2023

  1. Benoit Morel, Tom A. William, Alexandros Stamatakis, Gergely Szollosi: "AleRax: A tool for gene and species tree co-estimation and reconciliation under a probabilistic model of gene duplication, transfer and loss." BioRxiv preprint, 2023.
  2. Julia Haag, Lukas Hübner, Alexey M. Kozlov, Alexandros Stamatakis: "The Free Lunch is not over yet—systematic exploration of numerical thresholds in maximum likelihood phylogenetic inference." Bioinformatics Advances 3, no. 1 (2023): vbad124.
  3. Anastasis Togkousidis, Olga Chernomor, Alexandros Stamatakis: "Parallel Inference of Phylogenetic Stands with Gentrius", 2023 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW). IEEE, 2023.
  4. Tom A. Williams, Adrian A. Davin, Benoit Morel, Lenard L. Szantho, Anja Spang, Alexandros Stamatakis, Philip Hugenholtz, Gergely J. Szollosi: "Parameter estimation and species tree rooting using ALE and GeneRax" PDF, Genome Biology and Evolution, evad134, 2023.
  5. Johanna Trost, Julia Haag, Dimitri Hoehler, Luca Nesterenko, Laurent Jacob, Alexandros Stamatakis, Bastien Boussau: "Simulations of sequence evolution: how (un)realistic they really are and why", biorXiv preprint, 2023.
  6. Anastasis Togkousidis, Alexey M. Kozlov, Julia Haag, Dimitri Höhler, Alexandros Stamatakis: "Adaptive RAxML-NG: Accelerating Phylogenetic inference under Maximum Likelihood using dataset difficulty", biorXiv preprint, 2023.
  7. Tom A. Williams, Adrian A. Davin, Benoit Morel, Lenard L. Szantho, Anja Spang, Alexandros Stamatakis, Philip Hugenholtz, Gergely J. Szollosi: "The power and limitations of species tree-aware phylogenetics", biorXiv preprint, 2023.
  8. Ben Bettisworth, Alexander I. Jordan, Alexandros Stamatakis: "Phylourny: efficiently calculating elimination tournament win probabilities via phylogenetic methods", open access, Statistics and Computing:33(80), 2023.