Yannis Nevers

OMAnnotator: a novel approach to building an annotated consensus genome sequence

OMAnnotator improves genome annotation by integrating multiple evidence sources using evolutionary information, outperforming existing pipelines in re-annotating Drosophila and other genomes.

Structural phylogenetics unravels the evolutionary diversification of communication systems in gram-positive bacteria and their viruses

The paper introduces a structure-informed phylogenetic framework to study the evolutionary diversification of RRNPPA quorum sensing receptors in gram-positive bacteria and their viruses.

EdgeHOG: fine-grained ancestral gene order inference at tree-of-life scale

EdgeHOG infers ancestral gene order across the tree of life, producing 1,133 ancestral genomes and revealing conserved and rapidly evolving gene adjacencies.

Orthology inference at scale with FastOMA

FastOMA scales orthology inference to handle large genome datasets efficiently while maintaining accuracy.

Multifaceted quality assessment of gene repertoire annotation with OMArk

OMArk evaluates gene repertoire quality by assessing completeness, consistency, and contamination across species, identifying issues in reference proteomes.

A Linear-Time Solution to the Labeled Robinson-Foulds Distance Problem

The paper introduces a linear-time algorithm for computing the Labeled Robinson-Foulds edit distance between trees with labeled internal nodes, showing it improves upon previous methods.