Benjamin J. Buchfink

Independent computer scientist. Developer of the DIAMOND protein aligner.

[Nature Methods @naturemethods]

OrthoFinder v3: a tool for phylogenetic orthology inference with boosted accuracy and scalability for massive datasets. @Steve__Kelly @dr_belcher @David__Emms

https://t.co/rig74Y6iT7

[Tominaga K. (tomiken) @pacyc1841]

OrthoFinder: improved phylogenetic orthology inference with enhanced accuracy and scalability | Nature Methods https://t.co/fHTiBe8Ws6

[Ben WoOdcroft @wwood]

Sandpiper 2 is up. 913,000 metagenomic community profiles w GTDB R232 via SingleM, 200k more than 1.0. https://t.co/YYxXe1l8Cz

GlobDB coming.

Thanks to @aroney_samuel @IAmTotesBrett Josh Mitchell and especially the new kid @StefanHerh

[SPEC @spec_perf]

The SPEC CPU 2026 benchmark suites are here! As the industry standard for vendor-neutral performance, this suite uses 52 real-world apps to help server buyers evaluate how the latest CPUs, memory & compilers handle intense workloads. 🔗 https://t.co/XmEV1L9XjZ #SPEC #Server #CPU

[Benjamin J. Buchfink @bbuchfink]

Honored to announce that DIAMOND is one of 52 benchmarks in SPEC CPU®2026 🎉🥳🍾https://t.co/IlYNqNRERE

[Benjamin J. Buchfink @bbuchfink]

Me coding using Claude and Codex @AnthropicAI @OpenAI

[Benjamin J. Buchfink @bbuchfink]

@miangoar Software available since January 2023, you can compute clusterings like that yourself if you want 😉

[Nature Methods @naturemethods]

DIAMOND DeepClust: an ultrafast clustering method for organizing the protein universe of life.

https://t.co/X2rssNWhYu

[Benjamin J. Buchfink @bbuchfink]

Clustering proteins using DIAMOND is out now @naturemethods https://t.co/YFcfUuVWfB

[Benjamin J. Buchfink @bbuchfink]

nr database @NCBI hits one billion sequences 🤩

[Oliver Schwengers 🇩🇪🇪🇺🇺🇦 @oschwengers1]

🦠🧬🖥️ Bakta v1.12.0 is out

with tons of tiny improvements and bug fixes, too many to list all:
- partial genes on linear seqs
- improved errror handlings & runtimes
- support Python 3.12 & 3.13
- ...

Thank you to all bug reporters and contributors!

https://t.co/FVBqmqRSRn

[Benjamin J. Buchfink @bbuchfink]

DIAMOND v2.1.17 has new output fields sRANK to print taxonomy nodes of the given rank associated with the subject sequence, where RANK can be any rank in the NCBI taxonomy, e.g. sdomain, skingdom, sphylum, sorder, sgenus, sspecies, etc. https://t.co/YtVTQlDQ1N

[Antonio Camargo @apcamargo_]

🚨New preprint out!
We present a foundational genomic resource of human gut microbiome viruses. It delivers high-quality, deeply curated data spanning taxonomy, predicted hosts, structures, and functions, providing a reference for gut virome research (1/8) https://t.co/BejXcSxauc

[Javier Santoyo @jsantoyo]

HI-FEVER: a Nextflow pipeline for the high-throughput discovery and annotation of endogenous viral elements. #EndogenousViralElements #EukaryoticHostGenomes #Genomics #Bioinformatics
https://t.co/PnXKkIRaRc

[Martin Larralde @althonos]

Sup' #python #bioinformatics ! Didn't announce it so far, but now that it's working, I'm pleased to say you can now pip install BLAST+ (and more)! Technicalities below🧶 1/12

[Benjamin J. Buchfink @bbuchfink]

DIAMOND v2.1.15 now supports all taxonomy features for BLAST databases, and support for using BLAST databases has also been added to the Bioconda version https://t.co/YtVTQlDicf

[IntegralAnswers @IntegralAnswers]

🚨 BREAKING NEWS: Breast & Formula Fed Toddlers Linked to Autism Diagnosis 🚨

[Nature Biotechnology @NatureBiotech]

Predicting functions of uncharacterized gene products from microbial communities https://t.co/qFsLinUwhN

[bioRxiv Bioinfo @biorxiv_bioinfo]

Ragnarok: a flexible and RApid GeNe Annotation (ROcKs) pipeline deployed through Nextflow https://t.co/YyLph0NdoQ #biorxiv_bioinfo

[antisense. @razoralign]

CluSeek: Bioinformatics Tool to Identify and Analyze Gene Clusters https://t.co/sFiaCUgooQ