A Fast and Efficient Method for Estimating Amino Acid Substitution Models. - Van Dat Le; Cuong Cao Dang; Si Quang Le; Le Sy Vinh (KSE, 2011)

Protein Type Specific Amino Acid Substitution Models for Influenza Viruses. - Nguyen Van Sau; Cuong Cao Dang; Si Quang Le; Le Sy Vinh (KSE, 2011)

ReplacementMatrix: a web server for maximum-likelihood estimation of amino acid replacement rate matrices. - Cuong Cao Dang; Vincent Lefort; Le Sy Vinh; Si Quang Le; Olivier Gascuel (Bioinform., 2011)

FastMG: a simple, fast, and accurate maximum likelihood procedure to estimate amino acid replacement rate matrices from large data sets. - Cuong Cao Dang; Le Sy Vinh; Olivier Gascuel; Bart Hazes; Si Quang Le (BMC Bioinform., 2014)

Building a Specific Amino Acid Substitution Model for Dengue Viruses. - Thu Le Kim; Cuong Cao Dang; Le Sy Vinh (KSE, 2018)

pQMaker: empirically estimating amino acid substitution models in a parallel environment. - Nguyen Duc Canh; Cuong Cao Dang; Le Sy Vinh; Bui Quang Minh; Diep Thi Hoang (KSE, 2020)

Rooting Phylogenetic Trees from Protein Alignments. - Tinh H. Nguyen; Cuong Cao Dang; Le Sy Vinh (KSE, 2023)

QMix: An Efficient Program to Automatically Estimate Multi-Matrix Mixture Models for Amino Acid Substitution Process. - Nguyen Huy Tinh; Cuong Cao Dang; Le Sy Vinh (J. Comput. Biol., 2024)