Likelihood approximations of implied weights parsimony can be selected over the Mk model by the Akaike information criterion

Bayesian and parsimony approaches reconstruct informative trees from simulated morphological datasets

(2019) Martin R. Smith   Biology Letters

Parsimony, not Bayesian analysis, recovers more stratigraphically congruent phylogenetic trees

(2018) Robert S. Sansom et al.   Biology Letters

On defining a unique phylogenetic tree with homoplastic characters

(2018) Pablo A. Goloboff et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Parsimony and model-based phylogenetic methods for morphological data: comments on O'Reilly et al .

(2018) Pablo A. Goloboff et al.   PALAEONTOLOGY

Empirical realism of simulated data is more important than the model used to generate it: a reply to Goloboff et al .

(2018) Joseph E. O'Reilly et al.   PALAEONTOLOGY

Probabilistic methods outperform parsimony in the phylogenetic analysis of data simulated without a probabilistic model

(2018) Mark N. Puttick et al.   PALAEONTOLOGY

Morphological Data Sets Fit a Common Mechanism Much More Poorly than DNA Sequences and Call Into Question the Mkv Model

(2018) Pablo A Goloboff et al.   SYSTEMATIC BIOLOGY

Uncertain-tree: discriminating among competing approaches to the phylogenetic analysis of phenotype data

(2017) Mark N. Puttick et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Bayesian methods outperform parsimony but at the expense of precision in the estimation of phylogeny from discrete morphological data

(2016) Joseph E. O'Reilly et al.   Biology Letters

TNT version 1.5, including a full implementation of phylogenetic morphometrics

(2016) Pablo A. Goloboff et al.   CLADISTICS

Implied weighting and its utility in palaeontological datasets: a study using modelled phylogenetic matrices

(2016) Curtis R. Congreve et al.   PALAEONTOLOGY

POY version 5: phylogenetic analysis using dynamic homologies under multiple optimality criteria

(2014) Ward C. Wheeler et al.   CLADISTICS

A confounding effect of missing data on character conflict in maximum likelihood and Bayesian MCMC phylogenetic analyses

(2014) Mark P. Simmons   MOLECULAR PHYLOGENETICS AND EVOLUTION

Bayesian Analysis Using a Simple Likelihood Model Outperforms Parsimony for Estimation of Phylogeny from Discrete Morphological Data

(2014) April M. Wright et al.   PLoS One

Extended implied weighting

(2013) Pablo A. Goloboff   CLADISTICS

An artifact caused by undersampling optimal trees in supermatrix analyses of locally sampled characters

(2013) Mark P. Simmons et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Incorporating phylogenetic uncertainty on phylogeny-based palaeontological dating and the timing of turtle diversification

(2012) Juliana Sterli et al.   CLADISTICS

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

Radical instability and spurious branch support by likelihood when applied to matrices with non-random distributions of missing data

(2011) Mark P. Simmons   MOLECULAR PHYLOGENETICS AND EVOLUTION

Biologically Inspired Phylogenetic Models Strongly Outperform the No Common Mechanism Model

(2011) John P. Huelsenbeck et al.   SYSTEMATIC BIOLOGY

The Akaike Information Criterion Will Not Choose the No Common Mechanism Model

(2010) Mark T. Holder et al.   SYSTEMATIC BIOLOGY

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

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

Weighting against homoplasy improves phylogenetic analysis of morphological data sets

(2008) Pablo A. Goloboff et al.   CLADISTICS

TNT, a free program for phylogenetic analysis

(2008) Pablo A. Goloboff et al.   CLADISTICS

A Bayesian Perspective on a Non-parsimonious Parsimony Model

(2008) John P. Huelsenbeck et al.   SYSTEMATIC BIOLOGY