Who Let the CAT Out of the Bag? Accurately Dealing with Substitutional Heterogeneity in Phylogenomic Analyses

The Interrelationships of Placental Mammals and the Limits of Phylogenetic Inference

(2016) James E. Tarver et al.   Genome Biology and Evolution

New deep-sea species of Xenoturbella and the position of Xenacoelomorpha

(2016) Greg W. Rouse et al.   NATURE

Xenacoelomorpha is the sister group to Nephrozoa

(2016) Johanna Taylor Cannon et al.   NATURE

Miscues misplace sponges

(2016) Kenneth M. Halanych et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phylogenomics of tubeworms (Siboglinidae, Annelida) and comparative performance of different reconstruction methods

(2016) Yuanning Li et al.   ZOOLOGICA SCRIPTA

Extracting phylogenetic signal and accounting for bias in whole-genome data sets supports the Ctenophora as sister to remaining Metazoa

(2015) Marek L. Borowiec et al.   BMC GENOMICS

A Transcriptomic-Phylogenomic Analysis of the Evolutionary Relationships of Flatworms

(2015) Bernhard Egger et al.   CURRENT BIOLOGY

Phylogenomic Insights into Animal Evolution

(2015) Maximilian J. Telford et al.   CURRENT BIOLOGY

Employing Phylogenomics to Resolve the Relationships among Cnidarians, Ctenophores, Sponges, Placozoans, and Bilaterians

(2015) N. V. Whelan et al.   INTEGRATIVE AND COMPARATIVE BIOLOGY

The Effects of Partitioning on Phylogenetic Inference

(2015) David Kainer et al.   MOLECULAR BIOLOGY AND EVOLUTION

Hemichordate genomes and deuterostome origins

(2015) Oleg Simakov et al.   NATURE

Genomic data do not support comb jellies as the sister group to all other animals

(2015) Davide Pisani et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Error, signal, and the placement of Ctenophora sister to all other animals

(2015) Nathan V. Whelan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic insights into the evolutionary origin of Myxozoa within Cnidaria

(2015) E. Sally Chang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The phylogenetic utility and functional constraint of microRNA flanking sequences

(2015) N. J. Kenny et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Phylogenetic Signal Dissection Identifies the Root of Starfishes

(2015) Roberto Feuda et al.   PLoS One

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Evolutionary relationships of the Critically Endangered frog Ericabatrachus baleensis Largen, 1991 with notes on incorporating previously unsampled taxa into large-scale phylogenetic analyses

(2014) Karen Siu-Ting et al.   BMC EVOLUTIONARY BIOLOGY

Selecting optimal partitioning schemes for phylogenomic datasets

(2014) Robert Lanfear et al.   BMC EVOLUTIONARY BIOLOGY

Phylogenomic Resolution of the Hemichordate and Echinoderm Clade

(2014) Johanna T. Cannon et al.   CURRENT BIOLOGY

Phylogenomic Resolution of the Class Ophiuroidea Unlocks a Global Microfossil Record

(2014) Timothy D. O’Hara et al.   CURRENT BIOLOGY

Evolutionary origin of a streamlined marine bacterioplankton lineage

(2014) Haiwei Luo   ISME Journal

Platyzoan Paraphyly Based on Phylogenomic Data Supports a Noncoelomate Ancestry of Spiralia

(2014) Torsten H. Struck et al.   MOLECULAR BIOLOGY AND EVOLUTION

The ctenophore genome and the evolutionary origins of neural systems

(2014) Leonid L. Moroz et al.   NATURE

Mixture Models of Nucleotide Sequence Evolution that Account for Heterogeneity in the Substitution Process Across Sites and Across Lineages

(2014) Vivek Jayaswal et al.   SYSTEMATIC BIOLOGY

Deep metazoan phylogeny: When different genes tell different stories

(2013) Tetyana Nosenko et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Agent of Whirling Disease Meets Orphan Worm: Phylogenomic Analyses Firmly Place Myxozoa in Cnidaria

(2013) Maximilian P. Nesnidal et al.   PLoS One

The Genome of the Ctenophore Mnemiopsis leidyi and Its Implications for Cell Type Evolution

(2013) J. F. Ryan et al.   SCIENCE

PhyloBayes MPI: Phylogenetic Reconstruction with Infinite Mixtures of Profiles in a Parallel Environment

(2013) Nicolas Lartillot et al.   SYSTEMATIC BIOLOGY

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

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

PartitionFinder: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic Analyses

(2012) R. Lanfear et al.   MOLECULAR BIOLOGY AND EVOLUTION

Broad Phylogenomic Sampling and the Sister Lineage of Land Plants

(2012) Ruth E. Timme et al.   PLoS One

Accuracy of phylogeny reconstruction methods combining overlapping gene data sets

(2011) Anne Kupczok et al.   Algorithms for Molecular Biology

Resolving phylogenetic signal from noise when divergence is rapid: A new look at the old problem of echinoderm class relationships

(2011) Davide Pisani et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Acoelomorph flatworms are deuterostomes related to Xenoturbella

(2011) Hervé Philippe et al.   NATURE

phytools: an R package for phylogenetic comparative biology (and other things)

(2011) Liam J. Revell   Methods in Ecology and Evolution

Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough

(2011) Hervé Philippe et al.   PLOS BIOLOGY

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

Multigene Phylogeny of the Green Lineage Reveals the Origin and Diversification of Land Plants

(2010) Cédric Finet et al.   CURRENT BIOLOGY

Improved Phylogenomic Taxon Sampling Noticeably Affects Nonbilaterian Relationships

(2010) K. S. Pick et al.   MOLECULAR BIOLOGY AND EVOLUTION

FASconCAT: Convenient handling of data matrices

(2010) Patrick Kück et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Phylogenetic analysis of 83 plastid genes further resolves the early diversification of eudicots

(2010) M. J. Moore et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Phylogenomic analyses predict sistergroup relationship of nucleariids and Fungi and paraphyly of zygomycetes with significant support

(2009) Yu Liu et al.   BMC EVOLUTIONARY BIOLOGY

An updated 18S rRNA phylogeny of tunicates based on mixture and secondary structure models

(2009) Georgia Tsagkogeorga et al.   BMC EVOLUTIONARY BIOLOGY

Phylogenomics Revives Traditional Views on Deep Animal Relationships

(2009) Hervé Philippe et al.   CURRENT BIOLOGY

INDELible: A Flexible Simulator of Biological Sequence Evolution

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

Biological Sequence Simulation for Testing Complex Evolutionary Hypotheses: indel-Seq-Gen Version 2.0

(2009) Cory L. Strope et al.   MOLECULAR BIOLOGY AND EVOLUTION

Assessing the root of bilaterian animals with scalable phylogenomic methods

(2009) A. Hejnol et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Additional molecular support for the new chordate phylogeny

(2008) Frédéric Delsuc et al.   GENESIS

An Improved General Amino Acid Replacement Matrix

(2008) S. Q. Le et al.   MOLECULAR BIOLOGY AND EVOLUTION

Broad phylogenomic sampling improves resolution of the animal tree of life

(2008) Casey W. Dunn et al.   NATURE

Evaluating the robustness of phylogenetic methods to among-site variability in substitution processes

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

Phylogenetic mixture models for proteins

(2008) S. Q. Le et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES