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

Wed Jan 11 16:34:01 UTC 2017

Probably not helpful, but kaks() in the seqinr package of r will do something better than Nei-gojobori, but worse than PAML.

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________________________________
From: Bioperl-l <bioperl-l-bounces+darren.obbard=ed.ac.uk at mailman.open-bio.org> on behalf of Roy Chaudhuri <roy.chaudhuri at gmail.com>
Sent: Wednesday, January 11, 2017 3:13:01 PM
To: Mark A. Jensen; bioperl-l at mailman.open-bio.org; carandraug+dev at gmail.com
Subject: Re: [Bioperl-l] free software to estimate dS and dN in pairwise comparisons

Should probably note that the Nei-Gojobori and LWL methods are quite
old, and do not take account of transition/transversion rate variation
so may produce misleading results. The more sophisticated models
implemented in PAML (codeml and yn00) are probably a better bet if you
can sort out the licence issue.

Cheers,
Roy.

On 11/01/2017 04:45, Mark A. Jensen wrote:
> 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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