Network Biology

• Heinz and xHeinz are tools for single- and multi-species biological network module discovery. Availability: open source under the MIT license at GitHub (heinz) and GitHub (xheinz).  
• eXamine is a Cytoscape or standalone app for a set-oriented visual analysis approach for annotated modules that displays set membership as contours on top of a node-link layout. Availability: open source under the GPL at GitHub.  
• Natalie is a tool for restricted global pairwise network alignment. Availability: open source under the MIT license at GitHub.

Genomics

• WhatsHap is a software for haplotype assembly, that is, phasing genomic variants using DNA sequencing reads. It is especially suitable for long reads, but works also well with short reads. Availability: open source under the MIT license at BitBucket.

Trees and Clustering

• JRF compares two trees using the generalized Robinson-Foulds metric, a concept we developed. Availability: open source under the MIT license at GitHub. 
• yoshiko is a graph-based clustering tool and groups data points by solving the weighted cluster editing problem. Availability: open source under the MIT license at GitHub.

Other areas

• HuGS. Human-Guided Search (HuGS) is a framework for helping the computer solve computational problems by human interaction. The code was developed around the year 2001 by Neal Lesh, Gunnar Klau, Michael Mitzenmacher and Joe Marks while the authors were at MERL, Cambridge (MA). Availability: open source under the MIT license at GitHub.