Hi George,

Yes, there’s RNeXML. Glad you found it on your own, I’ve been occupied with a 
workshop. Note that there’s a publication on RNeXML too, as you’ve probably 
seen in the README on Github.

Personally, I think it’d be great to have phyloXML support as well in the R 
ecosystem. However, I’d argue that while the two exchange standards have 
different strengths (and NeXML is not without its own “warts”), for the benefit 
of the user (typically a biology scientist-developer) it would seem to be 
vastly preferable if these standards converge at the R API level. So maybe 
phyloXML support could be added on to RNeXML, or if its own package, at least 
the R API signature could be kept in synchrony?

  -hilmar

> On Dec 14, 2017, at 3:41 PM, George Vega Yon <g.vega...@gmail.com> wrote:
> 
> Hey,
> 
> Just for the record. I just found two alternatives that seem to be in
> active development, nexml (www.nexml.org) and RecPhyloXML (
> https://urldefense.proofpoint.com/v2/url?u=http-3A__phylariane.univ-2Dlyon1.fr_recphyloxml_&d=DwIGaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=eGWUXrFTNKFQ_7iv2ZZTsTpqF6jBUoOs67dzNTy0W_Y&m=izAgipXSIMSu-6nAHEQLMuJAo1iol6odf6w4kB7xE4I&s=5CdlhUFqJAcw9qGduCmWrGXPwhWFUhZMcOss0uysZ34&e=
>  ). nexml is supported by
> rOpenSci 
> (https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_ropensci_RNeXML&d=DwIGaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=eGWUXrFTNKFQ_7iv2ZZTsTpqF6jBUoOs67dzNTy0W_Y&m=izAgipXSIMSu-6nAHEQLMuJAo1iol6odf6w4kB7xE4I&s=E2KdcumsPG-JacTs6EbDx9PNds1g15J0lpbZVFgcnLs&e=
>  ), and both have C++/phython
> APIs that can be useful for R package development.
> 
> I still may try to get something done on PhyloXML since jsPhyloSVG, which
> I'm working on now 
> https://urldefense.proofpoint.com/v2/url?u=https-3A__uscbiostats.github.io_jsPhyloSVG_&d=DwIGaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=eGWUXrFTNKFQ_7iv2ZZTsTpqF6jBUoOs67dzNTy0W_Y&m=izAgipXSIMSu-6nAHEQLMuJAo1iol6odf6w4kB7xE4I&s=qCOKU5kc59kVmuDmY13hm0h_F0-5VtB-8YC5dp3Nc_I&e=
>  , only supports
> annotations in PhyloXML (it does support nexml trees, but I don't think it
> support annotations).
> 
> Best,
> 
> George G. Vega Yon
> +1 (626) 381 8171 <(626)%20381-8171>
> https://urldefense.proofpoint.com/v2/url?u=http-3A__ggvy.cl&d=DwIGaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=eGWUXrFTNKFQ_7iv2ZZTsTpqF6jBUoOs67dzNTy0W_Y&m=izAgipXSIMSu-6nAHEQLMuJAo1iol6odf6w4kB7xE4I&s=GH2YmJwH3j59FpvbwH0pJu3-LJHbo4BTkG73yMtknFw&e=
>  
> 
> On Wed, Dec 13, 2017 at 11:35 AM, George Vega Yon <g.vega...@gmail.com>
> wrote:
> 
>> That's a good suggestion. I'll reach out  the rOpenSci people/
>> 
>> Still, I'm starting a repo here: 
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_USCBiostats_rphyloxml&d=DwIGaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=eGWUXrFTNKFQ_7iv2ZZTsTpqF6jBUoOs67dzNTy0W_Y&m=izAgipXSIMSu-6nAHEQLMuJAo1iol6odf6w4kB7xE4I&s=ZI73M-7QB4r4wS6k6y4ZjA4nQsF0MMbpxv-IATJ8VuI&e=
>>  
>> will start dropping stuff there.
>> 
>> Best,
>> 
>> George G. Vega Yon
>> +1 (626) 381 8171 <(626)%20381-8171>
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__ggvy.cl&d=DwIGaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=eGWUXrFTNKFQ_7iv2ZZTsTpqF6jBUoOs67dzNTy0W_Y&m=izAgipXSIMSu-6nAHEQLMuJAo1iol6odf6w4kB7xE4I&s=GH2YmJwH3j59FpvbwH0pJu3-LJHbo4BTkG73yMtknFw&e=
>>  
>> 
>> On Tue, Dec 12, 2017 at 4:31 PM, Daniel Fulop <dfulop....@gmail.com>
>> wrote:
>> 
>>> Sounds like a good idea. Not sure if you’re reinventing the wheel or not.
>>> Sounds like something ROpenSci might support; see:
>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_ropensci_onboarding&d=DwIGaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=eGWUXrFTNKFQ_7iv2ZZTsTpqF6jBUoOs67dzNTy0W_Y&m=izAgipXSIMSu-6nAHEQLMuJAo1iol6odf6w4kB7xE4I&s=Xaz1EafJxnCZMDhwVbMq39-DSlGClnlW10wmp8307EA&e=
>>>  
>>> 
>>> 
>>> 
>>> 
>>> From: George Vega Yon <g.vega...@gmail.com> <g.vega...@gmail.com>
>>> Reply: George Vega Yon <g.vega...@gmail.com> <g.vega...@gmail.com>
>>> Date: December 12, 2017 at 4:13:59 PM
>>> To: Group R-sig-phylo <r-sig-phylo@r-project.org>
>>> <r-sig-phylo@r-project.org>
>>> Subject:  [R-sig-phylo] Will phyloXML in R be useful?
>>> 
>>> Hey,
>>> 
>>> Right now, I'm working on a wrapper for jsPhyloSVG (a javascript library
>>> for visualizing phylogenetic trees on the web browser) in R, and just got
>>> to learn about the phyloXML format. Googling around and checking out this
>>> email list archives it seems that there's no support for this format in
>>> R.
>>> 
>>> My question is: how useful do you think having this in R will be? I'm
>>> willing to write an R package to read/write trees in this format (done
>>> before with GEXF, which is for networks in general). But I just want to
>>> make sure that (1) this will be useful for the community, and (2) I'm not
>>> reinventing the wheel (is anybody working on this now?). What are your
>>> thoughts?
>>> 
>>> Best,
>>> 
>>> George G. Vega Yon
>>> +1 (626) 381 8171 <(626)%20381-8171>
>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__ggvy.cl&d=DwIGaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=eGWUXrFTNKFQ_7iv2ZZTsTpqF6jBUoOs67dzNTy0W_Y&m=izAgipXSIMSu-6nAHEQLMuJAo1iol6odf6w4kB7xE4I&s=GH2YmJwH3j59FpvbwH0pJu3-LJHbo4BTkG73yMtknFw&e=
>>>  
>>> 
>>> [[alternative HTML version deleted]]
>>> 
>>> _______________________________________________
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>>>  
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>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_r-2D&d=DwIGaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=eGWUXrFTNKFQ_7iv2ZZTsTpqF6jBUoOs67dzNTy0W_Y&m=izAgipXSIMSu-6nAHEQLMuJAo1iol6odf6w4kB7xE4I&s=ysaFlE8Zm70teQET_RVPd9xB5EvNFPojxC-Pt7Ekpuk&e=
>>>  
>>> sig-ph...@r-project.org/
>>> 
>>> 
>> 
> 
>       [[alternative HTML version deleted]]
> 
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-- 
Hilmar Lapp -:- genome.duke.edu -:- lappland.io

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