TANDEM: integrating automated allele binning into genetics and genomics workflows. - Michael Matschiner; Walter Salzburger (Bioinform., 2009)

Fitchi: haplotype genealogy graphs based on the Fitch algorithm. - Michael Matschiner (Bioinform., 2016)

BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. - Remco R. Bouckaert; Timothy G. Vaughan; Joëlle Barido-Sottani; Sebastián Duchêne; Mathieu Fourment; Alexandra Gavryushkina; Joseph Heled; Graham Jones; Denise Kühnert; Nicola De Maio; Michael Matschiner; Fábio K. Mendes; et al. (PLoS Comput. Biol., 2019)