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

[Thibaut Jombart]

Haha, sorry, I just realized I replied to the opposite problem, and missed
Eric's reply.
My bad.
I need coffee.

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>
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On 14 January 2017 at 19:27, Eric Archer - NOAA Federal <
eric.archer at noaa.gov> wrote:

> 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.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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>
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