Bad Clade Deletion (BCD) Supertrees is a java library and command line tool providing the bad character deletion supertree algorithm for rooted input trees. It provides several strategies to weight the character that have to be removed during the mincut phase. BCD Supertrees can use the Greedy Strict Consensus Merger (GSCM) algorithm to preprocess the input trees.
PEACE (Parameterized and Exact Algorithms for Cluster Editing) is a project for clustering experimental data using a weighted graph derived from pairwise similarity information.