PoMo: An Allele Frequency-Based Approach for Species Tree Estimation

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Linking Great Apes Genome Evolution across Time Scales Using Polymorphism-Aware Phylogenetic Models

(2013) Nicola De Maio et al.   MOLECULAR BIOLOGY AND EVOLUTION

Great ape genetic diversity and population history

(2013) Javier Prado-Martinez et al.   NATURE

Unified modeling of gene duplication, loss, and coalescence using a locus tree

(2012) M. D. Rasmussen et al.   GENOME RESEARCH

Genome-scale coestimation of species and gene trees

(2012) B. Boussau et al.   GENOME RESEARCH

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

(2012) Alexei J. Drummond et al.   MOLECULAR BIOLOGY AND EVOLUTION

Inferring Species Trees Directly from Biallelic Genetic Markers: Bypassing Gene Trees in a Full Coalescent Analysis

(2012) David Bryant et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

Is Recombination a Problem for Species-Tree Analyses?

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

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

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

(2011) Yufeng Wu   EVOLUTION

Estimating species trees using approximate Bayesian computation

(2011) Helen Hang Fan et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

PoPoolation: A Toolbox for Population Genetic Analysis of Next Generation Sequencing Data from Pooled Individuals

(2011) Robert Kofler et al.   PLoS One

MSMS: a coalescent simulation program including recombination, demographic structure and selection at a single locus

(2010) Gregory Ewing et al.   BIOINFORMATICS

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

(2010) Bret R. Larget et al.   BIOINFORMATICS

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

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

(2010) Liang Liu et al.   BMC EVOLUTIONARY BIOLOGY

Composite likelihood-based inferences on genetic data from dependent loci

(2010) Arindam RoyChoudhury   JOURNAL OF MATHEMATICAL BIOLOGY

Reconstructing Population Histories from Single Nucleotide Polymorphism Data

(2010) J. Siren et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

Ancestral Population Genomics: The Coalescent Hidden Markov Model Approach

(2009) J. Y. Dutheil et al.   GENETICS

Incomplete Lineage Sorting: Consistent Phylogeny Estimation from Multiple Loci

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

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

Estimating Species Trees: Methods of Phylogenetic Analysis When There Is Incongruence across Genes

(2009) L. Lacey Knowles   SYSTEMATIC BIOLOGY

Maximum Likelihood Estimates of Species Trees: How Accuracy of Phylogenetic Inference Depends upon the Divergence History and Sampling Design

(2009) John E. McCormack 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

Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data

(2009) Ryan N. Gutenkunst et al.   PLoS Genetics

ESTIMATING SPECIES TREES USING MULTIPLE-ALLELE DNA SEQUENCE DATA

(2008) Liang Liu et al.   EVOLUTION

IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING?

(2008) Scott V. Edwards   EVOLUTION

A Two-Stage Pruning Algorithm for Likelihood Computation for a Population Tree

(2008) A. RoyChoudhury et al.   GENETICS