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!

  • $\begingroup$ 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. $\endgroup$
    – Community Bot
    May 10, 2022 at 19:12
  • 1
    $\begingroup$ Are you looking for identity, or are you variant calling, or finally perhaps looking a consensus sequence? $\endgroup$
    – M__
    May 10, 2022 at 19:15
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    $\begingroup$ 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! $\endgroup$
    – ksw
    May 10, 2022 at 19:44


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