Defining populations for Arlequin input
Hello, you can do this easily in adegenet, though there is no direct conversion from the Arlequin format. Workflow would be something like: 1. read sequences using fasta2DNAbin 2. extract SNPs into a genind using DNAbin2genind 3. read your population assignment data from a text file using read.table or read.csv 4. assign the populations to you genind using 'pop', e.g. pop(x) <- the_new_pop where 'x' is you genind and 'the_new_pop' is a vector of group assignments, matching against 'indNames(x)'. Check the 'basics' tutorial for more info: https://github.com/thibautjombart/adegenet/wiki/Tutorials Best Thibaut -- Dr Thibaut Jombart Lecturer, Department of Infectious Disease Epidemiology, Imperial College London Head of RECON: repidemicsconsortium.org sites.google.com/site/thibautjombart/ github.com/thibautjombart Twitter: @TeebzR <http://twitter.com/TeebzR> +44(0)20 7594 3658 On 12 January 2017 at 13:59, Katharine Walter <katharine.walter at yale.edu> wrote:
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,
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