clustalo-python

This is just a simple Python wrapper around Clustal Omega (http://www.clustal.org/omega/), used internally at Benchling, then modified for easier building by Cyrus Biotechnology.

Support for OSX requires the libomp library, and automake from brew. You may install it via:

brew install libomp automake

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.