Thank you all for the suggestions. Creating a vector with the species works very well. :)
2015-07-15 17:59 GMT+01:00 Sergio Ferreira Cardoso < sff.card...@campus.fct.unl.pt>: > Thank you very much Nicholas. Works perfectly!!! :) > > 2015-07-15 17:22 GMT+01:00 Nicholas Crouch <ncro...@uic.edu>: > >> Sergio, >> >> You can use ape's 'drop.tip', e.g. >> >> # Phylogeny is object 'phy' >> # Species interested in in object 'my.species' >> >> v <- phy$tip.label %in% my.species >> drop <- phy$tip.label[v==FALSE] >> >> trimmed.phy <- drop.tip(phy, drop) >> >> On Wed, Jul 15, 2015 at 11:15 AM, Sergio Ferreira Cardoso < >> sff.card...@campus.fct.unl.pt> wrote: >> >>> Dear members, >>> >>> I have a tree with almost 10.000 species and I want to prune it. The >>> problem is I only want a tree with 59 of those species. Is there any >>> possible way to make this in R? Is there any code to prune all taxa >>> except >>> the ones on my data? >>> >>> 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 >>> ᐧ >>> >>> [[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/ >> >> >> >> >> -- >> Nicholas Crouch >> Graduate Student, Igić Lab >> Department of Biological Sciences >> University of Illinois at Chicago >> > > > > -- > 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 - 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/
