OrthologID: automation of genome-scale ortholog identification within a parsimony framework. - Joanna C. Chiu; Ernest K. Lee; Mary G. Egan; Indra Neil Sarkar; Gloria M. Coruzzi; Robert DeSalle (Bioinform., 2006)

Automated simultaneous analysis phylogenetics (ASAP): an enabling tool for phlyogenomics. - Indra Neil Sarkar; Mary G. Egan; Gloria M. Coruzzi; Ernest K. Lee; Robert DeSalle (BMC Bioinform., 2008)

OrthoReD: a rapid and accurate orthology prediction tool with low computational requirement. - Kai Battenberg; Ernest K. Lee; Joanna C. Chiu; Alison M. Berry; Daniel Potter (BMC Bioinform., 2017)