Very Fast Tree: speeding up the estimation of phylogenies for large alignments through parallelization and vectorization strategies

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

Lam-Tung Nguyen, Heiko A. Schmidt, Arndt von Haeseler et al. · Molecular Biology and Evolution · 2014 · 25.9K citations · Full text

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

Stéphane Guindon, Jean-François Dufayard, Vincent Lefort et al. · Systematic Biology · 2010 · 18.4K citations · Full text

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

Morgan N. Price, Paramvir Dehal, Adam P. Arkin · PLoS ONE · 2010 · 15.1K citations · Full text

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

Alexey M. Kozlov, Diego Darriba, Tomáš Flouri et al. · Bioinformatics · 2019 · 4.2K citations · Full text

Evaluating Fast Maximum Likelihood-Based Phylogenetic Programs Using Empirical Phylogenomic Data Sets

Xiaofan Zhou, Xing‐Xing Shen, Chris Todd Hittinger et al. · Molecular Biology and Evolution · 2017 · 172 citations · Full text

Genetics, Genomics, Sequence Alignment +17