Easy and reliable genome annotation.

Annotate your sequence!

⁕⁕ NEW ⁕⁕ Animal cell structure en

Fungi - Protozoa - Vectors

Wide selection of eukaryotic reference genomes

Annotate Example
No longer supported HYPHAE


Annotate your sequence against fungi reference genomes

Annotate Example
No longer supported OSC Microbio 05 01 locom


Annotate your sequence against protozoa reference genomes

Annotate Example

Now in Glasgow

To further develop Companion, we implemented a new instance at the University of Glasgow. The server has more resources, so jobs should run twice as fast.


Annotation results are typically ready in a couple of hours. Submit multiple jobs at once and we will keep you up to date about their progress.


Annotation of a new genome could be as easy as uploading your scaffold sequences (FASTA, EMBL, GenBank), choosing a reference and pushing a button!


The pipeline spans many aspects of new genome production: from pseudo-chromosome contiguation, structural and functional gene annotation, through to comparative analyses and visualization.

Standards compliant

Annotation results are provided in validated GFF3 format for gene model and product annotations, and GAF format for GO associations.

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for the lastest developments and updates.

High quality

Data-generating components of the pipeline are built on time-tested de facto standard software.


Want to tweak the pipeline or perform large-scale annotations on your compute cluster? Get Nextflow, the pipeline code under the hood and the Docker dependencies and run the whole workflow on your own machine!

Please cite!

Our update paper featuring Companion version 2 has been accepted for publication by Nucleic Acids Research!

If you are using Companion in your research, please cite the following publication:

William Haese-Hill, Kathryn Crouch, Thomas D. Otto
Annotation and visualisation of parasite, fungi and arthropod genomes with Companion.
Nucleic Acids Research, 2024; gkae378.
DOI: 10.1093/nar/gkae378