Misleading results of likelihood-based phylogenetic analyses in the presence of missing data

A supermatrix analysis of genomic, morphological, and paleontological data from crown Cetacea

(2011) Jonathan H Geisler et al.   BMC EVOLUTIONARY BIOLOGY

Spurious 99% bootstrap and jackknife support for unsupported clades

(2011) Mark P. Simmons et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Missing Data in Phylogenetic Analysis: Reconciling Results from Simulations and Empirical Data

(2011) John J. Wiens et al.   SYSTEMATIC BIOLOGY

The conflation of ignorance and knowledge in the inference of clade posteriors

(2010) Christopher P. Randle et al.   CLADISTICS

Branch support via resampling: an empirical study

(2010) John V. Freudenstein et al.   CLADISTICS

The deterministic effects of alignment bias in phylogenetic inference

(2010) Mark P. Simmons et al.   CLADISTICS

Alignment of, and phylogenetic inference from, random sequences: The susceptibility of alternative alignment methods to creating artifactual resolution and support

(2010) Mark P. Simmons et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Effects of data incompleteness on the relative performance of parsimony and Bayesian approaches in a supermatrix phylogenetic reconstruction of Mustelidae and Procyonidae (Carnivora)

(2009) Mieczyslaw Wolsan et al.   CLADISTICS

Long-Branch Attraction Bias and Inconsistency in Bayesian Phylogenetics

(2009) Bryan Kolaczkowski et al.   PLoS One

The Effect of Ambiguous Data on Phylogenetic Estimates Obtained by Maximum Likelihood and Bayesian Inference

(2009) Alan R. Lemmon et al.   SYSTEMATIC BIOLOGY

Multigene phylogeny of the Mustelidae: Resolving relationships, tempo and biogeographic history of a mammalian adaptive radiation

(2008) Klaus-Peter Koepfli et al.   BMC BIOLOGY

jModelTest: Phylogenetic Model Averaging

(2008) D. Posada   MOLECULAR BIOLOGY AND EVOLUTION