Dear Karla,

First, I suggest you manage your alignment files in FASTA rather than in NEXUS: this is much more efficient in practice.


You may read an alignment in a NEXUS file using read.nexus.data() in ape, then convert it in "DNAbin" class with as.DNAbin(). The cbind() funtion in ape allows you some flexibility in managing several alignments. See the help page ?cbind.DNAbin. If your data are in FASTA files, then you'll read directly "DNAbin" objects.

An alternative is to use the package alex on CRAN.

Cheers,

Emmanuel

Le 18/11/2016 à 12:21, Karla Shikev a écrit :
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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