free software to estimate dS and dN in pairwise comparisons

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free software to estimate dS and dN in pairwise comparisons

Carnë Draug-2
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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Re: free software to estimate dS and dN in pairwise comparisons

Horacio Montenegro
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 <[hidden email]> 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
> [hidden email]
> http://mailman.open-bio.org/mailman/listinfo/bioperl-l

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Re: 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=[hidden email] on behalf of [hidden email]> 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 <[hidden email]> 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
    > [hidden email]
    > http://mailman.open-bio.org/mailman/listinfo/bioperl-l
   
    _______________________________________________
    Bioperl-l mailing list
    [hidden email]
    http://mailman.open-bio.org/mailman/listinfo/bioperl-l


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

Horacio Montenegro
     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
<[hidden email]> 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=[hidden email] on behalf of [hidden email]> 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 <[hidden email]> 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
>     > [hidden email]
>     > http://mailman.open-bio.org/mailman/listinfo/bioperl-l
>
>     _______________________________________________
>     Bioperl-l mailing list
>     [hidden email]
>     http://mailman.open-bio.org/mailman/listinfo/bioperl-l
>

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

Fields, Christopher J
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" <[hidden email]> 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
><[hidden email]> 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=[hidden email] on behalf of [hidden email]> 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 <[hidden email]> 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
>>     > [hidden email]
>>     > http://mailman.open-bio.org/mailman/listinfo/bioperl-l
>>
>>     _______________________________________________
>>     Bioperl-l mailing list
>>     [hidden email]
>>     http://mailman.open-bio.org/mailman/listinfo/bioperl-l
>>

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

Mark A. Jensen
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" <[hidden email]>
> 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
>><[hidden email]> 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=[hidden email] on
>>> behalf of [hidden email]> 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
>>> <[hidden email]> 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
>>>     > [hidden email]
>>>     > http://mailman.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>>     _______________________________________________
>>>     Bioperl-l mailing list
>>>     [hidden email]
>>>     http://mailman.open-bio.org/mailman/listinfo/bioperl-l
>>>
>
> _______________________________________________
> Bioperl-l mailing list
> [hidden email]
> http://mailman.open-bio.org/mailman/listinfo/bioperl-l

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

Mark A. Jensen
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" <[hidden email]>
>> 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
>>><[hidden email]> 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=[hidden email] on
>>>> behalf of [hidden email]> 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
>>>> <[hidden email]> 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
>>>>     > [hidden email]
>>>>     > http://mailman.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>>     _______________________________________________
>>>>     Bioperl-l mailing list
>>>>     [hidden email]
>>>>     http://mailman.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> [hidden email]
>> http://mailman.open-bio.org/mailman/listinfo/bioperl-l
>
> _______________________________________________
> Bioperl-l mailing list
> [hidden email]
> http://mailman.open-bio.org/mailman/listinfo/bioperl-l

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

Carnë Draug-2
In reply to this post by Fields, Christopher J
On 11 January 2017 at 01:30, Fields, Christopher J
<[hidden email]> wrote:

> On 10 January 2017 at 23:05, Horacio Montenegro <[hidden email]> 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

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

Carnë Draug-2
In reply to this post by Mark A. Jensen
On 11 January 2017 at 04:45, Mark A. Jensen <[hidden email]> wrote:
> And here it is -- still runs! No BioPerl required, as it turns out.
>
> https://github.com/majensen/dnds
>
> MAJ

This is great thank you.  Since you are not packaging it, can I just
copy it into my project?  Or maybe adapt it to bioperl (any suggestion
where it should go?)  Also, can you please specify a license?

Thank you
Carnë

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

Mark A. Jensen

Sure, go for it. I might work it up into a module but no need to wait for me. Let's go with the Perl license.
Cheers MAJ

On Wed, Jan 11, 2017 at 9:45am, Carnë Draug <[hidden email]> wrote:

On 11 January 2017 at 04:45, Mark A. Jensen <[hidden email]> wrote:
> And here it is -- still runs! No BioPerl required, as it turns out.
>
> https://github.com/majensen/dnds
>
> MAJ

This is great thank you.  Since you are not packaging it, can I just
copy it into my project?  Or maybe adapt it to bioperl (any suggestion
where it should go?)  Also, can you please specify a license?

