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

Fast and accurate multiple-protein-sequence alignment at scale with FAMSA2 - Nature Biotechnology

FAMSA2 accurately aligns millions of protein sequences at high speed.

go.nature.com

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...

Fast and accurate multiple-protein-sequence alignment at scale with FAMSA2 - Nature Biotechnology

FAMSA2 accurately aligns millions of protein sequences at high speed.

nature.com

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.

MDCompress: better, faster compression of molecular dynamics simulation trajectories

Motivation: Molecular dynamics (MD) simulations model the physical movements of atoms in biomolecular systems over time, providing atomic-resolution insight into conformational changes, binding events...

biorxiv.org

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/...

FAMSA2 enables accurate multiple sequence alignment at protein-universe scale

We introduce FAMSA2, an algorithm that produces high-accuracy multiple protein sequence alignments with unprecedented speed. Across structural, phylogenetic, and functional benchmarks, FAMSA2 matches ...

biorxiv.org

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

Ultrafast and accurate sequence alignment and clustering of viral genomes - Nature Methods

Vclust generates fast and accurate estimation of average nucleotide identity for viral genomes, scaling clustering to millions of genomes.

nature.com

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!

Scalable and unsupervised discovery from raw sequencing reads using SPLASH2 - Nature Biotechnology

SPLASH2 speeds up analysis of sequence variation in massive datasets.

nature.com

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/...

GitHub - refresh-bio/agc: Assembled Genomes Compressor

Assembled Genomes Compressor. Contribute to refresh-bio/agc development by creating an account on GitHub.

github.com