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Scoring Multiple Sequence Alignments with Python

Build Status PyPI PyPI

PyMSA is an open source software tool aimed at providing a number of scores for multiple sequence alignment (MSA) problems. This project is a development of the students of the third course students of the degree on Bioinformatics of the E.T.S. de Ingeniería Informática of the University of Málaga.


The scores that are currently available are:

  • Sum of pairs,
  • Star,
  • Minimum entropy,
  • Percentage of non-gaps and
  • Percentage of totally conserved columns.


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

$ git clone
$ python install

Alternatively, you can install with pip:

$ pip install pyMSA


PyMSA has been developed with Python 3.6.0 :: Anaconda 4.3.0 (x86_64).

To install all dependencies use:

$ pip install -r requirements.txt


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


Last changes (July 2017)

  • pyMSAScoring project is now renamed to pyMSA!
  • All the scores are now computed using a list of sequences instead of a list of pairs.
  • Tests for Percentage of non-gaps added.


Active development team

Thanks to

  • Maria José Muñoz - Project Manager
  • Miguel Ángel Gallardo - Developer of the Star score
  • Daniel Torres - Developer of the Star code
  • René Betancor - Developer of the Sum of Pairs score
  • Pablo Rodríguez - Developer of the Entropy score
  • Guillermo López - Developer of the Entropy score
  • Juan Ignacio Álvarez - Developer of the of Non-Gaps score


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