We have a non-R tool that can do the job: https://github.com/FePhyFoFum/phyx
After compiling, command is (assuming fasta (extension ".fas") input, but any input format will work): ./pxcat -s *.fas -o my_concatenated_alignment.fas -p partition_info.txt (The partition_info.txt logs how sites/partitions are ordered). If you need these in out another format (say, phylip), do: ./pxcat -s *.fas -o my_concatenated_alignment.fas | ./pxs2phy -o my_concatenated_alignment.phy HTH. JWB ________________________________________ Joseph W. Brown Post-doctoral Researcher, Smith Laboratory University of Michigan Department of Ecology & Evolutionary Biology Room 2071, Kraus Natural Sciences Building Ann Arbor MI 48109-1079 josep...@umich.edu > On 12 Sep, 2016, at 06:41, Bhuller, Ravneet > <ravneet.bhulle...@imperial.ac.uk> wrote: > > Dear Members, > > Any suggestions on how to concatenate the aligned gene sequences in fasta > format so as to get whole genome alignments? > I need whole genome alignments as an input to a phylogenetic tool. > > Many thanks, > > Rav > > _______________________________________________ > 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/ [[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/