ParGenes¶

Description¶

A massively parallel tool for model selection and tree inference on thousands of genes

Run module spider pargenes to find out what environment modules are available for this application.

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

phylogenetics