Clustering tools / software

The spectra-cluster toolsuite currently contains four tools to cluster MS/MS based proteomics data:

• `Proteome Discoverer node`_: Proteome Discoverer node of the spectra-cluster algorithm
• spectra-cluster-cli: Command line version
• spectra-cluster-gui: Graphical user interface
• spectra-cluster-hadoop: Hadoop version

All of these tools use the spectra-cluster Java API to perform the actual clustering and should produce comparable results.

Our own development focuses on the spectra-cluster-cli tool. Therefore, this tool is always at the latest development stage.

Developing own algorithms

The spectra-cluster toolsuite provides several ready-to-use APIs that support the development of MS/MS clustering algorithms as well as own analaysis tools.

• clustering-file-reader: Java API to read the .clustering format
• spectra-cluster-py: Tools to analyse .clustering files as well as a Python API to process .clustering files

The spectra-cluster Java API contains the core clustering functionality used by the implementations of the spectra-cluster algorithm. To test the effect of a, for example, different spectrum similarity method it is only necessary to implement a single interface. This new code will then be fully compatible with all existing tools (for example the spectra-cluster-cli command-line interface) which allows the user to immediately test the new implementation.