Thank you
Carnë


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

Roy Chaudhuri-3
In reply to this post by Mark A. Jensen
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" <[hidden email]>
>>> 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
>>>> <[hidden email]> 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=[hidden email] on
>>>>> behalf of [hidden email]> 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
>>>>> <[hidden email]> 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
>>>>>     > [hidden email]
>>>>>     > http://mailman.open-bio.org/mailman/listinfo/bioperl-l
>>>>>
>>>>>     _______________________________________________
>>>>>     Bioperl-l mailing list
>>>>>     [hidden email]
>>>>>     http://mailman.open-bio.org/mailman/listinfo/bioperl-l
>>>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> [hidden email]
>>> http://mailman.open-bio.org/mailman/listinfo/bioperl-l
>>
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Re: free software to estimate dS and dN in pairwise comparisons

Fields, Christopher J
In reply to this post by Carnë Draug-2
On 1/11/17, 8:44 AM, "Bioperl-l on behalf of Carnë Draug" <bioperl-l-bounces+cjfields=[hidden email] on behalf of [hidden email]> wrote:



>On 11 January 2017 at 04:45, Mark A. Jensen <[hidden email]> wrote:
>> And here it is -- still runs! No BioPerl required, as it turns out.
>>
>> https://github.com/majensen/dnds
>>
>> MAJ
>
>This is great thank you.  Since you are not packaging it, can I just
>copy it into my project?  Or maybe adapt it to bioperl (any suggestion
>where it should go?)  Also, can you please specify a license?
>
>Thank you
>Carnë

This might be something to ask Jason (cc’d).  Jason, any ideas where dN/dS functionality might fit best in bioperl?

chris
>

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

Fields, Christopher J
In reply to this post by Carnë Draug-2
On 1/11/17, 8:43 AM, "[hidden email] on behalf of Carnë Draug" <[hidden email] on behalf of [hidden email]> wrote:



>On 11 January 2017 at 01:30, Fields, Christopher J
><[hidden email]> wrote:
>> On 10 January 2017 at 23:05, Horacio Montenegro <[hidden email]> 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

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

Fields, Christopher J
In reply to this post by Fields, Christopher J
Thanks Jason!

I think the idea (which may have been trimmed out in the replies) was to potentially incorporate this into bioperl; I guess the question now is whether this is still necessary.

chris

From: Jason Stajich <[hidden email]>
Date: Wednesday, January 11, 2017 at 9:52 AM
To: Chris Fields <[hidden email]>
Cc: Carnë Draug <[hidden email]>, Mark Jensen <[hidden email]>, bioperl mailing list <[hidden email]>
Subject: Re: [Bioperl-l] free software to estimate dS and dN in pairwise comparisons

Hi - As standalone non-bioperl dependent it seems like it needs it own repo?

Currently we have Ka/Ks calculation in Bio::Align::DNAStatistics - not sure if this implementation is faster? 

FYI Carnë -  you might also see my fast C implementation pairwise dnds as well that is a hybrid of the yn00 code.
The main app for already aligned CDS is yn00_cds_prealigned also generates a table of the pairwise values I find this useful for generating fast pairwise e.g.

scripts for the step are in here:


On Wed, Jan 11, 2017 at 7:38 AM, Fields, Christopher J <[hidden email]> wrote:
On 1/11/17, 8:44 AM, "Bioperl-l on behalf of Carnë Draug" <bioperl-l-bounces+cjfields=[hidden email] on behalf of [hidden email]> wrote:



>On 11 January 2017 at 04:45, Mark A. Jensen <[hidden email]> wrote:
>> And here it is -- still runs! No BioPerl required, as it turns out.
>>
>> https://github.com/majensen/dnds
>>
>> MAJ
>
>This is great thank you.  Since you are not packaging it, can I just
>copy it into my project?  Or maybe adapt it to bioperl (any suggestion
>where it should go?)  Also, can you please specify a license?
>
>Thank you
>Carnë

