Dear Liam, I can easily read in mutiple alignments and concatenate them using apex. But the problem is how to save the concatenated file in a FASTA format so that I can use it in a different phylogenetic tool like Gubbins. Any suggestions?
Regards, Rav > On 12 Sep 2016, at 13:42, Liam J. Revell <liam.rev...@umb.edu> wrote: > > Hi Ravneet (& Joseph). > > I'm not sure if this is what you had in mind, but you could investigate the > apex package (https://cran.r-project.org/package=apex). It seems to have > functionality to read in multiple alignments using custom object classes, and > then concatenate these alignments into a single matrix. > > All the best, Liam > > Liam J. Revell, Associate Professor of Biology > University of Massachusetts Boston > web: http://faculty.umb.edu/liam.revell/ > email: liam.rev...@umb.edu > blog: http://blog.phytools.org > > On 9/12/2016 6:20 AM, Joseph W. Brown wrote: >> 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/ >> _______________________________________________ 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/