CliXO Code, Version 0.3

CliXO algorithm implementation version 0.3 (doi: 10.1093/bioinformatics/btu282)

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Clique Extracted Ontologies (CliXO), Version 0.3

Author: Michael Kramer ( Trey Ideker lab, UCSD.
Release Date: 5/20/2015
CliXO release 0.3
Please cite: Kramer M, Dutkowski J, Yu M, Bafna V, Ideker T. Inferring gene ontologies from pairwise similarity data. Bioinformatics, 30: i34-i42. 2014. doi: 10.1093/bioinformatics/btu282

This code can be used to infer a directed, acyclic graph (DAG) / ontology from a set of pairwise similarity data. Please see for a full description of the CliXO algorithm implemented here.

Please feel free to contact the author with any questions, comments, or concerns.

Code for aligning two ontologies (such as the ontologies created by the CliXO algorithm) can be found here: