<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>

CC BY-SA 4.0
2022-05-10T19:12:22.960Z
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.
Community
CC BY-SA 4.0
2022-05-10T19:15:08.830Z
Are you looking for identity, or are you variant calling, or finally perhaps looking a consensus sequence?
M__
CC BY-SA 4.0
2022-05-10T19:44:44.733Z
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!
ksw
<phylogenetics><variants>
Extract SNPs from multiple sequence alignment
# 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

