clustalo 0.1.1

This is just a simple Python wrapper around Clustal Omega (http://www.clustal.org/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 setup.py file to leave out gomp and -fopenmp when installing.

Usage

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.