Re: free software to estimate dS and dN in pairwise comparisons

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" <[email protected] on behalf of [email protected]> 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 <[email protected]> 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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