MANTIS: a phylogenetic framework for multi-species genome comparisons. - Athanasia C. Tzika; Raphaël Helaers; Yves Van de Peer; Michel C. Milinkovitch (Bioinform., 2008)

MetaPIGA v2.0: maximum likelihood large phylogeny estimation using the metapopulation genetic algorithm and other stochastic heuristics. - Raphaël Helaers; Michel C. Milinkovitch (BMC Bioinform., 2010)

Excalibur: A new ensemble method based on an optimal combination of aggregation tests for rare-variant association testing for sequencing data. - Simon Boutry; Raphaël Helaers; Tom Lenaerts; Miikka Vikkula (PLoS Comput. Biol., 2023)

Rare variant association on unrelated individuals in case-control studies using aggregation tests: existing methods and current limitations. - Simon Boutry; Raphaël Helaers; Tom Lenaerts; Miikka Vikkula (Briefings Bioinform., 2023)