Deal Liam and Emmanuel, Thank you very much. I tried to open the file this way:
obj<-scan(file="TimetreeOfLife2015.tre",n=1,skip=2,what="character") tree<-read.tree(text=obj) It worked but then there were other errors. Something is wrong with te edge lengths. I can't even plot the tree. I tried with read.tree but the errors persisted. When I used another tree, everything worked fine, so I guess I'll just use that one. Once again, thank you. Sérgio. 2016-05-23 20:55 GMT+01:00 Emmanuel Paradis <emmanuel.para...@ird.fr>: > Liam is probably right: there seems to be something missing in the NEXUS > file. > > The Newick file from the same site can also be read with read.tree. > > Emmanuel > > > Le 23/05/2016 18:21, Liam J. Revell a écrit : > >> It looks like the NEXUS file might be badly conformed. >> >> You could try: >> >> obj<-scan(file="TimetreeOfLife2015.tre",n=1,skip=2,what="character") >> tree<-read.tree(text=obj) >> >> That seemed to work for me. >> >> - Liam >> >> Liam J. Revell, Associate Professor of Biology >> University of Massachusetts Boston >> web: http://faculty.umb.edu/liam.revell/ >> email: liam.rev...@umb.edu >> blog: http://blog.phytools.org >> >> On 5/23/2016 12:11 PM, Sergio Ferreira Cardoso wrote: >> >>> Dear all, >>> >>> I am trying to open a .tre file with ape. I downloaded the tree from >>> http://www.timetree.org/book#treefiles. It's a .tre (not .nex) file, but >>> it's essentially a nexus. I tried to open it: >>> >>> tr <- read.nexus(file="TimetreeOfLife2015.tre") >>>> >>> Error in trees[[i]] : subscript out of bounds >>> >>> I tried to change the file name to .nex, but it wouldn't work. I saw some >>> previous threads but I couldn't solve the problem. >>> Does anyone know how can I solve this? >>> >>> Thanks in advance, >>> Sérgio. >>> >>> ps: I have the lastest 3.4 version of ape. >>> >>> >> _______________________________________________ >> R-sig-phylo mailing list - R-sig-phylo@r-project.org >> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo >> Searchable archive at >> http://www.mail-archive.com/r-sig-phylo@r-project.org/ >> > -- Com os melhores cumprimentos, Sérgio Ferreira Cardoso. -------------------- Best regards, Sérgio Ferreira Cardoso MSc. Paleontology Museu da Lourinhã, GEAL. Lisboa, Portugal [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
