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

[Eric Archer - NOAA Federal]

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


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Date: Fri, 13 Jan 2017 09:27:47 -0500
> From: Katharine Walter <katharine.walter at yale.edu>
> To: r-sig-genetics at r-project.org
> Subject: [R-sig-genetics] Defining populations for Arlequin input
> Message-ID:
>         <CACAXSaW1PtALesWgO5EY=+tdRYhxzBbF3O7rnvMwgNBO-5zXPg at 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,
>

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