The performance of coalescent-based species tree estimation methods under models of missing data

Species Tree Inference from Gene Splits by Unrooted STAR Methods

(2018) Elizabeth S. Allman et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

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

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

Bad Clade Deletion Supertrees: A Fast and Accurate Supertree Algorithm

(2017) Markus Fleischauer et al.   MOLECULAR BIOLOGY AND EVOLUTION

FastRFS: fast and accurate Robinson-Foulds Supertrees using constrained exact optimization

(2016) Pranjal Vachaspati 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

ASTRID: Accurate Species TRees from Internode Distances

(2015) Pranjal Vachaspati et al.   BMC GENOMICS

Data Requirement for Phylogenetic Inference from Multiple Loci: A New Distance Method

(2015) Gautam Dasarathy et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

The Impact of Missing Data on Species Tree Estimation

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

Avoiding Missing Data Biases in Phylogenomic Inference: An Empirical Study in the Landfowl (Aves: Galliformes)

(2015) Peter A. Hosner et al.   MOLECULAR BIOLOGY AND EVOLUTION

FastME 2.0: A Comprehensive, Accurate, and Fast Distance-Based Phylogeny Inference Program: Table 1.

(2015) Vincent Lefort et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

(2015) Sebastien Roch et al.   SYSTEMATIC BIOLOGY

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

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

Effects of missing data on species tree estimation under the coalescent

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

MRL and SuperFine+MRL: new supertree methods

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

iGLASS: An Improvement to the GLASS Method for Estimating Species Trees from Gene Trees

(2012) Ethan M. Jewett et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

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

Fast and accurate methods for phylogenomic analyses

(2011) Jimmy Yang et al.   BMC BIOINFORMATICS

Estimating Species Trees from Unrooted Gene Trees

(2011) Liang Liu et al.   SYSTEMATIC BIOLOGY

SuperFine: Fast and Accurate Supertree Estimation

(2011) M. Shel Swenson et al.   SYSTEMATIC BIOLOGY

A simulation study comparing supertree and combined analysis methods using SMIDGen

(2010) M Shel Swenson et al.   Algorithms for Molecular 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

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

(2009) Laura S. Kubatko et al.   BIOINFORMATICS

Consistency of Topological Moves Based on the Balanced Minimum Evolution Principle of Phylogenetic Inference

(2009) M. Bordewich et al.   IEEE-ACM Transactions on Computational Biology and 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

Estimating Species Phylogenies Using Coalescence Times among Sequences

(2009) Liang Liu et al.   SYSTEMATIC 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