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

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 surpass parsimony when assessing clade support in phylogenetic analyses of discrete morphological data

(2017) Joseph E. O'Reilly et al.   PALAEONTOLOGY

Bayesian and likelihood phylogenetic reconstructions of morphological traits are not discordant when taking uncertainty into consideration: a comment on Puttick et   al .

(2017) Joseph W. Brown et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Parsimony and maximum-likelihood phylogenetic analyses of morphology do not generally integrate uncertainty in inferring evolutionary history: a response to Brown et al.

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

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

The impact of fossil data on annelid phylogeny inferred from discrete morphological characters

(2016) Luke A. Parry et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Modeling Character Change Heterogeneity in Phylogenetic Analyses of Morphology through the Use of Priors

(2015) April M. Wright et al.   SYSTEMATIC BIOLOGY

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

Ultrafast Approximation for Phylogenetic Bootstrap

(2013) B. Q. Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Placental Mammal Ancestor and the Post-K-Pg Radiation of Placentals

(2013) M. A. O'Leary et al.   SCIENCE

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

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

TNT, a free program for phylogenetic analysis

(2008) Pablo A. Goloboff et al.   CLADISTICS