APE: Analyses of Phylogenetics and Evolution in R language. - Emmanuel Paradis; Julien Claude; Korbinian Strimmer (Bioinform., 2004)

pegas: an R package for population genetics with an integrated-modular approach. - Emmanuel Paradis (Bioinform., 2010)

ape 3.0: New tools for distance-based phylogenetics and evolutionary analysis in R. - Andrei-Alin Popescu; Katharina T. Huber; Emmanuel Paradis (Bioinform., 2012)

ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R. - Emmanuel Paradis; Klaus Schliep (Bioinform., 2019)

Modelling the geographical distributions of one native and two introduced species of crayfish in the French Alps. - Chantima Piyapong; Clara Tattoni; Marco Ciolli; Samuel Dembski; Emmanuel Paradis (Ecol. Informatics, 2020)

A review of computer tools for prediction of ecosystems and populations: We need more open-source software. - Emmanuel Paradis (Environ. Model. Softw., 2020)

Probabilistic unsupervised classification for large-scale analysis of spectral imaging data. - Emmanuel Paradis (Int. J. Appl. Earth Obs. Geoinformation, 2022)

Reduced multidimensional scaling. - Emmanuel Paradis (Comput. Stat., 2022)

Information-energy equivalence and the emergence of self-replicating biological systems. - Emmanuel Paradis (Biosyst., 2023)

An efficient algorithm to find all minimum spanning trees. - Emmanuel Paradis (J. Complex Networks, 2025)