Weighted ASTRID: fast and accurate species trees from weighted internode distances

Weighting by Gene Tree Uncertainty Improves Accuracy of Quartet-based Species Trees

(2022) Chao Zhang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Species tree estimation under joint modeling of coalescence and duplication: Sample complexity of quartet methods

(2022) Max Hill et al.   ANNALS OF APPLIED PROBABILITY

FASTRAL: Improving scalability of phylogenomic analysis

(2021) Payam Dibaeinia et al.   BIOINFORMATICS

Quartet-based inference is statistically consistent under the unified duplication-loss-coalescence model

(2021) Alexey Markin et al.   BIOINFORMATICS

wQFM: highly accurate genome-scale species tree estimation from weighted quartets

(2021) Mahim Mahbub et al.   BIOINFORMATICS

Bayesian-Weighted Triplet and Quartet Methods for Species Tree Inference

(2021) Andrew Richards et al.   BULLETIN OF MATHEMATICAL BIOLOGY

DISCO: Species Tree Inference using Multi-Copy gene family Tree Decomposition

(2021) James Willson et al.   SYSTEMATIC BIOLOGY

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

(2020) Bui Quang Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference

(2019) Alexey M Kozlov et al.   BIOINFORMATICS

Statistically consistent divide-and-conquer pipelines for phylogeny estimation using NJMerge

(2019) Erin K. Molloy et al.   Algorithms for Molecular Biology

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

(2018) Chao Zhang et al.   BMC BIOINFORMATICS

Species Tree Inference from Gene Splits by Unrooted STAR Methods

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

Renewing Felsenstein’s phylogenetic bootstrap in the era of big data

(2018) F. Lemoine et al.   NATURE

Long-branch attraction in species tree estimation: inconsistency of partitioned likelihood and topology-based summary methods

(2018) Sebastien Roch et al.   SYSTEMATIC BIOLOGY

UFBoot2: Improving the Ultrafast Bootstrap Approximation

(2017) Diep Thi Hoang et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2017) Huw A. Ogilvie et al.   MOLECULAR BIOLOGY AND EVOLUTION

To Include or Not to Include: The Impact of Gene Filtering on Species Tree Estimation Methods

(2017) Erin K Molloy et al.   SYSTEMATIC BIOLOGY

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

(2016) Pranjal Vachaspati et al.   BIOINFORMATICS

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

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

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

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

(2015) Vincent Lefort et al.   MOLECULAR BIOLOGY 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

Likelihood-based tree reconstruction on a concatenation of aligned sequence data sets can be statistically inconsistent

(2015) Sebastien Roch et al.   THEORETICAL POPULATION BIOLOGY

Phylogenomic analyses data of the avian phylogenomics project

(2015) Erich D Jarvis et al.   GigaScience

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

(2015) Md Shamsuzzoha Bayzid et al.   PLoS One

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

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

Accuracy Guarantees for Phylogeny Reconstruction Algorithms Based on Balanced Minimum Evolution

(2013) Magnus Bordewich et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Approximating the balanced minimum evolution problem

(2011) Samuel Fiorini et al.   OPERATIONS RESEARCH LETTERS

Survey of Branch Support Methods Demonstrates Accuracy, Power, and Robustness of Fast Likelihood-based Approximation Schemes

(2011) Maria Anisimova et al.   SYSTEMATIC BIOLOGY

Estimating Species Trees from Unrooted Gene Trees

(2011) Liang Liu et al.   SYSTEMATIC BIOLOGY

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

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

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

Fast NJ-like algorithms to deal with incomplete distance matrices

(2008) Alexis Criscuolo et al.   BMC BIOINFORMATICS

Branch Lengths, Support, and Congruence: Testing the Phylogenomic Approach with 20 Nuclear Loci in Snakes

(2008) John J. Wiens et al.   SYSTEMATIC BIOLOGY

A Rapid Bootstrap Algorithm for the RAxML Web Servers

(2008) Alexandros Stamatakis et al.   SYSTEMATIC BIOLOGY