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
>
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>
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-- 
Klaus Schliep
Postdoctoral Fellow
Revell Lab, University of Massachusetts Boston
http://www.phangorn.org/

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