The Impact of Missing Data on Species Tree Estimation

Estimating phylogenetic trees from genome-scale data

(2015) Liang Liu et al.   Annals of the New York Academy of Sciences

How Should Genes and Taxa be Sampled for Phylogenomic Analyses with Missing Data? An Empirical Study in Iguanian Lizards

(2015) Jeffrey W. Streicher et al.   SYSTEMATIC BIOLOGY

ASTRAL: genome-scale coalescent-based species tree estimation

(2014) S. Mirarab et al.   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Possible Loss of the Chloroplast Genome in the Parasitic Flowering Plant Rafflesia lagascae (Rafflesiaceae)

(2014) Jeanmaire Molina et al.   MOLECULAR BIOLOGY AND EVOLUTION

Coalescent Methods Are Robust to the Simultaneous Effects of Long Branches and Incomplete Lineage Sorting

(2014) L. Liu 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 confounding effect of missing data on character conflict in maximum likelihood and Bayesian MCMC phylogenetic analyses

(2014) Mark P. Simmons   MOLECULAR PHYLOGENETICS 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

GenBank

(2014) Dennis A. Benson et al.   NUCLEIC ACIDS RESEARCH

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

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

(2014) E. D. Jarvis et al.   SCIENCE

Coalescent versus Concatenation Methods and the Placement of Amborella as Sister to Water Lilies

(2014) Zhenxiang Xi et al.   SYSTEMATIC BIOLOGY

Evaluating Summary Methods for Multilocus Species Tree Estimation in the Presence of Incomplete Lineage Sorting

(2014) Siavash Mirarab et al.   SYSTEMATIC BIOLOGY

Land plant origins and coalescence confusion

(2014) Mark S. Springer et al.   TRENDS IN PLANT SCIENCE

The multispecies coalescent model and land plant origins: a reply to Springer and Gatesy

(2014) Bojian Zhong et al.   TRENDS IN PLANT SCIENCE

Next-Generation Sequencing Platforms

(2013) Elaine R. Mardis   Annual Review of Analytical Chemistry

High-Throughput Genomic Data in Systematics and Phylogenetics

(2013) Emily Moriarty Lemmon et al.   Annual Review of Ecology Evolution and Systematics

Naive binning improves phylogenomic analyses

(2013) Md Shamsuzzoha Bayzid et al.   BIOINFORMATICS

Phylogenomics of Annelida revisited: a cladistic approach using genome-wide expressed sequence tag data mining and examining the effects of missing data

(2013) Sebastian Kvist et al.   CLADISTICS

Phylogenomic Analyses Elucidate the Evolutionary Relationships of Bats

(2013) Georgia Tsagkogeorga et al.   CURRENT BIOLOGY

Effects of missing data on species tree estimation under the coalescent

(2013) Rasmus Hovmöller et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Three keys to the radiation of angiosperms into freezing environments

(2013) Amy E. Zanne et al.   NATURE

Inferring ancient divergences requires genes with strong phylogenetic signals

(2013) Leonidas Salichos et al.   NATURE

Phylogenomics and Coalescent Analyses Resolve Extant Seed Plant Relationships

(2013) Zhenxiang Xi et al.   PLoS One

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

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

The Evolutionary Root of Flowering Plants

(2012) Vadim V. Goremykin et al.   SYSTEMATIC BIOLOGY

A genome triplication associated with early diversification of the core eudicots

(2012) Yuannian Jiao et al.   GENOME BIOLOGY

Accuracy of phylogeny reconstruction methods combining overlapping gene data sets

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

Understanding angiosperm diversification using small and large phylogenetic trees

(2011) S. A. Smith et al.   AMERICAN JOURNAL OF BOTANY

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

(2011) Mark P. Simmons   CLADISTICS

COALESCENT-BASED SPECIES TREE INFERENCE FROM GENE TREE TOPOLOGIES UNDER INCOMPLETE LINEAGE SORTING BY MAXIMUM LIKELIHOOD

(2011) Yufeng Wu   EVOLUTION

Systematic Error in Seed Plant Phylogenomics

(2011) Bojian Zhong et al.   Genome Biology and Evolution

A large-scale phylogeny of Amphibia including over 2800 species, and a revised classification of extant frogs, salamanders, and caecilians

