Re: [Ncl-devel] [Nexml-discuss] NeXML website, and future plans

[Mark H. <mth...@ku...>]

Hi all,
	RAxML does not use NCL, I'm afraid. It might if NCL had been written in C rather than C++, but that ship has sailed.

	GARLI does.  As does the R package (http://cran.r-project.org/web/packages/phylobase/index.html	). 

	DendroPy used to have a working parse-with-NCL-option that read files much faster.  But that is broken (and may never come back).

all the best,
mark


On Jul 26, 2012, at 7:56 PM, Hilmar Lapp wrote:

> What I'm peripherally aware of is RAxML, RevBayes (the successor of MrBayes), Phycas. But that's probably incomplete, so I'm cross-posting this to the NCL list.
> 
> -hilmar
> 
> Sent with a tap.
> 
> On Jul 26, 2012, at 8:48 AM, Rutger Vos <rut...@gm...> wrote:
> 
>> I am not 100% sure that the GPL automatically applies to code that's
>> generated with the xsd tool (but it probably is). In any case, I
>> suppose NCL would be the way forward. Please remind me, which current
>> programs would then, theoretically, be able to consume/produce NeXML
>> provided they update their NCL?
>> 
>> On Thu, Jul 26, 2012 at 2:36 PM, Hilmar Lapp <hl...@ne...> wrote:
>>> I agree with the motivation behind further developing the C++ code, and would add that many phylogenetic analysis programs are written in C or C++ and hence this would be what they need to support NeXML more easily. However, I also think that the current C++ code is a dead end, at least if I understand correctly, for the licensing alone (GPL rather than LGPL), because it prevents uptake by commercial or otherwise closed source tools. I think further developing the NCL code, which was recently re-licensed as BSD, is the better way forward.
>>> 
>>> -hilmar
>>> 
>>> Sent with a tap.
>>> 
>>> On Jul 26, 2012, at 8:24 AM, Rutger Vos <rut...@gm...> wrote:
>>> 
>>>> Hi all,
>>>> 
>>>> following Anurag's excellent work in porting the NeXML source tree to
>>>> github (from sourceforge) and re-organizing it into smaller
>>>> sub-projects I have now finally got around to point the NeXML website
>>>> to this new source (including the static HTML for the site itself,
>>>> which I tweaked here and there).
>>>> 
>>>> In going through these changes it became clear there's a couple more
>>>> things that would perhaps be good to do:
>>>> 
>>>> * we have always used the link http://nexml.org/manual as a proxy for
>>>> our wiki page on sourceforge. Since that's the last thing that ties us
>>>> to them, we could safely move that wiki somewhere else (e.g. also to
>>>> github) and update the redirect. Not urgent, but would be nice.
>>>> 
>>>> * there is still that cpp attempt as part of the source tree. You know
>>>> what would be really great? If that was developed a little bit further
>>>> so that its xml bean-like facilities were exposed through swig so that
>>>> the scripting languages could, alternatively, build on this for their
>>>> nexml i/o. I suspect that might give spectacular performance
>>>> improvements.
>>>> 
>>>> * (And then there's of course all the bugfixes and enhancements we
>>>> know about in the back of our heads).
>>>> 
>>>> Best wishes,
>>>> 
>>>> Rutger
>>>> 
>>>> --
>>>> Dr. Rutger A. Vos
>>>> Bioinformaticist
>>>> NCB Naturalis
>>>> Visiting address: Office A109, Einsteinweg 2, 2333 CC, Leiden, the Netherlands
>>>> Mailing address: Postbus 9517, 2300 RA, Leiden, the Netherlands
>>>> http://rutgervos.blogspot.com
>>>> 
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>>>> _______________________________________________
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>>>> https://lists.sourceforge.net/lists/listinfo/nexml-discuss
>> 
>> 
>> 
>> -- 
>> Dr. Rutger A. Vos
>> Bioinformaticist
>> NCB Naturalis
>> Visiting address: Office A109, Einsteinweg 2, 2333 CC, Leiden, the Netherlands
>> Mailing address: Postbus 9517, 2300 RA, Leiden, the Netherlands
>> http://rutgervos.blogspot.com
> 
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and 
> threat landscape has changed and how IT managers can respond. Discussions 
> will include endpoint security, mobile security and the latest in malware 
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> _______________________________________________
> Nexml-discuss mailing list
> Nex...@li...
> https://lists.sourceforge.net/lists/listinfo/nexml-discuss
> 

Mark Holder

mth...@ku...
http://phylo.bio.ku.edu/mark-holder

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