Mastodawn

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!

SimPlot-CL: Automated Similarity Plotting from the Command Line

A lightweight, Python-based command-line tool for generating similarity plots directly from sequences.

EVE

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).

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).

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.

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

RE: https://mstdn.science/@firefoxx66/115887966535364834

Jan 19

Just a reminder - if you're in Zurich tonight and interested in open data sharing, come hear me speak at 18.00! (Only 20 minutes, in English!)

https://www.karldergrosse.ch/programm/veranstaltung/winterreden-2026-emma-hodcroft

Jan 13

In Zurich on Monday evening? Want to hear about #opendata & data sharing, and how critical it is for preparing for and responding to infectious diseases? 🔓🧬

Come hear me speak at Karl de Grosse Debattierhaus Winterreden! 🪟💬

👉🏻 19 Jan, 18.00, 20 mins, English

Jan 8

And look I'm sorry - but saying that maintaining COVID dashboards is focusing on unimportant things - is nothing less than purposefully missing the point.
Any scientist worth their salt knows we don't just stop monitoring viruses because they stop being pandemic.