Skip to main content
This is a pre-production deployment of Warehouse. Changes made here affect the production instance of PyPI (
Help us improve Python packaging - Donate today!

Python wrapper around libclustalo

Project Description

This is just a simple Python wrapper around Clustal Omega (, used internally at Benchling but casually open source, if it helps anybody. Also available via:

pip install clustalo

Requires libclustalo installed, version 1.2.0. On Linux, it’s recommended you build and install it yourself:

cd clustal-omega-1.2.0
./configure --with-pic --with-openmp
make && sudo make install

before installing this package.

Support for OSX is not quite there yet, mainly because OpenMP isn’t supported on clang. Homebrew is still on 1.1.0, so you’ll need to compile and install clustalo 1.2.0 yourself (–without-openmp). You’ll also need to modify the file to leave out gomp and -fopenmp when installing.


from clustalo import clustalo
input = {
    'seq1': 'AAATCGGAAA',
    'seq2': 'CGGA'
aligned = clustalo(input)
# aligned is a dict of aligned sequences:
#   seq1: AAATCGGAAA
#   seq2: ----CGGA--

At the moment, input sequences are assumed to not be aligned (i.e. there is no dealign option). See clustalo.clustalo.__doc__ or file clustaslo/clustalo.c for documentation.

Release History

This version
History Node


History Node


Download Files

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

Filename, Size & Hash SHA256 Hash Help File Type Python Version Upload Date
(260.0 kB) Copy SHA256 Hash SHA256
Dumb Binary 2.7 Jul 23, 2014
(3.0 kB) Copy SHA256 Hash SHA256
Source None Jul 23, 2014

Supported By

Elastic Elastic Search Pingdom Pingdom Monitoring Dyn Dyn DNS Sentry Sentry Error Logging CloudAMQP CloudAMQP RabbitMQ Kabu Creative Kabu Creative UX & Design Google Google Cloud Servers Fastly Fastly CDN StatusPage StatusPage Statuspage DigiCert DigiCert EV Certificate