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

[Sebastien Moretti]

Hi

There are also some new developments in order to improve codeml - code 
and models - which is part of PAML.
See 
https://academic.oup.com/bioinformatics/article/doi/10.1093/bioinformatics/btw632/2584480/State-aggregation-for-fast-likelihood-computations

- FastCodeml  https://gitlab.isb-sib.ch/phylo/fastcodeml
- godon       https://bitbucket.org/Davydov/godon


FastCodeml is GPLv3 and godon - still beta - will also be GPL.

Sébastien


On 1/11/17, 8:43 AM, "carandraug at gmail.com on behalf of Carnë Draug" 
<carandraug at gmail.com on behalf of carandraug+dev at gmail.com> wrote:



 >On 11 January 2017 at 01:30, Fields, Christopher J
 ><cjfields at illinois.edu> wrote:
 >> On 10 January 2017 at 23:05, 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:
 >>>
 >>> [...]
 >>>     The author may have changed his mind, but as far as I can see it
 >>> is still GPLed.
 >>>
 >>
 >> 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.
 >>
 >
 >There are other issues even if you use it for academic purposes.
 >I want to write free software for others and make it easily available
 >but the dependency on PAML prevents that.
 >
 >  * free software dependent on it inherits that lack of freedom.
 >
 >  * non-free software is not packaged by Linux distribution (or is
 >    packaged into the non-free repositories which are disabled by
 >    default).
 >
 >Carnë

Agreed.

-c