1/5
Introducing SimPlot-CL! 🧬
Recombination plays an important role in viral evolution. Similarity plots are a great way to visualize recombination patterns, but generating them across many genomes can be cumbersome
(Work with my student, Keno Strotjohann!)
📂 github.com/hodcroftlab/simplot-cl
2/5
We built a lightweight Python command-line tool for automated similarity plot (SimPlot) analyses. It performs sliding-window comparisons of one or multiple query sequences against a panel of reference sequences, designed with viral recombination analysis in mind.
3/5
SimPlot-CL makes it easy to generate similarity plots in bulk! It supports inputs where query and reference sequences are in the same or separate FASTA files, can optionally align sequences first, and offers customizable plotting parameters (window/step sizes, colors, etc).
4/5
The tool is inspired by great existing software like the original SimPlot (Lole et al., 1999), but provides a command-line implementation that enables smooth integration into bioinformatics pipelines (e.g. Snakemake or Nextflow workflows).
5/5
If you want to try it out, check out the documentation and open-source code here:
🌐 Website: https://eve-lab.org/blog/SimPlot-CL
📂 GitHub: https://github.com/hodcroftlab/simplot-cl
Feedback and feature suggestions are very welcome! 🙂
And again - huge thanks/credit to Keno for this great work!
Dr Emma Hodcroft 
