Dear Karla, what is exactly the problem and what did you try? There is a (generic) function cbind for "phyDat" objects in phangorn, which should exactly do this task.
library(phangorn) data(Laurasiatherian) (x1 <- subset(Laurasiatherian, 1:20)) (x2 <- subset(Laurasiatherian, 11:30)) cbind(x1, x2) As Emmanuel mentioned the package apex simplifies the whole process. library(apex) files <- dir(system.file(package="apex"),patter="patr", full=TRUE) files dat <- read.multiphyDat(files, format="FASTA") concatenate(dat) Regards, Klaus On Fri, Nov 18, 2016 at 6:21 AM, Karla Shikev <karlashi...@gmail.com> wrote: > Dear all, > > I got alignments for many loci as nexus files and I've been trying to > concatenate them into a single alignment. However, some taxa are missing > from some of the loci, so that simple alternatives such as cbinding > individual files in phangorn doesn't work. > > Any help with this will be greatly appreciated. > > Karla > > [[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-ph...@r-project.org/ > -- Klaus Schliep Postdoctoral Fellow Revell Lab, University of Massachusetts Boston http://www.phangorn.org/ [[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/