Adrian Altenhoff

This paper reports on the fourth CAFA challenge, showing improvements in Gene Ontology term prediction but highlighting challenges in new evaluation settings.

PhytClust partitions rooted phylogenetic trees into monophyletic clusters without user-defined thresholds, achieving optimal and reproducible results across diverse biological datasets.

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

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

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

Read2Tree processes raw sequencing reads to build phylogenetic trees, outperforming conventional methods in speed and accuracy across diverse datasets.

OMAMO selects the best simple model organism for studying a biological process based on orthologous relationships between humans and species.

This paper introduces ClusterMerge, a precise clustering algorithm that efficiently identifies homologous proteins by reducing computational complexity and enabling parallel processing.

OMA standalone is a tool for orthology inference across public and custom genomes, enabling analysis of both existing and user-provided data.

The paper introduces two phylogenetic tests to identify gene fragments in the wheat genome and finds 1221 likely gene fragment pairs in a draft assembly.

The paper shows taxon sampling unevenly impacts gene tree nodes and introduces a two-step method to construct more reliable model gene trees using SwissTree.