(2011) R. Alexander Pyron et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Radical instability and spurious branch support by likelihood when applied to matrices with non-random distributions of missing data

(2011) Mark P. Simmons   MOLECULAR PHYLOGENETICS AND EVOLUTION

Terraces in Phylogenetic Tree Space

(2011) M. J. Sanderson 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

Phylogenomic Analysis Resolves the Interordinal Relationships and Rapid Diversification of the Laurasiatherian Mammals

(2011) Xuming Zhou et al.   SYSTEMATIC BIOLOGY

Estimating Species Trees from Unrooted Gene Trees

(2011) Liang Liu et al.   SYSTEMATIC BIOLOGY

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

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

Phybase: an R package for species tree analysis

(2010) L. Liu et al.   BIOINFORMATICS

Phylogenomics with incomplete taxon coverage: the limits to inference

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

A maximum pseudo-likelihood approach for estimating species trees under the coalescent model

(2010) Liang Liu et al.   BMC EVOLUTIONARY BIOLOGY

Phylogenetic analyses reveal the shady history of C4 grasses

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

The Accuracy of Species Tree Estimation under Simulation: A Comparison of Methods

(2010) Adam D. Leaché et al.   SYSTEMATIC BIOLOGY

Methods for Genomic Partitioning

(2009) Emily H. Turner et al.   Annual Review of Genomics and Human Genetics

Characterizing phylogenetically decisive taxon coverage

(2009) Mike Steel et al.   APPLIED MATHEMATICS LETTERS

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

STEM: species tree estimation using maximum likelihood for gene trees under coalescence

(2009) Laura S. Kubatko et al.   BIOINFORMATICS

Removal of Noisy Characters from Chloroplast Genome-Scale Data Suggests Revision of Phylogenetic Placements of Amborella and Ceratophyllum

(2009) Vadim V. Goremykin et al.   JOURNAL OF MOLECULAR EVOLUTION

Bayesian Inference of Species Trees from Multilocus Data

(2009) J. Heled et al.   MOLECULAR BIOLOGY AND EVOLUTION

Coalescent methods for estimating phylogenetic trees

(2009) Liang Liu et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The Impact of Outgroup Choice and Missing Data on Major Seed Plant Phylogenetics Using Genome-Wide EST Data

(2009) Jose Eduardo de la Torre-Bárcena et al.   PLoS One

Assessing the root of bilaterian animals with scalable phylogenomic methods

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

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

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

Estimating Species Phylogenies Using Coalescence Times among Sequences

(2009) Liang Liu 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

Gene tree discordance, phylogenetic inference and the multispecies coalescent

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

BEST: Bayesian estimation of species trees under the coalescent model

(2008) L. Liu   BIOINFORMATICS

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

(2008) Stefanie Hartmann et al.   BMC EVOLUTIONARY BIOLOGY

IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING?

(2008) Scott V. Edwards   EVOLUTION

Integrating Phylogenetic and Population Genetic Analyses of Multiple Loci to Test Species Divergence Hypotheses in Passerina Buntings

(2008) Matt D. Carling et al.   GENETICS

Calculating Bootstrap Probabilities of Phylogeny Using Multilocus Sequence Data

(2008) T.-K. Seo   MOLECULAR BIOLOGY AND EVOLUTION

The phylogeny of Cetartiodactyla: The importance of dense taxon sampling, missing data, and the remarkable promise of cytochrome b to provide reliable species-level phylogenies

(2008) Ingi Agnarsson et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Developing markers for multilocus phylogenetics in non-model organisms: A test case with turtles

(2008) Robert C. Thomson et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Broad phylogenomic sampling improves resolution of the animal tree of life

(2008) Casey W. Dunn et al.   NATURE

Ancient Rapid Radiations of Insects: Challenges for Phylogenetic Analysis

(2007) James B. Whitfield et al.   Annual Review of Entomology