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The Journal of Heredity|October 28, 2017
Pinniped Diphyly and Bat Triphyly: More Homology Errors Drive Conflicts in the Mammalian TreeMark S Springer, John GatesyTrends in Ecology & Evolution|October 19, 2006
The supermatrix approach to systematicsAlan de Queiroz, John GatesyMolecular Phylogenetics and Evolution|September 17, 2008
Potential use of host-derived genome signatures to root virus phylogeniesMark P SimmonsMolecular Phylogenetics and Evolution|November 10, 2011
Radical instability and spurious branch support by likelihood when applied to matrices with non-random distributions of missing dataMark P SimmonsMolecular Phylogenetics and Evolution|May 4, 2004
Independence of alignment and tree searchMark P SimmonsCladistics : the International Journal of the Willi Hennig Society|November 2, 2021
Mutually exclusive phylogenomic inferences at the root of the angiosperms: Amborella is supported as sister and Observed Variability is biasedMark P SimmonsMolecular Phylogenetics and Evolution|February 18, 2014
Limitations of locally sampled characters in phylogenetic analyses of sparse supermatricesMark P SimmonsMolecular Phylogenetics and Evolution|September 1, 2014
A confounding effect of missing data on character conflict in maximum likelihood and Bayesian MCMC phylogenetic analysesMark P SimmonsCladistics : the International Journal of the Willi Hennig Society|December 7, 2021
Misleading results of likelihood-based phylogenetic analyses in the presence of missing dataMark P SimmonsCladistics : the International Journal of the Willi Hennig Society|December 14, 2021
A Fundamental Problem with Amino-Acid-Sequence Characters for Phylogenetic AnalysesMark P SimmonsPageof 14