I’ve posted a script and a basic readme here which allows users of the python bioinformatics toolkit PyCogent to run intermolecular coevolutionary analyses using PyCogent’s built-in coevolution module.
PyCogent’s coevolution module supports several tree-aware and tree-ignorant methods for identifying pairs of coevolving pairs within and between biological sequences. Additionally it contains support for pre- and post-processing coevolution input and results, such as recoding multiple sequence alignments with reduced-state amino acid alphabets. The script included in PyCogent supports intramolecular coevolutionary analysis, while this new script supports intermolecular coevolutionary analysis.
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