Citation

If you publish research that uses pargenes you have to cite it as follows:

When using ParGenes, please cite

• Benoit Morel, Alexey M. Kozlov and Alexandros Stamatakis (2018) ParGenes: a tool for massively parallel model selection and phylogenetic tree inference on thousands of genes. Bioinformatics. https://doi.org/10.1093/bioinformatics/bty839
• Alexey M. Kozlov, Diego Darriba, Tomáš Flouri, Benoit Morel, and Alexandros Stamatakis (2019) RAxML-NG: A fast, scalable, and user-friendly tool for maximum likelihood phylogenetic inference. Bioinformatics 35:4453-4455. https://doi.org/10.1093/bioinformatics/btz305

When using model selection feature, please additionally cite ModelTest-NG:

• Diego Darriba, David Posada, Alexey M. Kozlov, Alexandros Stamatakis, Benoit Morel and Tomáš Flouri (2020) ModelTest-NG: a new and scalable tool for DNA and protein model selection. Molecular Biology and Evolution 37: msz189. https://doi.org/10.1093/molbev/msz189

When using ASTRAL III (astral.jar), please additionally cite:

• Chao Zhang, Maryam Rabiee, Erfan Sayyari, and Siavash Mirarab (2018) ASTRAL-III: Polynomial Time Species Tree Reconstruction from Partially Resolved Gene Trees. BMC Bioinformatics 19 (S6): 153. https://doi.org/10.1186/s12859-018-2129-y

When using ASTER (astral, astral-pro, or astral-hybrid), please additionally cite:

• Chao Zhang and Siavash Mirarab (2022) Weighting by Gene Tree Uncertainty Improves Accuracy of Quartet-based Species Trees. Molecular Biology and Evolution 39: msac215. https://doi.org/10.1093/molbev/msac215