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Welcome to the PyPythia wiki!

Pythia is a lightweight python library to predict the difficulty of Multiple Sequence Alignments (MSAs).

Documentation

• Installation
  • Requirements
  • Install using pip
  • Install from source
  • Troubleshooting
• Usage
  • Command Line Tool
  • From Code
  • Usage without installation
  • Input data
  • Predictors

C Library

The same functionality is also available as C library here. Since the C library depends on Coraxlib it is not as easy and fast to use as this python library. If you are only interested in the difficulty of your MSA, we recommend using this Python library. If you want to incorporate the difficulty prediction in a phylogenetic tool, we recommend using the faster C library.

Support

If you encounter any trouble using Pythia, have a question, or you find a bug, please feel free to open an issue here.

Publication

The paper explaining the details of Pythia is published in MBE:
Haag, J., Höhler, D., Bettisworth, B., & Stamatakis, A. (2022). From Easy to Hopeless - Predicting the Difficulty of Phylogenetic Analyses. Molecular Biology and Evolution, 39(12). https://doi.org/10.1093/molbev/msac254

References

• A. M. Kozlov, D. Darriba, T. Flouri, B. Morel, and A. Stamatakis (2019) RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference Bioinformatics, 35(21): 4453–4455. https://doi.org/10.1093/bioinformatics/btz305

• D. Höhler, W. Pfeiffer, V. Ioannidis, H. Stockinger, A. Stamatakis (2022) RAxML Grove: an empirical phylogenetic tree database Bioinformatics, 38(6):1741–1742. https://doi.org/10.1093/bioinformatics/btab863