Sebastian Deorowicz

FAMSA can now be used in a web browser: refresh-bio.github.io/tools/famsa/ It is compiled to WebAssembly, so all computations run locally on the device - your data never leaves your machine. Sample timings (workstation, 16 threads) for cys family (56k seqs): 150s (default) or 20s (with medoids).

Product of a terrific collaboration with @sdeorowicz.bsky.social, Marek Kokot, and Amit Roy: doi.org/10.1093/bioi... MDCompress produces compressed trajectory files that are up to 37% smaller than in the widely-used XTC format. Nice software library interfaces for fast (de-)compression.

Fast and accurate multiple-protein-sequence alignment at scale with FAMSA2 - @sdeorowicz.bsky.social go.nature.com/4muAQsh

10 years after the first FAMSA paper, its successor is now published in Nat Biotech! We believe that FAMSA2 can enable analyses of large protein collections that were previously unattainable. Thank you, Andrzej and Cedric, for great collaboration www.nature.com/articles/s41...

MDCompress (www.biorxiv.org/content/10.6...) is our recent proposal for storing molecular dynamics simulations. Try if you feel that your XTC files are too big or need random access features. Great collaboration with Travis Wheeler's lab.

Interested in a tool that aligns millions of proteins in minutes with quality similar to or better than the state-of-the-art utilities? Please take a look at our FAMSA2 paper: www.biorxiv.org/content/10.1... and GH repo: github.com/refresh-bio/...

Vclust generates fast and accurate estimation of average nucleotide identity (ANI) for viral genomes, scaling clustering to millions of genomes. @sdeorowicz.bsky.social @bedutilh.bsky.social @prozwalak.bsky.social @uni-jena.de @microverse.bsky.social www.nature.com/articles/s41...

Vclust (the ultra-fast, high-accuracy tool for viral genome comparison & clustering) is now published: www.nature.com/articles/s41... Great collaboration with A.Zielezinki, UAM guys and @bedutilh.bsky.social

Recently, our SPLASH paper (www.nature.com/articles/s41...) was published in NatBiotech. Now, we release its extended version, sc-SPLASH (www.biorxiv.org/content/10.1...), which allows reference-free analysis of single-cell data. It was a great experience to work with our collaborators on that!

First post here. :-) AGC 3.2 (assembled genome compressor) has been released. Better speed, better ratio (at least for bacteria genomes), optional low-memory decompression. github.com/refresh-bio/...