Hy-Phy Users Manual Spencer Muse 1 North Carolina State University - Sergei Kosakovsky Pond 2 University of Arizona Abstract: Hy-Phy is a high-level programming language for performing molecular evolutionary analyses. Although Hy-Phy has a growing number of tree reconstruction features, its primary design is not to reconstruct phylogenetic trees. Instead, the object of Hy-Phy is to provide a flexible platform for studying rates and patterns of sequence change.
Sergei L. Kosakovsky Pond and Spencer V. Muse, 1997-2002