BAOBAB: a Java editor for large phylogenetic trees. - Julien Dutheil; Nicolas Galtier (Bioinform., 2002)

Bio++: a set of C++ libraries for sequence analysis, phylogenetics, molecular evolution and population genetics. - Julien Dutheil; Sylvain Gaillard; Eric Bazin; Sylvain Glemin; Vincent Ranwez; Nicolas Galtier; Khalid Belkhir (BMC Bioinform., 2006)

Evolutionary Modeling of Rate Shifts Reveals Specificity Determinants in HIV-1 Subtypes. - Osnat Penn; Adi Stern; Nimrod D. Rubinstein; Julien Dutheil; Eran Bacharach; Nicolas Galtier; Tal Pupko (PLoS Comput. Biol., 2008)

Detecting coevolving positions in a molecule: why and how to account for phylogeny. - Julien Dutheil (Briefings Bioinform., 2012)

Optimization of sequence alignments according to the number of sequences vs. number of sites trade-off. - Julien Y. Dutheil; Emeric Figuet (BMC Bioinform., 2015)

hotspot: software to support sperm-typing for investigating recombination hotspots. - Linda Odenthal-Hesse; Julien Y. Dutheil; Fabian Klötzl; Bernhard Haubold (Bioinform., 2016)

Being noisy in a crowd: Differential selective pressure on gene expression noise in model gene regulatory networks. - Natasa Puzovic; Tanvi Madaan; Julien Y. Dutheil (PLoS Comput. Biol., 2023)