Ok. I just solved the problem with adding "file=" when using wirte.nexus.
2015-07-15 14:56 GMT+01:00 Sergio Ferreira Cardoso < [email protected]>: > Thank you François, > > I was trying to use consensus() from ape, but when I try to write a nexus > file I get an error message: > > > trees<-read.nexus("1000_trees.nex") > > consensus(trees,p=1,check.labels=TRUE) > > write.nexus(my_tree,"consensus_birds.nex") > #NEXUS > [R-package APE, Wed Jul 15 14:49:14 2015] > > BEGIN TAXA; > DIMENSIONS NTAX = 59; > TAXLABELS > Rhynchotus_rufescens > Apteryx_haastii > Dromaius_novaehollandiae > (...) > ; > END; > BEGIN TREES; > TRANSLATE > Error in y$tip.label : $ operator is invalid for atomic vectors > > My only problem now is to create the file. I'm going to try the softwares > you pointed. > > Best regards, > Sérgio. > ᐧ > > 2015-07-15 14:49 GMT+01:00 François Michonneau < > [email protected]>: > >> Hi Sergio, >> >> Not in R, but you can use PAUP, MrBayes or Dendropy (my recommendation). >> >> Cheers, >> -- François >> >> 2015-07-15 7:53 GMT-04:00 Sergio Ferreira Cardoso >> <[email protected]>: >> > Dear all, >> > >> > I have a nexus file with 1000 trees on it with divergence times as >> branch >> > lengths. Does anyone know about a package that can make a consensus tree >> > out of my 1000 trees? >> > Thanks in advance. >> > >> > Best regards, >> > Sérgio. >> > >> > -- >> > Com os melhores cumprimentos, >> > Sérgio Ferreira Cardoso. >> > >> > -------------------- >> > >> > Best regards, >> > Sérgio Ferreira Cardoso >> > >> > >> > >> > >> > MSc. Paleontology candidate >> > Departamento de Ciências da Terra - FCT /Universidade Nova de Lisboa >> > Geociências - Universidade de Évora >> > >> > Lisboa, Portugal >> > >> > [[alternative HTML version deleted]] >> > >> > _______________________________________________ >> > R-sig-phylo mailing list - [email protected] >> > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo >> > Searchable archive at >> http://www.mail-archive.com/[email protected]/ >> > > > > -- > Com os melhores cumprimentos, > Sérgio Ferreira Cardoso. > > -------------------- > > Best regards, > Sérgio Ferreira Cardoso > > > > > MSc. Paleontology candidate > Departamento de Ciências da Terra - FCT /Universidade Nova de Lisboa > Geociências - Universidade de Évora > > Lisboa, Portugal > -- Com os melhores cumprimentos, Sérgio Ferreira Cardoso. -------------------- Best regards, Sérgio Ferreira Cardoso MSc. Paleontology candidate Departamento de Ciências da Terra - FCT /Universidade Nova de Lisboa Geociências - Universidade de Évora Lisboa, Portugal [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/[email protected]/
