PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating. - Nicolas Lartillot; Thomas Lepage; Samuel Blanquart (Bioinform., 2009)

MATAM: reconstruction of phylogenetic marker genes from short sequencing reads in metagenomes. - Pierre Pericard; Yoann Dufresne; Loïc Couderc; Samuel Blanquart; Hélène Touzet (Bioinform., 2018)

Phylogenetic inference of the emergence of sequence modules and protein-protein interactions in the ADAMTS-TSL family. - Olivier Dennler; François Coste; Samuel Blanquart; Catherine Belleannée; Nathalie Théret (PLoS Comput. Biol., 2023)

SPARTA: Interpretable functional classification of microbiomes and detection of hidden cumulative effects. - Baptiste Ruiz; Arnaud Belcour; Samuel Blanquart; Sylvie Buffet-Bataillon; Isabelle Le Huërou-Luron; Anne Siegel; Yann Le Cunff (PLoS Comput. Biol., 2024)