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

[Fields, Christopher J]

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
    >
    > _______________________________________________
    > Bioperl-l mailing list
    > Bioperl-l at mailman.open-bio.org
    > http://mailman.open-bio.org/mailman/listinfo/bioperl-l
    
    _______________________________________________
    Bioperl-l mailing list
    Bioperl-l at mailman.open-bio.org
    http://mailman.open-bio.org/mailman/listinfo/bioperl-l