Bayesian and parsimony approaches reconstruct informative trees from simulated morphological datasets

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

(2018) Pablo A. Goloboff 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

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

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

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

(2016) Curtis R. Congreve et al.   PALAEONTOLOGY

Identifying unstable taxa: Efficient implementation of triplet-based measures of stability, and comparison with Phyutility and RogueNaRok

(2015) Pablo A. Goloboff et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Total-Evidence Dating under the Fossilized Birth–Death Process

(2015) Chi Zhang et al.   SYSTEMATIC BIOLOGY

tqDist: a library for computing the quartet and triplet distances between binary or general trees

(2014) Andreas Sand et al.   BIOINFORMATICS

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

Rates of Phenotypic and Genomic Evolution during the Cambrian Explosion

(2013) Michael S.Y. Lee et al.   CURRENT BIOLOGY

Behaviour of resampling methods under different weighting schemes, measures and variable resampling strengths

(2009) Cecilia Kopuchian et al.   CLADISTICS

TNT, a free program for phylogenetic analysis

(2008) Pablo A. Goloboff et al.   CLADISTICS