There is a 'write.arlequin' function in the strataG package that will create an arlequin input file from a strataG gtypes object. You can create a gtypes object with sequence data read in from a FASTA file and stratifications described in a data.frame (see 'df2gtypes' or 'sequence2gtypes').
Cheers, eric ---- *Eric Archer, Ph.D.* Southwest Fisheries Science Center (NMFS/NOAA) 8901 La Jolla Shores Drive La Jolla, CA 92037 USA 858-546-7121 (work) 858-546-7003 (FAX) Marine Mammal Genetics Group: swfsc.noaa.gov/mmtd-mmgenetics GitHub: github/ericarcher & Adjunct Professor, Marine Biology Scripps Institution of Oceanography University of California, San Diego http://profiles.ucsd.edu/frederick.archer " *The universe doesn't care what you believe. The wonderful thing about science is that it doesn't ask for your faith, it just asks for your eyes.*" - Randall Munroe "*Lighthouses are more helpful than churches.*" - Benjamin Franklin "*...but I'll take a GPS over either one.*" - John C. "Craig" George Date: Fri, 13 Jan 2017 09:27:47 -0500 > From: Katharine Walter <katharine.wal...@yale.edu> > To: r-sig-genetics@r-project.org > Subject: [R-sig-genetics] Defining populations for Arlequin input > Message-ID: > <CACAXSaW1PtALesWgO5EY=+tdRYhxzBbF3O7rnvMwgNBO-5zXPg@mail. > gmail.com> > Content-Type: text/plain; charset="UTF-8" > > Hi all, > > I would like to use Arlequin to infer some pop gen statistics. I have an > input FASTA of sequence data and can convert to Arlequin format with > PGDSpider. I'm wondering if there is a script available or if anyone has > suggestions on how to define populations in the Arlequin input file (i.e. > from a matrix of sample names and population assignments). I know you can > do this manually in DNAsp but I'm hoping there is a way to do this without > the GUI. > > Thank you for your help! > Best, > [[alternative HTML version deleted]] _______________________________________________ R-sig-genetics mailing list R-sig-genetics@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-genetics
