Try FasConcat or Seaview. Cheers, Martin
Am 12.09.2016 um 14:51 schrieb Bhuller, Ravneet: > 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/ Dr. Martin Dohrmann Ludwig-Maximilians-University Munich Dept. of Earth & Environmental Sciences Palaeontology & Geobiology Molecular Geo- & Palaeobiology Lab Richard-Wagner-Str. 10 80333 Munich, Germany Phone: +49-(0)89-2180-6593 [[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/
