Super-tree Approach for Studying the Phylogeny of Prokaryotes: New Results on Completely Sequenced Genomes. - Alexandra Calteau; Vincent Daubin; Guy Perrière (International Conference on Computational Science, 2004)

Databases of homologous gene families for comparative genomics. - Simon Penel; Anne-Muriel Arigon; Jean-François Dufayard; Anne-Sophie Sertier; Vincent Daubin; Laurent Duret; Manolo Gouy; Guy Perrière (BMC Bioinform., 2009)

Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests. - Sophie S. Abby; Eric Tannier; Manolo Gouy; Vincent Daubin (BMC Bioinform., 2010)

Models, algorithms and programs for phylogeny reconciliation. - Jean-Philippe Doyon; Vincent Ranwez; Vincent Daubin; Vincent Berry (Briefings Bioinform., 2011)

Evolution of gene neighborhoods within reconciled phylogenies. - Sèverine Bérard; Coralie Gallien; Bastien Boussau; Gergely J. Szöllosi; Vincent Daubin; Eric Tannier (Bioinform., 2012)

High-quality sequence clustering guided by network topology and multiple alignment likelihood. - Vincent Miele; Simon Penel; Vincent Daubin; Franck Picard; Daniel Kahn; Laurent Duret (Bioinform., 2012)

TPMS: a set of utilities for querying collections of gene trees. - Thomas Bigot; Vincent Daubin; Florent Lassalle; Guy Perrière (BMC Bioinform., 2013)

Lateral gene transfer, rearrangement, reconciliation. - Murray Patterson; Gergely J. Szöllosi; Vincent Daubin; Eric Tannier (BMC Bioinform., 2013)

RecPhyloXML: a format for reconciled gene trees. - Wandrille Duchemin; Guillaume Gence; Anne-Muriel Arigon Chifolleau; Lars Arvestad; Mukul S. Bansal; Vincent Berry; Bastien Boussau; François Chevenet; Nicolas Comte; Adrián A. Davín; Christophe Dessimoz; David Dylus; et al. (Bioinform., 2018)

Treerecs: an integrated phylogenetic tool, from sequences to reconciliations. - Nicolas Comte; Benoit Morel; Damir Hasic; Laurent Guéguen; Bastien Boussau; Vincent Daubin; Simon Penel; Céline Scornavacca; Manolo Gouy; Alexandros Stamatakis; Eric Tannier; David P. Parsons (Bioinform., 2020)

Thirdkind: displaying phylogenetic encounters beyond 2-level reconciliation. - Simon Penel; Hugo Menet; Théo Tricou; Vincent Daubin; Eric Tannier (Bioinform., 2022)

Phylogenetic reconciliation. - Hugo Menet; Vincent Daubin; Eric Tannier (PLoS Comput. Biol., 2022)