Picking fruit from the tree of life: comments on taxonomic sampling and quartet methods. - Jonathan H. Badger; Paul E. Kearney (SAC, 2001)

An information-based sequence distance and its application to whole mitochondrial genome phylogeny. - Ming Li 001; Jonathan H. Badger; Xin Chen; Sam Kwong; Paul E. Kearney; Haoyong Zhang (Bioinform., 2001)

Selecting the branches for an evolutionary tree.: A polynomial time approximation scheme. - Jonathan H. Badger; Paul E. Kearney; Ming Li 001; John Tsang; Tao Jiang 001 (J. Algorithms, 2004)

A Collapsing Method for the Efficient Recovery of Optimal Edges in Phylogenetic Trees. - Michael Hu; Paul E. Kearney; Jonathan H. Badger (Int. J. Artif. Intell. Tools, 2005)

IDEA: Interactive Display for Evolutionary Analyses. - Amy Egan; Anup Mahurkar; Jonathan Crabtree; Jonathan H. Badger; Jane M. Carlton; Joana C. Silva (BMC Bioinform., 2008)