You need Java (version 6.10 or above) installed on your machine in order to be able to run this executable.
>>java -jar neighborSearchApp.jar inputFile queryVertex size outputFile
inputFile: name of the input file, which specifies an undirected network in edge-list format. This file should list one edge (as a tab-delimited pair of vertices) per line. You may also specify a weight for each edge (as the third tab-delimited value).
queryVertex: name of the queried vertex, the names are not case-sensitive.
size: the number of closest neighbors.
outputFile: name of the output file. The closest nodes to the queried vertex will be written to this file (in order, one per line).
>>java -jar neighborSearchApp.jar twoHybridNetwork.txt YMR181C 50 myNeighbors.txt
Finds the 50 nodes closest to YMR181C in twoHybridNetwork.txt, writes these vertices (in order, one per line) to myCluster.txt.