ArticleNature methods2026
Efficient evidence-based genome annotation with EviAnn.
Article in Nature methods, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Dissecting the genetic basis of climatic adaptation in wild relatives (Malus baccata) for climate-resilient apple breeding.Journal of integrative plant biology · 2026Article
- A high-quality haplotype-resolved genome of Pyrus calleryana provides insights into adaptive gene families.The plant genome · 2026Article
- Profiling maize embryonic leaf development and discovering new genes using high-resolution spatial long-read isoform sequencing.Nature plants · 2026Article
- Chromosome-Scale Genome of Zoonotic EyewormAnimals : an open access journal from MDPI · 2026Article
- Finishing a complete giraffe genome from telomere to telomere with Verkko-Fillet.Cell genomics · 2026Article
- Chromosome-Scale Genome Architecture and Historical Demography of the Southern White Rhinoceros.Biology · 2026Article
- A reference genome sequence for the exceptionally long-lived Great Basin bristlecone pine, Pinus longaeva.G3 (Bethesda, Md.) · 2026Article
- The Evolution and Origin of Allotetraploid Aegilops geniculata Revealed by the Homoeolog-Resolved Genome Assembly.Plant biotechnology journal · 2026Article
- Genomic insights into chromosomal fusion and its evolutionary implications for zokors.Molecular biology and evolution · 2026Article
- Whole-genome sequence of the African Common Reed Frog (Hyperolius viridiflavus viridiflavus) from Ethiopia.G3 (Bethesda, Md.) · 2026Article
- Finishing a complete giraffe genome from telomere to telomere with Verkko-Fillet.bioRxiv : the preprint server for biology · 2025Article
- Telomere-to-telomere genome assembly of the Fraxinus mandshurica Rupr.Scientific data · 2025Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Machine-learning-based ab initio gene finders have long been central to eukaryotic genome annotation, largely because gene expression data were historically expensive and limited. Modern sequencing technologies have transformed this landscape, making transcript evidence abundant and reliable, while proteins from many well-annotated genomes provide additional rich sources of evidence. Here we address the underutilization of these data by existing annotation tools by developing EviAnn (Evidence-based Annotator), an evidence-based eukaryotic gene annotation system. EviAnn takes a strongly data-driven approach, building exon-intron structures of protein coding and noncoding genes directly from transcript alignments or protein homology rather than relying primarily on ab initio predictions. Using identical input data, EviAnn consistently outperforms leading packages such as BRAKER3, MAKER2 and FINDER, while utilizing considerably less computer time. A mammalian genome can be annotated in under an hour on a single multicore server. EviAnn is open-source software available via GitHub at https://github.com/alekseyzimin/EviAnn_release and through Bioconda as 'eviann'.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.