Re: [Treebase-devel] Fwd: reading nexus file from treebase?

[Rutger V. <rut...@gm...>]

The additions are necessary because they specify the relationships
between multiple taxa blocks, characters blocks and tree blocks.
They're not part of the core standard per se, though - I think they
were introduced by mesquite. Maybe ape should switch to nexml instead?

On Fri, Mar 25, 2011 at 3:25 PM, Hilmar Lapp <hl...@ne...> wrote:
> FYI - the NEXUS download from TreeBASE seems to contain stuff that
> aren't understood by some (rather widely used) NEXUS parsers. I don't
> know whether these are part of the core standard or were added later
> as a "flavor", but it may be beneficial to get rid of them if they
> aren't crucial.
>
> Thoughts?
>
> (BTW the readNexus() function in the phylobase package - which can
> read this - is based on NCL. So presumably that means that in NCL's
> implementation of the standard this is correct. It's just that not
> everyone uses NCL :-)
>
>        -hilmar
>
> Begin forwarded message:
>
>> From: Emmanuel Paradis <Emm...@ir...>
>> Date: March 25, 2011 12:00:36 AM EDT
>> To: François Michonneau <fra...@gm...>
>> Cc: R-s...@r-...
>> Subject: Re: [R-sig-phylo] reading nexus file from treebase?
>>
>> Scott,
>>
>> readNexus (phylobase) can read your tree but not read.nexus (ape).
>> The problem is the two lines inserted within the TREES block:
>>
>> BEGIN TREES;
>> TITLE Tb10793;         <<<<<<
>> LINK TAXA = M4787;     <<<<<<
>> TREE Fig._3c = [&R]
>>
>> If you delete them, it's OK. FigTree also cannot read this file.
>>
>> Cheers,
>>
>> Emmanuel
>>
>> François Michonneau wrote on 25/03/2011 00:35:
>>> Hi Scott,
>>>  Which version of phylobase are you using and which architecture? I
>>> can
>>> read the file on my machine.
>>>  Cheers,
>>>  -- François
>>> On Thu, Mar 24, 2011 at 12:39, Scott Chamberlain <myr...@gm...
>>> >wrote:
>>>> Hello,
>>>>
>>>> I can't get read.nexus (ape) or readNexus (phylobase) to read
>>>> nexus files
>>>> downloaded from treebase with URLs parsed from xml files. I can't
>>>> manually
>>>> edit each file as I want to read a lot of these files. Is there an
>>>> easy fix?
>>>> One of the files is copied below.
>>>>
>>>> Thanks!
>>>> Scott Chamberlain
>>>> Rice University, EEB Dept.
>>>>
>>>>
>>>>
>>>>
>>>> #NEXUS
>>>>
>>>> [!This data set was downloaded from TreeBASE, a relational
>>>> database of
>>>> phylogenetic knowledge. TreeBASE has been supported by the NSF,
>>>> Harvard
>>>> University, Yale University, SDSC and UC Davis. Please do not
>>>> remove this
>>>> acknowledgment from the Nexus file.
>>>>
>>>>
>>>> Downloaded on March 24, 2011; 16:32 GMT
>>>>
>>>> TreeBASE (cc) 1994-2008
>>>>
>>>> Study reference:
>>>> Brown R., & Yang Z. 2010. Bayesian Dating of Shallow Phylogenies
>>>> with a
>>>> Relaxed Clock.
>>>> Systematic Biology, 59(2): 119-131.
>>>>
>>>> TreeBASE Study URI:
>>>> http://purl.org/phylo/treebase/phylows/study/TB2:S10165]
>>>>
>>>> BEGIN TAXA;
>>>> TITLE M4787;
>>>> DIMENSIONS NTAX=16;
>>>> TAXLABELS
>>>> Chalcides_coeruleopunctatus_E2806.20
>>>> Chalcides_coeruleopunctatus_E2806.22
>>>> Chalcides_manueli_E2506.1
>>>> Chalcides_mionecton_mionecton_E2506.10
>>>> Chalcides_mionecton_mionecton_E2506.12
>>>> Chalcides_mionecton_trifasciatus_E2506.18
>>>> Chalcides_polylepis_E14124.1
>>>> Chalcides_polylepis_E14124.2
>>>> Chalcides_polylepis_E2506.21
>>>> Chalcides_sexlineatus_bistriatus_E2806.6
>>>> Chalcides_sexlineatus_sexlineatus_E2806.8
>>>> Chalcides_simonyi_E3007.2
>>>> Chalcides_sphenopsiformis_E8121.26
>>>> Chalcides_sphenopsiformis_E8121.27
>>>> Chalcides_viridanus_E2806.10
>>>> Chalcides_viridanus_E2806.14
>>>> ;
>>>> END;
>>>>
>>>> BEGIN TREES;
>>>> TITLE Tb10793;
>>>> LINK TAXA = M4787;
>>>> TREE Fig._3c = [&R]
>>>> ((Chalcides_sphenopsiformis_E8121.26,Chalcides_sphenopsiformis_E8121.27),(((Chalcides_viridanus_E2806.10,Chalcides_viridanus_E2806.14),((Chalcides_sexlineatus_bistriatus_E2806.6,Chalcides_sexlineatus_sexlineatus_E2806.8),(Chalcides_coeruleopunctatus_E2806.22,Chalcides_coeruleopunctatus_E2806.20))),(Chalcides_simonyi_E3007.2,((Chalcides_mionecton_trifasciatus_E2506.18,(Chalcides_mionecton_mionecton_E2506.12,Chalcides_mionecton_mionecton_E2506.10)),(Chalcides_manueli_E2506.1,(Chalcides_polylepis_E14124.1,(Chalcides_polylepis_E14124.2,Chalcides_polylepis_E2506.21)))))));
>>>> [! TreeBASE tree URI:
>>>> http://purl.org/phylo/treebase/phylows/tree/TB2:Tr6136]
>>>>
>>>>
>>>> END;
>>>>
>>>>
>>>>       [[alternative HTML version deleted]]
>>>>
>>>> _______________________________________________
>>>> R-sig-phylo mailing list
>>>> R-s...@r-...
>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
>>>>
>>>      [[alternative HTML version deleted]]
>>> ------------------------------------------------------------------------
>>> _______________________________________________
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>>> R-s...@r-...
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>>
>> --
>> Emmanuel Paradis
>> IRD, Jakarta, Indonesia
>> http://ape.mpl.ird.fr/
>>
>> _______________________________________________
>> R-sig-phylo mailing list
>> R-s...@r-...
>> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
>
> --
> ===========================================================
> : Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
> ===========================================================
>
>
>
>
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-- 
Dr. Rutger A. Vos
School of Biological Sciences
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