Skip to main content
Join the official 2019 Python Developers SurveyStart the survey!

Scoring Multiple Sequence Alignments with Python

Project description

<p align="center">
<img src=resources/pymsa.png alt="pyMSA">

# 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.

## Features
The scores that are currently available are:
* Sum of pairs,
* Star,
* Minimum entropy,
* Percentage of non-gaps,
* Percentage of totally conserved columns *and*
* STRIKE (**S**ingle s**TR**ucture **I**nduced **E**valuation).

## Downloading
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

### STRIKE score
For computing the [STRIKE]( score,
the tool (v1.2) must be installed on the `usr/local/bin` folder.

*e.g.* After compiling run:

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

### Substitution matrices

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 the `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')

## Usage
An example of running all the included scores is located in the [`example`](example/) folder.

## Authors
### Active development team
* Antonio Benítez-Hidalgo <>
* Antonio J. Nebro <>

## License
This project is licensed under the terms of the MIT - see the [LICENSE](LICENSE) file for details.

Project details

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Files for pyMSA, version 0.5.1
Filename, size File type Python version Upload date Hashes
Filename, size pyMSA-0.5.1-py3-none-any.whl (12.4 kB) File type Wheel Python version py3 Upload date Hashes View hashes
Filename, size pyMSA-0.5.1.tar.gz (11.3 kB) File type Source Python version None Upload date Hashes View hashes

Supported by

Elastic Elastic Search Pingdom Pingdom Monitoring Google Google BigQuery Sentry Sentry Error logging AWS AWS Cloud computing DataDog DataDog Monitoring Fastly Fastly CDN SignalFx SignalFx Supporter DigiCert DigiCert EV certificate StatusPage StatusPage Status page