This repository contains the code used for evaluation of the methods decribed in:

K. Scheubert, F. Hufsky, and S. Böcker
Multiple mass spectrometry fragmentation trees revisited: boosting performance and quality
In Proc. of Workshop on Algorithms in Bioinformatics (WABI 2014), volume 8701 of Lect Notes Comput Sci, pages 217–231. Springer, Berlin, 2014
[DOI] [Preprint]

Java dependencies are managed with Gradle. Note: To use the ILP solvers the corresponding native libraries have to be configure appropriately.