[R-sig-genetics] Defining populations for Arlequin input

[Thibaut Jombart]

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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>
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