Answers.Body: <p>You can use <code>vegan</code> or <code>adegenet</code> to run AMOVA on haploid data and compare it with <code>poppr</code> results. I do not see why converting the input to <code>genclone</code> object would be a problem.</p>
  <p>nic</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2024-11-07T13:22:58.827Z
Answers.Text: Hi, thanks for your response. The reason why I don't want to convert it to a genclone object is because genclose is used for loci and SNPs, whereas I am working with haplotype, so sequence data.
Answers.UserDisplayName: Ana_wizard
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2024-11-05T16:54:02.097Z
Answers.LastActivityDate: 2024-11-05T16:54:02.097Z
Answers.UserDisplayName: nicolotellini
Body: <p>I have haplotype data from mitochondrial DNA, which is divided into different countries and different cities within the countries. I would like to do an AMOVA (analysis of molecular variance), to see if there is any significant differences between the countries or cities. Because I am working with molecular data (haplotypes) I want to see if there are signifcant differences based on the DNA sequences</p>
  <p>I have been doing some experimenting with the &quot;poppr&quot; package in Rstudio, however I am not sure if this package is appropriate because you have to transform your data into genclone object. So my question is, if it is possible to do an AMOVA with haploid data using the &quot;poppr&quot; package, or if there is another method that is more suitable for haploid data.</p>
  
Tags: <sequence-analysis><haplotypes><rstudio>
Title: AMOVA in Rstudio with haploid data
ThreadText: # AMOVA in Rstudio with haploid data
  
  (Asked by: username_0 on 2024-10-30)
  
  I have haplotype data from mitochondrial DNA, which is divided into different countries and different cities within the countries. I would like to do an AMOVA (analysis of molecular variance), to see if there is any significant differences between the countries or cities. Because I am working with molecular data (haplotypes) I want to see if there are signifcant differences based on the DNA sequences
  
  I have been doing some experimenting with the "poppr" package in Rstudio, however I am not sure if this package is appropriate because you have to transform your data into genclone object. So my question is, if it is possible to do an AMOVA with haploid data using the "poppr" package, or if there is another method that is more suitable for haploid data.
  
  **Tags:** sequence-analysis, haplotypes, rstudio
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2024-11-05. Score: 1
  
  You can use `vegan` or `adegenet` to run AMOVA on haploid data and compare it with `poppr` results. I do not see why converting the input to `genclone` object would be a problem.
  
  nic
  
  > **Comments:**
  > **username_0**: Hi, thanks for your response. The reason why I don't want to convert it to a genclone object is because genclose is used for loci and SNPs, whereas I am working with haplotype, so sequence data.  
  
  ---
  
  