Answers.Body: <p>Arlequin format is historically extremely difficult to manually manage. The group leader eventually wrote software to allow easy Arlequin format management and conversion. This is achieve by Population Genetics Data (format) Spider, or PGDSpider by <a href="https://academic.oup.com/bioinformatics/article/28/2/298/198891?login=false" rel="nofollow noreferrer">Lisher and Excoffier (2018)</a>. All information is available <a href="http://www.cmpg.unibe.ch/software/PGDSpider/" rel="nofollow noreferrer">here</a> and the manual is <a href="http://www.cmpg.unibe.ch/software/PGDSpider/PGDSpider%20manual_vers%202-1-1-5.pdf" rel="nofollow noreferrer">here</a>. I would personally avoid attempting to manually rectify population designation.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-02-09T10:17:57.540Z
Answers.LastActivityDate: 2023-02-09T10:17:57.540Z
Answers.UserDisplayName: M__
Body: <p>I have converted a VCF file to the arlequin file format. It consists of 20 samples that <em>should</em> belong to three populations, along with a few thousands SNPs. However, when I load the arlequin file into the software, it shows I only have 1 population. Any way to fix this?</p>
  <p>Thanks.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-02-09T18:06:48.957Z
Comments.Text: Can you please show a few lines from your Arlequin file?
Comments.UserDisplayName: gringer
Tags: <snp><format-conversion>
Title: Arlequin - How to assign samples to populations?
ThreadText: # Arlequin - How to assign samples to populations?
  
  (Asked by: username_0 on 2023-02-09)
  
  I have converted a VCF file to the arlequin file format. It consists of 20 samples that *should* belong to three populations, along with a few thousands SNPs. However, when I load the arlequin file into the software, it shows I only have 1 population. Any way to fix this?
  
  Thanks.
  
  **Tags:** snp, format-conversion
  
  > **Comments:**
  > **username_1**: Can you please show a few lines from your Arlequin file?  
  
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  ## 1 answers
  
  ### Answer by username_2 on 2023-02-09. Score: 0
  
  Arlequin format is historically extremely difficult to manually manage. The group leader eventually wrote software to allow easy Arlequin format management and conversion. This is achieve by Population Genetics Data (format) Spider, or PGDSpider by [Lisher and Excoffier (2018)](https://academic.oup.com/bioinformatics/article/28/2/298/198891?login=false). All information is available [here](http://www.cmpg.unibe.ch/software/PGDSpider/) and the manual is [here](http://www.cmpg.unibe.ch/software/PGDSpider/PGDSpider%20manual_vers%202-1-1-5.pdf). I would personally avoid attempting to manually rectify population designation.
  
  
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