Author

Jonathan Holmes

University of OxfordORCID 0009-0001-0440-8404Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

Click to filter author papers

Bioinformatics· 1 Evolutionary Biology· 1

Signature Assays, Organisms & Methods

Click to filter · or open tag

Research Focus:phylogenetics / evolution· 2 Assay:whole-genome sequencing· 2 Approach:benchmark study· 1 Research Focus:benchmarking· 1 Approach:deep learning· 1 Organism:multiple species· 1 Assay:protein sequence· 1 Research Focus:software / tool· 1

Frequent Co-Authors

Steven L. KellyiD· 2 shared David EmmsiD· 1 shared Laurence J. BelcheriD· 1 shared Yi LiuiD· 1 shared

Activity by Year

2025-2026 · peak 1/yr

Co-Author Collaboration Network

4 top collaborators · 6 mutual co-author links

Click any collaborator node to inspect or filter shared papers

Focal author (center)Selected co-authorORCID co-authorUnlinked name

Curved chords = mutual co-authorship

2 shared papersEvolutionary Biology

Steven L. KellyORCID

Mutual co-authors in cluster

Author profile →

2 papers

Recent·Most cited

Evolutionary BiologybioRxivPreprintJan 21, 2026

FastSpeciesTree: Fast and Scalable Species tree Inference

Jonathan Holmes, Steven L. Kelly

FastSpeciesTree rapidly and accurately infers species trees from large genomic datasets, outperforming existing methods in speed and scalability.

2 citations

whole-genome sequencingdeep learning

𝕏 PostBluesky

BioinformaticsbioRxivPreprintJul 15, 2025

✦ In-depth digest

OrthoFinder: scalable phylogenetic orthology inference for comparative genomics

David Emms, Yi Liu, Laurence J. Belcher…·Steven L. Kelly

OrthoFinder v3 splits orthogroups at duplications predating the species-tree root, raising OrthoBench accuracy, and assigns extra species to a core run, finishing 1024 species in 128 hours.

44 citations

multiple speciesprotein sequence

𝕏 PostBluesky