首都大学東京
MEGA version 2 (MEGA2), which was coauthored by an additional investigator Ingrid Jakobson, was released in 2001. All the computer programs and the readme files of this version could be sent electronically due to advances in computer technology. Around this time, the leadership of the MEGA project was taken over by Kumar (now at Temple University) and Tamura (now at Tokyo Metropolitan University). The monograph "Molecular Evolutionary Genetics Analysis" was often used as a textbook for new ways to study molecular evolution.