RRTree: Relative-Rate Tests between groups of sequences on a phylogenetic tree. - Marc Robinson-Rechavi; Dorothée Huchon (Bioinform., 2000)

GLOOME: gain loss mapping engine. - Ofir Cohen; Haim Ashkenazy; Frida Belinky; Dorothée Huchon; Tal Pupko (Bioinform., 2010)

GenomeFLTR: filtering reads made easy. - Edo Dotan; Michael Alburquerque; Elya Wygoda; Dorothée Huchon; Tal Pupko (Nucleic Acids Res., 2023)

A machine-learning-based alternative to phylogenetic bootstrap. - Noa Ecker; Dorothée Huchon; Yishay Mansour; Itay Mayrose; Tal Pupko (Bioinform., 2024)