This might be something to ask Jason (cc’d).  Jason, any ideas where dN/dS functionality might fit best in bioperl?

chris
>



--
Jason E Stajich, PhD 
Associate Professor
University of California, Riverside
http://lab.stajich.org http://fungalgenomes.org http://fungidb.org http://zygolife.org
@stajichlab @hyphaltip @fungalgenomes @fungidb @zygolife
office: 951.827.2363



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

Darren Obbard
In reply to this post by Roy Chaudhuri-3

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

Get Outlook for Android


From: Bioperl-l <bioperl-l-bounces+darren.obbard=[hidden email]> on behalf of Roy Chaudhuri <[hidden email]>
Sent: Wednesday, January 11, 2017 3:13:01 PM
To: Mark A. Jensen; [hidden email]; carandraug+[hidden email]
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" <[hidden email]>
>>> 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
>>>> <[hidden email]> 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=[hidden email] on
>>>>> behalf of [hidden email]> 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+[hidden email]> 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
>>>>>     > [hidden email]
>>>>>     > http://mailman.open-bio.org/mailman/listinfo/bioperl-l
>>>>>
>>>>>     _______________________________________________
>>>>>     Bioperl-l mailing list
>>>>>     [hidden email]
>>>>>     http://mailman.open-bio.org/mailman/listinfo/bioperl-l
>>>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> [hidden email]
>>> http://mailman.open-bio.org/mailman/listinfo/bioperl-l
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> [hidden email]
>> http://mailman.open-bio.org/mailman/listinfo/bioperl-l
>
> _______________________________________________
> Bioperl-l mailing list
> [hidden email]
> http://mailman.open-bio.org/mailman/listinfo/bioperl-l
_______________________________________________
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Re: free software to estimate dS and dN in pairwise comparisons

Mark A. Jensen
In reply to this post by Fields, Christopher J

Roy's comment was a good one, either way there may be an opportunity to update the algorithms with ones that incorporate tvts rate variation and such.
Mark

On Wed, Jan 11, 2017 at 1:25pm, Fields, Christopher J <[hidden email]> wrote:

Thanks Jason!

I think the idea (which may have been trimmed out in the replies) was to potentially incorporate this into bioperl; I guess the question now is whether this is still necessary.

chris

From: Jason Stajich <[hidden email]>
Date: Wednesday, January 11, 2017 at 9:52 AM
To: Chris Fields <[hidden email]>
Cc: Carnë Draug <[hidden email]>, Mark Jensen <[hidden email]>, bioperl mailing list <[hidden email]>
Subject: Re: [Bioperl-l] free software to estimate dS and dN in pairwise comparisons

Hi - As standalone non-bioperl dependent it seems like it needs it own repo?

Currently we have Ka/Ks calculation in Bio::Align::DNAStatistics - not sure if this implementation is faster? 

FYI Carnë -  you might also see my fast C implementation pairwise dnds as well that is a hybrid of the yn00 code.
The main app for already aligned CDS is yn00_cds_prealigned also generates a table of the pairwise values I find this useful for generating fast pairwise e.g.

scripts for the step are in here:


On Wed, Jan 11, 2017 at 7:38 AM, Fields, Christopher J <[hidden email]> wrote:
On 1/11/17, 8:44 AM, "Bioperl-l on behalf of Carnë Draug" <bioperl-l-bounces+cjfields=[hidden email] on behalf of [hidden email]> wrote:



>On 11 January 2017 at 04:45, Mark A. Jensen <[hidden email]> wrote:
>> And here it is -- still runs! No BioPerl required, as it turns out.
>>
>> https://github.com/majensen/dnds
>>
>> MAJ
>
>This is great thank you.  Since you are not packaging it, can I just
>copy it into my project?  Or maybe adapt it to bioperl (any suggestion
>where it should go?)  Also, can you please specify a license?
>
>Thank you
>Carnë

This might be something to ask Jason (cc’d).  Jason, any ideas where dN/dS functionality might fit best in bioperl?

