Comparative evaluation of maximum parsimony and Bayesian phylogenetic reconstruction using empirical morphological data

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

Dating placentalia: Morphological clocks fail to close the molecular fossil gap

(2016) Mark N. Puttick et al.   EVOLUTION

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

Phylogenetic inference using discrete characters: performance of ordered and unordered parsimony and of three-item statements

(2013) Anaïs Grand et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Efficacy or convenience? Model-based approaches to phylogeny estimation using morphological data

(2013) Marc R. Spencer et al.   CLADISTICS

Combining fossil and molecular data to date the diversification of New World Primates

(2013) C. G. Schrago et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Highly Incomplete Taxa Can Rescue Phylogenetic Analyses from the Negative Impacts of Limited Taxon Sampling

(2012) John J. Wiens et al.   PLoS One

Experimental Design in Phylogenetics: Testing Predictions from Expected Information

(2012) Diego San Mauro et al.   SYSTEMATIC BIOLOGY

A Total-Evidence Approach to Dating with Fossils, Applied to the Early Radiation of the Hymenoptera

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

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

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

MorphoBank: phylophenomics in the “cloud”

(2011) Maureen A. O’Leary et al.   CLADISTICS

Divergence Time Estimation Using Fossils as Terminal Taxa and the Origins of Lissamphibia

(2011) R. Alexander Pyron   SYSTEMATIC BIOLOGY

Do model-based phylogenetic analyses perform better than parsimony? A test with empirical data

(2010) Eirik Rindal et al.   CLADISTICS

INDELible: A Flexible Simulator of Biological Sequence Evolution

(2009) W. Fletcher et al.   MOLECULAR BIOLOGY AND EVOLUTION

TNT, a free program for phylogenetic analysis

(2008) Pablo A. Goloboff et al.   CLADISTICS