Answers.Body: <p>At present I would simply use iqtree</p>
  <pre><code>iqtree -s file -m GTR+I+G -T 6 -B 1000 
  </code></pre>
  <p>This will parallelise across 6 CPUs and results in 1000 bootstraps, whilst GTR is the mutation model, which models invariant sites under a 4 category gamma distribution. This is a robust model.</p>
  <p>You can view the tree in <a href="http://tree.bio.ed.ac.uk/software/figtree/" rel="nofollow noreferrer">FigTree</a>.</p>
  <p>The DNA file is in fasta format</p>
  <pre><code>&gt; seq1
  AGACGT
  &gt;seq2
  AGAAAT
  </code></pre>
  <p>If there's an 'unknown' format bug let me know because I only work in  data pipeline so I forget if I've shifted the format.</p>
  <p>The result will be in the treefile and is a professional quality tree, complete with bootstraps.</p>
  <p>The <code>I</code> parameter here could omitted for this dataset because I assume all none of the sites are invariant.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-05-24T00:35:56.707Z
Answers.Text: @M_ Thank you for you answer. DArTseq is one of the cheap and easy but efficient genotyping-by-sequencing platforms which allow genome-wide marker discovery through restriction enzyme-mediated genome complexity reduction and sequencing of the restriction fragments (Edet et.al. 2018). I am attempting to construct a phylogenetic tree using the results of DArTseq rather than the FASTA sequences.
Answers.UserDisplayName: Lama
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Answers.CreationDate: 2023-05-24T00:52:11.103Z
Answers.Text: @Lama its a simple format shift. Maybe conversion of DArTseq to fasta is a good question to raise? At the end of the day the theory is universal if the output is nucleotide data. We'd need to see the new type first, but it's likely very easy. You can build trees from anything and everything - its the underlying theory that counts.
Answers.UserDisplayName: M__
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-05-22T14:07:13.827Z
Answers.LastActivityDate: 2023-05-22T15:32:22.807Z
Answers.LastEditDate: 2023-05-22T15:32:22.807Z
Answers.UserDisplayName: M__
Body: <p>I would like to make an evolutionary tree using the SNP data from DArTseq. Are there any software or packages available for this purpose? I came across the software SNphylo, but its home page is not updated. Your suggestions would be appreciated.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-05-22T07:04:26.420Z
Comments.Text: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.
Comments.UserDisplayName: Community
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-05-22T07:12:09.663Z
Comments.Text: Welcome @Lama You would need to explain DArTseq and the data set size
Comments.UserDisplayName: M__
Tags: <phylogenetics><phylogeny>
Title: Evolutionary tree from SNP data
ThreadText: # Evolutionary tree from SNP data
  
  (Asked by: username_0 on 2023-05-22)
  
  I would like to make an evolutionary tree using the SNP data from DArTseq. Are there any software or packages available for this purpose? I came across the software SNphylo, but its home page is not updated. Your suggestions would be appreciated.
  
  **Tags:** phylogenetics, phylogeny
  
  > **Comments:**
  > **username_1**: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.  
  > **username_2**: Welcome @username_0 You would need to explain DArTseq and the data set size  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2023-05-22. Score: 1
  
  At present I would simply use iqtree
  
  ```
  iqtree -s file -m GTR+I+G -T 6 -B 1000 
  
  ```
  
  This will parallelise across 6 CPUs and results in 1000 bootstraps, whilst GTR is the mutation model, which models invariant sites under a 4 category gamma distribution. This is a robust model.
  
  You can view the tree in [FigTree](http://tree.bio.ed.ac.uk/software/figtree/).
  
  The DNA file is in fasta format
  
  ```
  > seq1
  AGACGT
  >seq2
  AGAAAT
  
  ```
  
  If there's an 'unknown' format bug let me know because I only work in data pipeline so I forget if I've shifted the format.
  
  The result will be in the treefile and is a professional quality tree, complete with bootstraps.
  
  The `I` parameter here could omitted for this dataset because I assume all none of the sites are invariant.
  
  > **Comments:**
  > **username_0**: @M_ Thank you for you answer. DArTseq is one of the cheap and easy but efficient genotyping-by-sequencing platforms which allow genome-wide marker discovery through restriction enzyme-mediated genome complexity reduction and sequencing of the restriction fragments (Edet et.al. 2018). I am attempting to construct a phylogenetic tree using the results of DArTseq rather than the FASTA sequences.  
  > **username_2**: @username_0 its a simple format shift. Maybe conversion of DArTseq to fasta is a good question to raise? At the end of the day the theory is universal if the output is nucleotide data. We'd need to see the new type first, but it's likely very easy. You can build trees from anything and everything - its the underlying theory that counts.  
  
  ---
  
  