Scoring Multiple Sequence Alignments with Python

Build Status PyPI License PyPI Python version

pyMSA is an open source software tool aimed at providing a number of scores for multiple sequence alignment (MSA) problems. A tutorial about pyMSA is available in the resources folder of the proyect.


Score functions implemented:

  • Sum of pairs,
  • Star,
  • Minimum entropy,
  • Percentage of non-gaps,
  • Percentage of totally conserved columns and
  • STRIKE (Single sTRucture Induced Evaluation).


To download PyMSA just clone the Git repository hosted in GitHub:

$ git clone
$ python install

Alternatively, you can install it with pip:

$ pip install pyMSA


An example of running all the included scores is located in the example folder.

Terminal session


Active development team


This project is licensed under the terms of the MIT - see the LICENSE file for details.


Scoring multiple sequence alignments with Python

Pymsa Info

⭐ Stars 13
🔗 Source Code
🕒 Last Update 7 months ago
🕒 Created 5 years ago
🐞 Open Issues 3
➗ Star-Issue Ratio 4
😎 Author benhid