Reconciling taxonomy and phylogenetic inference: formalism and algorithms for describing discord and inferring taxonomic roots. - Frederick A. Matsen IV; Aaron Gallagher (Algorithms Mol. Biol., 2012)

Minimizing the average distance to a closest leaf in a phylogenetic tree - Frederick A. Matsen IV; Aaron Gallagher; Connor McCoy (CoRR, 2012)

nestly - a framework for running software with nested parameter choices and aggregating results. - Connor McCoy; Aaron Gallagher; Noah G. Hoffman; Frederick A. Matsen IV (Bioinform., 2013)