Body: <p>I’m wondering if folks have recommendations for tools/scripts to extract SNP sites from a multiple sequence alignment of consensus bacterial genomes? Specifically, I am interested in a multiple sequence alignment containing variant (SNP) positions only, to be used as input for phylogeny-building programs including RAxML and BEAST.</p>
  <p>I was previously using <a href="https://github.com/sanger-pathogens/snp-sites" rel="nofollow noreferrer">https://github.com/sanger-pathogens/snp-sites</a>, but this is not being maintained and I’m running into errors that it seems many others are having (with regards to sequences being different lengths, although I have confirmed they are the same length).</p>
  <p>Any recommendations would be great, thank you!</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-05-10T19:12:22.960Z
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: 2022-05-10T19:15:08.830Z
Comments.Text: Are you looking for identity, or are you variant calling, or finally perhaps looking a consensus sequence?
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-05-10T19:44:44.733Z
Comments.Text: Yes, apologies for the lack of clarity. I have aligned consensus sequences, I'm hoping to extract SNP sites only into an alignment of SNP positions. Thank you!
Comments.UserDisplayName: ksw
Tags: <phylogenetics><variants>
Title: Extract SNPs from multiple sequence alignment
ThreadText: # Extract SNPs from multiple sequence alignment
  
  (Asked by: username_0 on 2022-05-10)
  
  I’m wondering if folks have recommendations for tools/scripts to extract SNP sites from a multiple sequence alignment of consensus bacterial genomes? Specifically, I am interested in a multiple sequence alignment containing variant (SNP) positions only, to be used as input for phylogeny-building programs including RAxML and BEAST.
  
  I was previously using <https://github.com/sanger-pathogens/snp-sites>, but this is not being maintained and I’m running into errors that it seems many others are having (with regards to sequences being different lengths, although I have confirmed they are the same length).
  
  Any recommendations would be great, thank you!
  
  **Tags:** phylogenetics, variants
  
  > **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**: Are you looking for identity, or are you variant calling, or finally perhaps looking a consensus sequence?  
  > **username_0**: Yes, apologies for the lack of clarity. I have aligned consensus sequences, I'm hoping to extract SNP sites only into an alignment of SNP positions. Thank you!  
  
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  ## 0 answers
  
  