chris
>



--
Jason E Stajich, PhD 
Associate Professor
University of California, Riverside
http://lab.stajich.org http://fungalgenomes.org http://fungidb.org http://zygolife.org
@stajichlab @hyphaltip @fungalgenomes @fungidb @zygolife
office: 951.827.2363



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

Carnë Draug-2
In reply to this post by Roy Chaudhuri-3
On 11 January 2017 at 15:13, Roy Chaudhuri <[hidden email]> wrote:
> [...] The more sophisticated models implemented in
> PAML (codeml and yn00) are probably a better bet if you can sort out the
> licence issue.
>

Since it seems they do want to change the licence to GPL, I sent an
email to Professor Ziheng Yang offering my help to solve this issue
for them.  If someone happens to know him personally, would be nice
if you could nudge him and suggest him to accept my help (under my
real name David).

Carnë

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

Roy Chaudhuri-3
Hi Carnë,

Not sure if you have seen this thread on the PAML Google group?:
https://groups.google.com/forum/#!topic/pamlsoftware/NFu_lNBoAEA

Perhaps you could offer to help there? Professor Yang specifically
states on the website that he will not answer queries about PAML by e-mail.

Cheers,
Roy.

On 12/01/2017 14:27, Carnë Draug wrote:

> On 11 January 2017 at 15:13, Roy Chaudhuri <[hidden email]> wrote:
>> [...] The more sophisticated models implemented in
>> PAML (codeml and yn00) are probably a better bet if you can sort out the
>> licence issue.
>>
>
> Since it seems they do want to change the licence to GPL, I sent an
> email to Professor Ziheng Yang offering my help to solve this issue
> for them.  If someone happens to know him personally, would be nice
> if you could nudge him and suggest him to accept my help (under my
> real name David).
>
> Carnë
>
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Re: free software to estimate dS and dN in pairwise comparisons

Carnë Draug-2
On 12 January 2017 at 14:54, Roy Chaudhuri <[hidden email]> wrote:
> Hi Carnë,
>
> Not sure if you have seen this thread on the PAML Google group?:
> https://groups.google.com/forum/#!topic/pamlsoftware/NFu_lNBoAEA
>
> Perhaps you could offer to help there? Professor Yang specifically states on
> the website that he will not answer queries about PAML by e-mail.
>

I did see that thread.  I also saw that he hasn't replied on that
group for a while.

I did not read that on his website.  My interpretation was that it's
ok to email him about PAML such as reporting bugs, but not questions
about how to use the programs.  Anyway, I will add my voice to
that thread on the google group too.

Carnë

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

Fields, Christopher J
In reply to this post by Roy Chaudhuri-3
Hi Roy,

Yup, this is the thread that touched off a lot of this current discussion.  The concern I have is that the intent seems to be there to GPL it all, but there has been a fair lack of momentum (the discussion spans about a year).

chris

On 1/12/17, 8:54 AM, "Bioperl-l on behalf of Roy Chaudhuri" <bioperl-l-bounces+cjfields=[hidden email] on behalf of [hidden email]> wrote:

    Hi Carnë,
   
    Not sure if you have seen this thread on the PAML Google group?:
    https://groups.google.com/forum/#!topic/pamlsoftware/NFu_lNBoAEA
   
    Perhaps you could offer to help there? Professor Yang specifically
    states on the website that he will not answer queries about PAML by e-mail.
   
    Cheers,
    Roy.
   
    On 12/01/2017 14:27, Carnë Draug wrote:
    > On 11 January 2017 at 15:13, Roy Chaudhuri <[hidden email]> wrote:
    >> [...] The more sophisticated models implemented in
    >> PAML (codeml and yn00) are probably a better bet if you can sort out the
    >> licence issue.
    >>
    >
    > Since it seems they do want to change the licence to GPL, I sent an
    > email to Professor Ziheng Yang offering my help to solve this issue
    > for them.  If someone happens to know him personally, would be nice
    > if you could nudge him and suggest him to accept my help (under my
    > real name David).
    >
    > Carnë
    >
    _______________________________________________
    Bioperl-l mailing list
    [hidden email]
    http://mailman.open-bio.org/mailman/listinfo/bioperl-l


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