About genomeRxiv
Every genome
gets an address.
genomeRxiv assigns your assembly a Life Identification Number (LIN), a precise, reproducible position among all sequenced microbes, from genus down to clonal lineage, in minutes.
> field_isolate_42.fna · 5.8 Mb · 112 contigs
99.92% ANI · position H resolved · 8 of 20 positions assigned
The mission
Names change.
Addresses should not.
genomeRxiv is a database built to accelerate the description of Earth's microbial diversity, at a precision that includes, and goes beyond, named species.
Anyone can circumscribe, describe, and name a group of bacteria, a LINgroup, at or below the genus level, even when the group is a single clonal lineage. Validly published species names are linked to peer-reviewed publications; everything else still gets a stable, genome-based address. Uploaded genomes are placed into the similarity framework next to every genome already in the database, and short gene sequences can be searched directly, so identification is precise even when a whole genome is not available. genomeRxiv is under active development; meet the team behind it.
genomeRxiv is a family of databases, one per domain of life, that share the LIN framework, the placement pipeline, and this interface. You are on the Fungi database; the Prokaryotes database is a click away from the switcher beside the logo, and a LIN means the same thing in each.
The core idea
The Life Identification Number
A LIN is a series of 20 positions, A through T. Each position corresponds to a threshold of average nucleotide identity (ANI): sharing a longer prefix means being more similar. The first positions separate genera; the last ones separate members of the same outbreak.
Two genomes that agree through position H are at least 97% identical across their whole genomes. Agreement through position T means they are effectively the same strain.
How it works
Three steps from file to placement
The pipeline is a real sequence: each step feeds the next.
Signature, not sequence
Your assembly is reduced to a compact sourmash signature. For private identification, the sequence never leaves your machine.
Ranked against the database
The signature is ranked against every genome in genomeRxiv by average nucleotide identity.
A LIN is assigned
Your genome receives its LIN, the nearest LINgroups and species, and a tree of its neighborhood.
The result
What you get back
Every identification returns the assigned LIN, the closest genome with its ANI, and the LINgroups your isolate belongs to, with charts, maps, and a phylogenetic tree one click away.
A live sample of the result table: each genome carries its color-coded 20-position LIN under the banded ANI scale, longest shared prefix meaning closest relative. Sort, search, and pick columns right here; the real page adds charts, maps, and trees.
Explore
Explore the database from any angle
Who it serves
One address, many uses
History
A decade of genome-based naming
The LIN concept
A system to automatically classify and name any individual genome-sequenced organism, independently of current taxonomy, is proposed by the Vinatzer and Heath labs at Virginia Tech.
LINbase goes online
The first web server for genome-based identification of prokaryotes as members of crowdsourced taxa, introducing LINgroups as a way to circumscribe and describe groups.
LINflow
The Vinatzer lab releases LINflow, a standalone pipeline that computes and assigns LINs from assemblies on its own database schema. It is the engine genomeRxiv's backend still runs on today.
The genomeRxiv collaboration
An NSF-funded partnership between Virginia Tech, UC Davis, and the University of Strathclyde to scale the platform: faster placement with sourmash sketching, private identification, and a public API.
Open for submissions
genomeRxiv places new genomes in minutes and welcomes uploads, LINgroup descriptions, and feedback while the platform is under active development.
Publications
How to cite
If you have found genomeRxiv or LINbase useful, please cite:
genomeRxiv: a genome-based identification web server that bridges the gap between taxonomy and strain typing
Reza Mazloom, Rituraj Sharma, Janet S. H. Lorv, Sehgeet Kaur, Parul Sharma, C. Titus Brown, N. Tessa Pierce-Ward, Leighton Pritchard, Lenwood S. Heath, and Boris A. Vinatzer. bioRxiv (2026), preprint. doi:10.64898/2026.10.09.757156
LINbase: a web server for genome-based identification of prokaryotes as members of crowdsourced taxa
Long Tian, Chengjie Huang, Reza Mazloom, Lenwood S. Heath, and Boris A. Vinatzer. Nucleic Acids Research (2020). doi:10.1093/nar/gkaa190
A proposal for a portal to make earth's microbial diversity easily accessible and searchable
Boris A. Vinatzer, Long Tian, and Lenwood S. Heath. Antonie van Leeuwenhoek (2017). doi:10.1007/s10482-017-0849-z
A proposal for a genome similarity-based taxonomy for plant-pathogenic bacteria that is sufficiently precise to reflect phylogeny, host range, and outbreak affiliation applied to Pseudomonas syringae sensu lato as a proof of concept
Boris A. Vinatzer, Alexandra J. Weisberg, Caroline L. Monteil, Haitham A. Elmarakeby, Samuel K. Sheppard, and Lenwood S. Heath. Phytopathology (2016). doi:10.1094/PHYTO-07-16-0252-R
Similarity-based codes sequentially assigned to ebolavirus genomes are informative of species membership, associated outbreaks, and transmission chains
Alexandra J. Weisberg, Haitham A. Elmarakeby, Lenwood S. Heath, and Boris A. Vinatzer. Open Forum Infectious Diseases (2015). doi:10.1093/ofid/ofv024
A system to automatically classify and name any individual genome-sequenced organism independently of current biological classification and nomenclature
Haitham Marakeby, Eman Badr, Hanaa Torkey, Yuhyun Song, Caroline L. Monteil, Lenwood S. Heath, and Boris A. Vinatzer. PLOS ONE (2014). doi:10.1371/journal.pone.0089142
Have an unknown on your bench?
Upload a FASTA file and get its address, or try it first with our example genome.
Genome Identify
genomerxiv.cs.vt.edu