BUCKy: Gene tree/species tree reconciliation with Bayesian concordance analysis. - Bret R. Larget; Satish K. Kotha; Colin N. Dewey; Cécile Ané (Bioinform., 2010)

Phase transition on the convergence rate of parameter estimation under an Ornstein-Uhlenbeck diffusion on a tree. - Cécile Ané; Lam Si Tung Ho; Sebastien Roch (CoRR, 2014)

Assessing the fit of the multi-species network coalescent to multi-locus data. - Ruoyi Cai; Cécile Ané (Bioinform., 2021)

KIMGENS: a novel method to estimate kinship in organisms with mixed haploid diploid genetic systems robust to population structure. - Yen-Wen Wang; Cécile Ané (Bioinform., 2022)

Identifying circular orders for blobs in phylogenetic networks. - John A. Rhodes; Hector Baños; Jingcheng Xu; Cécile Ané (Adv. Appl. Math., 2025)