This folder contains the code that was used to measure the runtimes of 
* CDK/Round Robin algorithm (Dührkop et al., 2013)
* PFG (Zhang et al., 2016)
* HR2 (Kind and Fiehn, 2007)

PFG sources were downloaded from https://github.com/zmzhang/PFG

HR2 sources were downloaded from http://fiehnlab.ucdavis.edu/projects/Seven_Golden_Rules/Software/ and modified to remove all filtering rules.

To run the evaluation: 

1) Compile the programs by running 'make' in the CDK, PFG, and HR2 folders.

2) Run ./measure_all.sh

Tested on Ubuntu Linux.

