BiNA: a visual analytics tool for biological network data. by Andreas Gerasch, Daniel Faber, Jan Küntzer, Peter Niermann, Oliver Kohlbacher, Hans-Peter Lenhof, Michael Kaufmann

“…BiNA is available under the 3-clause BSD license at http://bina.unipax.info/.…”
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Exploring neighborhoods in large metagenome assembly graphs using spacegraphcats reveals hidden sequence diversity by C. Titus Brown, Dominik Moritz, Michael P. O’Brien, Felix Reidl, Taylor Reiter, Blair D. Sullivan

“…Our software implementation is available at https://github.com/spacegraphcats/spacegraphcats under the 3-Clause BSD License.…”
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AutoClassWeb: a simple web interface for Bayesian clustering of omics data by Pierre Poulain, Jean-Michel Camadro

“…AutoClassWeb is implemented in Python and is published under the 3-Clauses BSD license. The source code is available at https://github.com/pierrepo/autoclassweb along with a detailed documentation.…”
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sbml-diff: A tool for visually comparing SBML models in synthetic biology. by Scott-Brown, J, Papachristodoulou, A

“…An abstract view represents species as ellipses and draws edges between them to indicate whether a species increases or decreases the production or degradation of another species. sbml-diff is freely licensed under the three-clause BSD license and can be downloaded from https://github.com/jamesscottbrown/sbml-diff and used as a python package called from other software, as a free-standing command-line application, or online using the form at http://sysos.eng.ox.ac.uk/tebio/upload.…”