Scoring Multiple Sequence Alignments with Python
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,
- 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 https://github.com/ajnebro/pyMSA.git $ python setup.py 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
Last changes (July 2017)
pyMSAScoringproject is now renamed to
- 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
- 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.