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

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

(2018) F. Lemoine et al.   NATURE

EPA-ng: Massively Parallel Evolutionary Placement of Genetic Sequences

(2018) Pierre Barbera et al.   SYSTEMATIC BIOLOGY

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

(2017) Xiaofan Zhou et al.   MOLECULAR BIOLOGY AND EVOLUTION

ExaML version 3: a tool for phylogenomic analyses on supercomputers

(2015) Alexey M. Kozlov et al.   BIOINFORMATICS

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

Modeling Protein Evolution with Several Amino Acid Replacement Matrices Depending on Site Rates

(2012) S. Q. Le et al.   MOLECULAR BIOLOGY AND EVOLUTION

Terraces in Phylogenetic Tree Space

(2011) M. J. Sanderson et al.   SCIENCE

Using Non-Reversible Context-Dependent Evolutionary Models to Study Substitution Patterns in Primate Non-Coding Sequences

(2010) Guy Baele et al.   JOURNAL OF MOLECULAR EVOLUTION

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

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

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Empirical profile mixture models for phylogenetic reconstruction

(2008) Le Si Quang et al.   BIOINFORMATICS