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; > > > [[alternative HTML version deleted]] > > _______________________________________________ > R-sig-phylo mailing list > R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > [[alternative HTML version deleted]]
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