The prevalence of terraced treescapes in analyses of phylogenetic data sets

Speciation dynamics during the global radiation of extant bats

(2015) Jeff J. Shi et al.   EVOLUTION

Consequences of Common Topological Rearrangements for Partition Trees in Phylogenomic Inference

(2015) Olga Chernomor et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

The Impact of Missing Data on Species Tree Estimation

(2015) Zhenxiang Xi et al.   MOLECULAR BIOLOGY AND EVOLUTION

Dissecting Molecular Evolution in the Highly Diverse Plant Clade Caryophyllales Using Transcriptome Sequencing

(2015) Ya Yang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Building the avian tree of life using a large-scale, sparse supermatrix

(2015) J. Gordon Burleigh et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Probabilistic models of eukaryotic evolution: time for integration

(2015) Nicolas Lartillot   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Impacts of Terraces on Phylogenetic Inference

(2015) Michael J. Sanderson et al.   SYSTEMATIC BIOLOGY

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Should genes with missing data be excluded from phylogenetic analyses?

(2014) Wei Jiang et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

A multigene phylogenetic synthesis for the class Lecanoromycetes (Ascomycota): 1307 fungi representing 1139 infrageneric taxa, 317 genera and 66 families

(2014) Jolanta Miadlikowska et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Dubious resolution and support from published sparse supermatrices: The importance of thorough tree searches

(2014) Mark P. Simmons et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Limitations of locally sampled characters in phylogenetic analyses of sparse supermatrices

(2014) Mark P. Simmons   MOLECULAR PHYLOGENETICS AND EVOLUTION

Phylotranscriptomic analysis of the origin and early diversification of land plants

(2014) Norman J. Wickett et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phylogenomics resolves the timing and pattern of insect evolution

(2014) B. Misof et al.   SCIENCE

Bias in Tree Searches and its Consequences for Measuring Group Supports

(2014) Pablo A. Goloboff et al.   SYSTEMATIC BIOLOGY

Analysis and Visualization of Complex Macroevolutionary Dynamics: An Example from Australian Scincid Lizards

(2014) Daniel L. Rabosky et al.   SYSTEMATIC BIOLOGY

Phylogenetic relationships and character evolution analysis of Saxifragales using a supermatrix approach

(2013) D. E. Soltis et al.   AMERICAN JOURNAL OF BOTANY

Three keys to the radiation of angiosperms into freezing environments

(2013) Amy E. Zanne et al.   NATURE

Large-scale phylogeny of chameleons suggests African origins and Eocene diversification

(2013) K. A. Tolley et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Impact of Missing Data on Phylogenies Inferred from Empirical Phylogenomic Data Sets

(2012) Béatrice Roure et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

Macroevolutionary Dynamics and Historical Biogeography of Primate Diversification Inferred from a Species Supermatrix

(2012) Mark S. Springer et al.   PLoS One

Phylogenomics and a posteriori data partitioning resolve the Cretaceous angiosperm radiation Malpighiales

(2012) Z. Xi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

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

(2011) Mark P. Simmons   CLADISTICS

Spurious 99% bootstrap and jackknife support for unsupported clades

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

Terraces in Phylogenetic Tree Space

(2011) M. J. Sanderson et al.   SCIENCE

Impacts of the Cretaceous Terrestrial Revolution and KPg Extinction on Mammal Diversification

(2011) R. W. Meredith et al.   SCIENCE

Can Deliberately Incomplete Gene Sample Augmentation Improve a Phylogeny Estimate for the Advanced Moths and Butterflies (Hexapoda: Lepidoptera)?

(2011) Soowon Cho et al.   SYSTEMATIC BIOLOGY

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

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

Phylogenomics with incomplete taxon coverage: the limits to inference

(2010) Michael J Sanderson et al.   BMC EVOLUTIONARY BIOLOGY

Characterizing phylogenetically decisive taxon coverage

(2009) Mike Steel et al.   APPLIED MATHEMATICS LETTERS

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

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

Sparse Supermatrices for Phylogenetic Inference: Taxonomy, Alignment, Rogue Taxa, and the Phylogeny of Living Turtles

(2009) Robert C. Thomson et al.   SYSTEMATIC BIOLOGY

Using ESTs for phylogenomics: can one accurately infer a phylogenetic tree from a gappy alignment?

(2008) Stefanie Hartmann et al.   BMC EVOLUTIONARY BIOLOGY

A Mixed Branch Length Model of Heterotachy Improves Phylogenetic Accuracy

(2008) Bryan Kolaczkowski et al.   MOLECULAR BIOLOGY AND EVOLUTION

Modelling heterotachy in phylogenetic inference by reversible-jump Markov chain Monte Carlo

(2008) M. Pagel et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Optimal Data Partitioning and a Test Case for Ray-Finned Fishes (Actinopterygii) Based on Ten Nuclear Loci

(2008) Chenhong Li et al.   SYSTEMATIC BIOLOGY

A Rapid Bootstrap Algorithm for the RAxML Web Servers

(2008) Alexandros Stamatakis et al.   SYSTEMATIC BIOLOGY