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 set OPENMP_DISABLED=true in env vars before running build/install.
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.
Update setup.py to the new desired version number.
Run make upload to build and upload to PyPI.