Chunk #9 — INTRODUCTION — Improved hidden Markov Models and phylogenetic trees, and ortholog identification — Orthologs: identification of complete set of orthologs and best one-to-one (least diverged) ortholog
of the copies are thought to be neofunctionalization (in which one copy retains the ancestral function, while the other adapts to a new function) and subfunctionalization (in which each copy specializes in a subset of the ancestral functions) (9). If neofunctionalization has occurred, the LDO is the copy predicted to retain the ancestral function, i.e. the ‘same gene’ as the ancestor. An example of ortholog and LDO identification is shown in Figure 2.
