StarBEAST2 Brings Faster Species Tree Inference and Accurate Estimates of Substitution Rates

Efficient Bayesian species tree inference under the multispecies coalescent

(2017) Bruce Rannala et al.   SYSTEMATIC BIOLOGY

Challenges in Species Tree Estimation Under the Multispecies Coalescent Model

(2016) Bo Xu et al.   GENETICS

Algorithmic improvements to species delimitation and phylogeny estimation under the multispecies coalescent

(2016) Graham Jones   JOURNAL OF MATHEMATICAL BIOLOGY

The gene tree delusion

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

Convergence across a continent: adaptive diversification in a recent radiation of Australian lizards

(2016) Mozes P. K. Blom et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Gene Tree Discordance Causes Apparent Substitution Rate Variation

(2016) Fábio K. Mendes et al.   SYSTEMATIC BIOLOGY

Computational Performance and Statistical Accuracy of *BEAST and Comparisons with Other Methods

(2016) Huw A. Ogilvie et al.   SYSTEMATIC BIOLOGY

Challenges in Species Tree Estimation Under the Multispecies Coalescent Model

(2016) Bo Xu et al.   GENETICS

Estimating phylogenetic trees from genome-scale data

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

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

(2015) Siavash Mirarab et al.   BIOINFORMATICS

The BPP program for species tree estimation and species delimitation

(2015) Ziheng Yang   Current Zoology

When do species-tree and concatenated estimates disagree? An empirical analysis with higher-level scincid lizard phylogeny

(2015) Shea M. Lambert et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Genes with minimal phylogenetic information are problematic for coalescent analyses when gene tree estimation is biased

(2015) Zhenxiang Xi et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

(2015) L. Liu et al.   SCIENCE

The Challenges of Resolving a Rapid, Recent Radiation: Empirical and Simulated Phylogenomics of Philippine Shrews

(2015) Thomas C. Giarla et al.   SYSTEMATIC BIOLOGY

The BPP program for species tree estimation and species delimitation

(2015) Ziheng Yang   Current Zoology

Quartet Inference from SNP Data Under the Coalescent Model

(2014) Julia Chifman et al.   BIOINFORMATICS

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

BBCA: Improving the scalability of *BEAST using random binning

(2014) Théo Zimmermann et al.   BMC GENOMICS

ExaBayes: Massively Parallel Bayesian Tree Inference for the Whole-Genome Era

(2014) Andre J. Aberer et al.   MOLECULAR BIOLOGY AND EVOLUTION

Unguided Species Delimitation Using DNA Sequence Data from Multiple Loci

(2014) Z. Yang et al.   MOLECULAR BIOLOGY AND EVOLUTION

A comprehensive multilocus phylogeny of the Neotropical cotingas (Cotingidae, Aves) with a comparative evolutionary analysis of breeding system and plumage dimorphism and a revised phylogenetic classification

(2014) Jacob S. Berv et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Species tree estimation of North American chorus frogs (Hylidae: Pseudacris) with parallel tagged amplicon sequencing

(2014) Lisa N. Barrow et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

(2014) S. Mirarab et al.   SCIENCE

The Inference of Gene Trees with Species Trees

(2014) Gergely J. Szöllősi et al.   SYSTEMATIC BIOLOGY

Why does diversification slow down?

(2014) Daniel Moen et al.   TRENDS IN ECOLOGY & EVOLUTION

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

High-Throughput Genomic Data in Systematics and Phylogenetics

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

Looking for trees in the forest: summary tree from posterior samples

(2013) Joseph Heled et al.   BMC EVOLUTIONARY BIOLOGY

Selection-Driven Evolution of Sex-Biased Genes Is Consistent with Sexual Selection in Arabidopsis thaliana

(2013) Toni I. Gossmann et al.   MOLECULAR BIOLOGY AND EVOLUTION

Concatenation versus coalescence versus "concatalescence"

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

Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales

(2012) Brant C. Faircloth et al.   SYSTEMATIC BIOLOGY

The genome as a life-history character: why rate of molecular evolution varies between mammal species

(2011) L. Bromham   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Bayesian random local clocks, or one rate to rule them all

(2010) Alexei J Drummond et al.   BMC BIOLOGY

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

(2010) Liang Liu et al.   BMC EVOLUTIONARY BIOLOGY

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

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Bayesian Inference of Species Trees from Multilocus Data

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

Molecules, morphology, and ecology indicate a recent, amphibious ancestry for echidnas

(2009) M. J. Phillips et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

ESTIMATING SPECIES TREES USING MULTIPLE-ALLELE DNA SEQUENCE DATA

(2008) Liang Liu et al.   EVOLUTION

The conditioned reconstructed process

(2008) Tanja Gernhard   JOURNAL OF THEORETICAL BIOLOGY

A tutorial on adaptive MCMC

(2008) Christophe Andrieu et al.   STATISTICS AND COMPUTING