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

ASTRAL: genome-scale coalescent-based species tree estimation

(2014) S. Mirarab et al.   BIOINFORMATICS

Land plant origins and coalescence confusion

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

Naive binning improves phylogenomic analyses

(2013) Md Shamsuzzoha Bayzid et al.   BIOINFORMATICS

Discordance of Species Trees with Their Most Likely Gene Trees: A Unifying Principle

(2013) N. A. Rosenberg   MOLECULAR BIOLOGY AND EVOLUTION

Identifying localized biases in large datasets: A case study using the avian tree of life

(2013) Rebecca T. Kimball et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Inferring ancient divergences requires genes with strong phylogenetic signals

(2013) Leonidas Salichos et al.   NATURE

A Phylogeny of Birds Based on Over 1,500 Loci Collected by Target Enrichment and High-Throughput Sequencing

(2013) John E. McCormack et al.   PLoS One

Coalescent-Based Genome Analyses Resolve the Early Branches of the Euarchontoglires

(2013) Vikas Kumar et al.   PLoS One

Robustness to Divergence Time Underestimation When Inferring Species Trees from Estimated Gene Trees

(2013) Michael DeGiorgio et al.   SYSTEMATIC BIOLOGY

The Influence of Gene Flow on Species Tree Estimation: A Simulation Study

(2013) Adam D. Leaché et al.   SYSTEMATIC BIOLOGY

Target Capture and Massively Parallel Sequencing of Ultraconserved Elements for Comparative Studies at Shallow Evolutionary Time Scales

(2013) Brian Tilston Smith et al.   SYSTEMATIC BIOLOGY

Computational approaches to species phylogeny inference and gene tree reconciliation

(2013) Luay Nakhleh   TRENDS IN ECOLOGY & EVOLUTION

Origin of land plants using the multispecies coalescent model

(2013) Bojian Zhong et al.   TRENDS IN PLANT SCIENCE

MRL and SuperFine+MRL: new supertree methods

(2012) Nam Nguyen et al.   Algorithms for Molecular Biology

Phylogenomic analyses support the position of turtles as the sister group of birds and crocodiles (Archosauria)

(2012) Ylenia Chiari et al.   BMC BIOLOGY

Genome-scale coestimation of species and gene trees

(2012) B. Boussau et al.   GENOME RESEARCH

Estimating Optimal Species Trees from Incomplete Gene Trees Under Deep Coalescence

(2012) MD. Shamsuzzoha Bayzid et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Full modeling versus summarizing gene-tree uncertainty: Method choice and species-tree accuracy

(2012) L. Lacey Knowles et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

Is Recombination a Problem for Species-Tree Analyses?

(2012) Hayley C. Lanier et al.   SYSTEMATIC BIOLOGY

Fast and accurate methods for phylogenomic analyses

(2011) Jimmy Yang et al.   BMC BIOINFORMATICS

Algorithms for MDC-Based Multi-Locus Phylogeny Inference: Beyond Rooted Binary Gene Trees on Single Alleles

(2011) Yun Yu et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Consistency Properties of Species Tree Inference by Minimizing Deep Coalescences

(2011) Cuong V. Than et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

BUCKy: Gene tree/species tree reconciliation with Bayesian concordance analysis

(2010) Bret R. Larget et al.   BIOINFORMATICS

DendroPy: a Python library for phylogenetic computing

(2010) J. Sukumaran et al.   BIOINFORMATICS

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

(2010) Liang Liu et al.   BMC EVOLUTIONARY BIOLOGY

Identifying the rooted species tree from the distribution of unrooted gene trees under the coalescent

(2010) Elizabeth S. Allman et al.   JOURNAL OF MATHEMATICAL BIOLOGY

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

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

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

(2009) Laura S. Kubatko et al.   BIOINFORMATICS

Incomplete Lineage Sorting: Consistent Phylogeny Estimation from Multiple Loci

(2009) E. Mossel et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Fast and Consistent Estimation of Species Trees Using Supermatrix Rooted Triples

(2009) Michael DeGiorgio et al.   MOLECULAR BIOLOGY AND EVOLUTION

Bayesian Inference of Species Trees from Multilocus Data

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

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

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

Properties of Consensus Methods for Inferring Species Trees from Gene Trees

(2009) James H. Degnan et al.   SYSTEMATIC BIOLOGY

Estimating Species Phylogenies Using Coalescence Times among Sequences

(2009) Liang Liu et al.   SYSTEMATIC BIOLOGY

Gene tree discordance, phylogenetic inference and the multispecies coalescent

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

Species Tree Inference by Minimizing Deep Coalescences

(2009) Cuong Than et al.   PLoS Computational Biology

BEST: Bayesian estimation of species trees under the coalescent model

(2008) L. Liu   BIOINFORMATICS

IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING?

(2008) Scott V. Edwards   EVOLUTION

Calculating Bootstrap Probabilities of Phylogeny Using Multilocus Sequence Data

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