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 <myrmecocys...@gmail.com>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;
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--
Emmanuel Paradis
IRD, Jakarta, Indonesia
http://ape.mpl.ird.fr/
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