Using a GTR+Γ substitution model for dating sequence divergence when stationarity and time-reversibility assumptions are violated. - Jose Barba-Montoya; Qiqing Tao; Sudhir Kumar 001 (Bioinform., 2020)

A new method for inferring timetrees from temporally sampled molecular sequences. - Sayaka Miura; Koichiro Tamura; Qiqing Tao; Louise A. Huuki; Sergei L. Kosakovsky Pond; Jessica Priest; Jiamin Deng; Sudhir Kumar 001 (PLoS Comput. Biol., 2020)

Data-driven speciation tree prior for better species divergence times in calibration-poor molecular phylogenies. - Qiqing Tao; Jose Barba-Montoya; Sudhir Kumar 001 (Bioinform., 2021)

TopHap: rapid inference of key phylogenetic structures from common haplotypes in large genome collections with limited diversity. - Marcos A. Caraballo-Ortiz; Sayaka Miura; Maxwell D. Sanderford; Tenzin Dolker; Qiqing Tao; Steven Weaver; Sergei L. Kosakovsky Pond; Sudhir Kumar 001 (Bioinform., 2022)