The Tree Snipping algorithms

were designed to improve the biological significance of the clusters produced by hierarchical clustering.
These algorithms partition the hierarchical-tree by snipping: cutting selected edges at variable levels.
[Bioinformatics, 2007]

A zip file with the java package implementing the two algorithms is available here. Please download and extract.
Windows: double click the RUNME file
Unix: run it with the command: java -jar Xmx500m TreeSnipping.jar

Some example files are available here, (given in the same order as requested by the program):

  • h-tree (hierarchical clustering dendrogram)
  • GO biological process annotations of the genes
  • mapping of leaves of the tree to genes
  • GO-terms descriptions

  • The format of the required input files is explained in help files accessible from the program pop-up.