Méthodes et algorithmes pour l'approche statistique en phylogénie. (Methods and algorithms for a statistical approach in phylogenetics). - Stéphane Guindon (2003)

PHYML Online - a web server for fast maximum likelihood-based phylogenetic inference. - Stéphane Guindon; Franck Lethiec; Patrice Duroux; Olivier Gascuel (Nucleic Acids Res., 2005)

Phylogeny.fr: robust phylogenetic analysis for the non-specialist. - Alexis Dereeper; Valentin Guignon; Guillaume Blanc; Stéphane Audic; S. Buffet; François Chevenet; Jean-François Dufayard; Stéphane Guindon; Vincent Lefort; Magali Lescot; Jean-Michel Claverie; Olivier Gascuel (Nucleic Acids Res., 2008)

Accounting for ambiguity in ancestral sequence reconstruction. - Adrien Oliva; Sylvain Pulicani; Vincent Lefort; Laurent Bréhélin; Olivier Gascuel; Stéphane Guindon (Bioinform., 2019)

EvoLaps: a web interface to visualize continuous phylogeographic reconstructions. - François Chevenet; Denis Fargette; Stéphane Guindon; Anne-Laure Bañuls (BMC Bioinform., 2021)

Sampling bias and model choice in continuous phylogeography: Getting lost on a random walk. - Antanas Kalkauskas; Umberto Perron; Yuxuan Sun; Nick Goldman; Guy Baele; Stéphane Guindon; Nicola De Maio (PLoS Comput. Biol., 2021)