Skip to main content

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.

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 clustalo, version 0.1.1
Filename, size File type Python version Upload date Hashes
Filename, size clustalo-0.1.1.macosx-10.9-x86_64.tar.gz (260.0 kB) File type Dumb Binary Python version 2.7 Upload date Hashes View
Filename, size clustalo-0.1.1.tar.gz (3.0 kB) File type Source Python version None Upload date Hashes View

Supported by

Pingdom Pingdom Monitoring Google Google Object Storage and Download Analytics Sentry Sentry Error logging AWS AWS Cloud computing DataDog DataDog Monitoring Fastly Fastly CDN DigiCert DigiCert EV certificate StatusPage StatusPage Status page