Phylogenetic Analyses of SARS-CoV-2 Strains Reveal Its Link to the Spread of COVID-19 Across the Globe. - Shashata Sawmya; Arpita Saha; Sadia Tasnim; Naser Anjum Samudro; Md. Toufikuzzaman; Ali Haisam Muhammad Rafid; Mohammad Saifur Rahman 001; M. Sohel Rahman; Tanvir Alam (MedInfo, 2021)

PASTA with many application-aware optimization criteria for alignment based phylogeny inference. - Muhammad Ali Nayeem; Md. Shamsuzzoha Bayzid; Naser Anjum Samudro; Mohammad Saifur Rahman 001; M. Sohel Rahman (Comput. Biol. Chem., 2022)

MAMMLE: A Framework for Phylogeny Estimation Based on Multiobjective Application-aware Multiple Sequence Alignment and Maximum Likelihood Ensemble. - Muhammad Ali Nayeem; Naser Anjum Samudro; Mohammad Saifur Rahman 001; M. Sohel Rahman (J. Comput. Biol., 2023)