pyMSA is an open source software tool aimed at providing a number of scores for multiple sequence alignment (MSA) problems.

The scores that are currently available are:

• 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 https://github.com/benhid/pyMSA.git
$ python setup.py install

Alternatively, you can install it with pip:

$ pip install pyMSA

For computing the STRIKE score, the package (v1.2) must be installed on the usr/local/bin folder.

e.g. After compiling run:

$ sudo cp bin/strike /usr/local/bin

pyMSA has only two available substitution matrices: PAM250 and Blosum62.

Other substitution matrices can be used by reading a matrix file with read_matrix_from_file() (from pymsa.util.substitution_matrix module).

FileMatrix implements this method by default:

from pymsa.core.substitution_matrix import PAM250, Blosum62, FileMatrix

pam250 = PAM250()
blosum62 = Blosum62()
pam380 = FileMatrix('PAM380.txt')

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

• Antonio Benítez-Hidalgo [email protected]
• Antonio J. Nebro [email protected]

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