Molecular Clocks Perhaps the most common hypothesis tested using molecular data is that a sequence has evolved according to a molecular clock. It now seems quite clear that a global molecular clock exists for few, if any, gene sequences. In contrast, the existence of local molecular clocks among more closely related species is more probable. Hy-Phy allows for both types of constraints, including the possibility of testing for multiple local clocks for different user-defined clades in the same tree.
Sergei L. Kosakovsky Pond and Spencer V. Muse, 1997-2002