>>>> sets, executables, and this documentation, is maintained by Ziheng<br>
>>>> Yang and distributed under the GNU GPL v3.<br>
>>>><br>
>>>> The author may have changed his mind, but as far as I can see it<br>
>>>> is still GPLed.<br>
>>>><br>
>>>> On Tue, Jan 10, 2017 at 8:32 PM, Fields, Christopher J<br>
>>>> <cjfields@illinois.edu> wrote:<br>
>>>>> This is based on the text from the README.txt file with the<br>
>>>>> distribution, which contradicts the license in the ‘src’ directory:<br>
>>>>><br>
>>>>> ‘PAML is distributed free of charge for academic use only’<br>
>>>>><br>
>>>>> There are others expressing licensing concerns as well, note this<br>
>>>>> thread from the Debian folks:<br>
>>>>> <a href="https://groups.google.com/d/msg/pamlsoftware/NFu_lNBoAEA/VonOWvh6CgAJ">
https://groups.google.com/d/msg/pamlsoftware/NFu_lNBoAEA/VonOWvh6CgAJ</a><br>
>>>>><br>
>>>>> BioPerl will always be open and free; Carnë knows this though, he’s<br>
>>>>> a bioperl contributor (and I would consider him a core developer).<br>
>>>>><br>
>>>>> chris<br>
>>>>><br>
>>>>> On 1/10/17, 2:38 PM, "Bioperl-l on behalf of Horacio Montenegro"<br>
>>>>> <bioperl-l-bounces+cjfields=illinois.edu@mailman.open-bio.org on<br>
>>>>> behalf of h.montenegro@gmail.com> wrote:<br>
>>>>><br>
>>>>> What is free for academic use only? PAML is distributed under<br>
>>>>> GNU GPL<br>
>>>>> v3 (see "introduction" at [1]), so not restricted to academic<br>
>>>>> use. And<br>
>>>>> BioPerl is distributed under a dual-license GNU / Artistic License<br>
>>>>> (see "license" at [2]).<br>
>>>>><br>
>>>>> best, Horacio<br>
>>>>><br>
>>>>> [1] <a href="http://abacus.gene.ucl.ac.uk/software/paml.html">http://abacus.gene.ucl.ac.uk/software/paml.html</a><br>
>>>>> [2] <a href="http://search.cpan.org/~cjfields/BioPerl-Run-1.007001/">http://search.cpan.org/~cjfields/BioPerl-Run-1.007001/</a><br>
>>>>><br>
>>>>> On Tue, Jan 10, 2017 at 6:19 PM, Carnë Draug<br>
>>>>> <carandraug+dev@gmail.com> wrote:<br>
>>>>> > I am looking for a piece of free software to estimate<br>
>>>>> synonymous and<br>
>>>>> > non-synonymous (dS and dN) distances between aligned sequences.<br>
>>>>> ><br>
>>>>> > I have found codeml on Bio::Tools::Run::Phylo::PAML::Codeml<br>
>>>>> but that<br>
>>>>> > is not free software (it's for academic use only). Can<br>
>>>>> anyone suggest<br>
>>>>> > an alternative?<br>
>>>>> ><br>
>>>>> > Thank you<br>
>>>>> > Carnë<br>
>>>>> ><br>
>>>>> > _______________________________________________<br>
>>>>> > Bioperl-l mailing list<br>
>>>>> > Bioperl-l@mailman.open-bio.org<br>
>>>>> > <a href="http://mailman.open-bio.org/mailman/listinfo/bioperl-l">http://mailman.open-bio.org/mailman/listinfo/bioperl-l</a><br>
>>>>><br>
>>>>> _______________________________________________<br>
>>>>> Bioperl-l mailing list<br>
>>>>> Bioperl-l@mailman.open-bio.org<br>
>>>>> <a href="http://mailman.open-bio.org/mailman/listinfo/bioperl-l">http://mailman.open-bio.org/mailman/listinfo/bioperl-l</a><br>
>>>>><br>
>>><br>
>>> _______________________________________________<br>
>>> Bioperl-l mailing list<br>
>>> Bioperl-l@mailman.open-bio.org<br>
>>> <a href="http://mailman.open-bio.org/mailman/listinfo/bioperl-l">http://mailman.open-bio.org/mailman/listinfo/bioperl-l</a><br>
>><br>
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