ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees

Species tree estimation using ASTRAL: how many genes are enough?

(2017) Shubhanshu Shekhar et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Contentious relationships in phylogenomic studies can be driven by a handful of genes

(2017) Xing-Xing Shen et al.   Nature Ecology & Evolution

Anchoring quartet-based phylogenetic distances and applications to species tree reconstruction

(2016) Erfan Sayyari et al.   BMC GENOMICS

The Interrelationships of Placental Mammals and the Limits of Phylogenetic Inference

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

Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies

(2016) Erfan Sayyari et al.   MOLECULAR BIOLOGY AND EVOLUTION

Implementing and testing the multispecies coalescent model: A valuable paradigm for phylogenomics

(2016) Scott V. Edwards et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The gene tree delusion

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

Analysis of a Rapid Evolutionary Radiation Using Ultraconserved Elements: Evidence for a Bias in Some Multispecies Coalescent Methods

(2016) Kelly A. Meiklejohn et al.   SYSTEMATIC BIOLOGY

ExaML version 3: a tool for phylogenomic analyses on supercomputers

(2015) Alexey M. Kozlov et al.   BIOINFORMATICS

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

(2015) Siavash Mirarab et al.   BIOINFORMATICS

Phylogenomic species tree estimation in the presence of incomplete lineage sorting and horizontal gene transfer

(2015) Ruth Davidson et al.   BMC GENOMICS

ASTRID: Accurate Species TRees from Internode Distances

(2015) Pranjal Vachaspati et al.   BMC GENOMICS

On the Robustness to Gene Tree Estimation Error (or lack thereof) of Coalescent-Based Species Tree Methods

(2015) Sebastien Roch et al.   SYSTEMATIC BIOLOGY

SimPhy: Phylogenomic Simulation of Gene, Locus, and Species Trees

(2015) Diego Mallo et al.   SYSTEMATIC BIOLOGY

Nuclear genomic signals of the ‘microturbellarian’ roots of platyhelminth evolutionary innovation

(2015) Christopher E Laumer et al.   eLife

Weighted Statistical Binning: Enabling Statistically Consistent Genome-Scale Phylogenetic Analyses

(2015) Md Shamsuzzoha Bayzid et al.   PLoS One

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

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

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

Statistical binning enables an accurate coalescent-based estimation of the avian tree

(2014) S. Mirarab et al.   SCIENCE

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

(2014) E. D. Jarvis et al.   SCIENCE

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

(2014) Siavash Mirarab et al.   SYSTEMATIC BIOLOGY

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

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

Determining species tree topologies from clade probabilities under the coalescent

(2011) Elizabeth S. Allman et al.   JOURNAL OF THEORETICAL BIOLOGY

Estimating Species Trees from Unrooted Gene Trees

(2011) Liang Liu et al.   SYSTEMATIC BIOLOGY

The Newick utilities: high-throughput phylogenetic tree processing in the UNIX shell

(2010) T. Junier et al.   BIOINFORMATICS

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

(2010) Liang Liu et al.   BMC EVOLUTIONARY BIOLOGY

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Incomplete Lineage Sorting: Consistent Phylogeny Estimation from Multiple Loci

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

INDELible: A Flexible Simulator of Biological Sequence Evolution

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

Bayesian Inference of Species Trees from Multilocus Data

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

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

IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING?

(2008) Scott V. Edwards   EVOLUTION