Analysis of Phylogenomic Tree Space Resolves Relationships Among Marsupial Families

New Statistical Criteria Detect Phylogenetic Bias Caused by Compositional Heterogeneity

(2017) David A. Duchêne et al.   MOLECULAR BIOLOGY AND EVOLUTION

An Evaluation of Different Partitioning Strategies for Bayesian Estimation of Species Divergence Times

(2017) Konstantinos Angelis et al.   SYSTEMATIC BIOLOGY

Chromosomal Speciation in the Genomics Era: Disentangling Phylogenetic Evolution of Rock-wallabies

(2017) Sally Potter et al.   Frontiers in Genetics

Genome-wide interrogation advances resolution of recalcitrant groups in the tree of life

(2017) Dahiana Arcila et al.   Nature Ecology & Evolution

The Interrelationships of Placental Mammals and the Limits of Phylogenetic Inference

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

TreeScaper: Visualizing and Extracting Phylogenetic Signal from Sets of Trees

(2016) Wen Huang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Clustering Genes of Common Evolutionary History

(2016) Kevin Gori et al.   MOLECULAR BIOLOGY AND EVOLUTION

The gene tree delusion

(2016) Mark S. Springer et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Detecting the Anomaly Zone in Species Trees and Evidence for a Misleading Signal in Higher-Level Skink Phylogeny (Squamata: Scincidae).

(2016) Charles W. Linkem et al.   SYSTEMATIC BIOLOGY

ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes

(2015) Siavash Mirarab et al.   BIOINFORMATICS

Exon capture phylogenomics: efficacy across scales of divergence

(2015) Jason G. Bragg et al.   Molecular Ecology Resources

Can We Identify Genes with Increased Phylogenetic Reliability?

(2015) Vinson P. Doyle et al.   SYSTEMATIC BIOLOGY

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Molecular Phylogeny, Biogeography, and Habitat Preference Evolution of Marsupials

(2014) Kieren J. Mitchell et al.   MOLECULAR BIOLOGY AND EVOLUTION

Phylogenetic analysis at deep timescales: Unreliable gene trees, bypassed hidden support, and the coalescence/concatalescence conundrum

(2014) John Gatesy et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Whole-genome analyses resolve early branches in the tree of life of modern birds

(2014) E. D. Jarvis et al.   SCIENCE

The changing face of the molecular evolutionary clock

(2014) Simon Y.W. Ho   TRENDS IN ECOLOGY & EVOLUTION

Less Is More in Mammalian Phylogenomics: AT-Rich Genes Minimize Tree Conflicts and Unravel the Root of Placental Mammals

(2013) Jonathan Romiguier et al.   MOLECULAR BIOLOGY AND EVOLUTION

Unlocking the vault: next-generation museum population genomics

(2013) Ke Bi et al.   MOLECULAR ECOLOGY

Inferring ancient divergences requires genes with strong phylogenetic signals

(2013) Leonidas Salichos et al.   NATURE

Inferring Kangaroo Phylogeny from Incongruent Nuclear and Mitochondrial Genes

(2013) Matthew J. Phillips et al.   PLoS One

Concatenation versus coalescence versus "concatalescence"

(2013) J. Gatesy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ensembl 2013

(2012) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model

(2012) S. Song 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

TreeOfTrees Method to Evaluate the Congruence Between Gene Trees

(2011) Pierre Darlu et al.   JOURNAL OF CLASSIFICATION

MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons

(2011) Vincent Ranwez et al.   PLoS One

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

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

Guided Tree Topology Proposals for Bayesian Phylogenetic Inference

(2011) Sebastian Höhna et al.   SYSTEMATIC BIOLOGY

Phybase: an R package for species tree analysis

(2010) L. Liu et al.   BIOINFORMATICS

Sources of Error Inherent in Species-Tree Estimation: Impact of Mutational and Coalescent Effects on Accuracy and Implications for Choosing among Different Methods

(2010) Huateng Huang et al.   SYSTEMATIC BIOLOGY

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

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Tracking Marsupial Evolution Using Archaic Genomic Retroposon Insertions

(2010) Maria A. Nilsson et al.   PLOS BIOLOGY

A phylogeny of Diprotodontia (Marsupialia) based on sequences for five nuclear genes

(2009) Robert W. Meredith et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Gene tree discordance, phylogenetic inference and the multispecies coalescent

(2009) James H. Degnan et al.   TRENDS IN ECOLOGY & EVOLUTION

A Dated Phylogeny of Marsupials Using a Molecular Supermatrix and Multiple Fossil Constraints

(2008) Robin M. D. Beck   JOURNAL OF MAMMALOGY

Trees of Trees: An Approach to Comparing Multiple Alternative Phylogenies

(2008) Tom M. W. Nye   SYSTEMATIC BIOLOGY

Family-level relationships among the Australasian marsupial “herbivores” (Diprotodontia: Koala, wombats, kangaroos and possums)

(2007) Matthew J. Phillips et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION