[Bioperl-l] free software to estimate dS and dN in pairwise comparisons
Fields, Christopher J
cjfields at illinois.edu
Tue Jan 10 22:32:29 UTC 2017
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).
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 ), so not restricted to academic use. And
BioPerl is distributed under a dual-license GNU / Artistic License
(see "license" at ).
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
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