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clustalo 0.1

Python wrapper around libclustalo

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

Homebrew (might) be still on 1.1.0, so if on Mac you might need to build it yourself also. OpenMP isn't available for clang, so you can either install gcc:

brew tap homebrew/versions
brew install gcc48

or just install without it. Just know that num_threads won't do anything.

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.

 
File Type Py Version Uploaded on Size
clustalo-0.1.tar.gz (md5) Source 2013-12-14 2KB
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