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To run Incremental Mitosis, please type the following in the command line:
Java -jar incrementalMitosis.jar [f] [k] [inputFilename] [patternNumber] [distanceMethod(euclidean,cosine,pearson,KLD,jaccard)] [outlierHandlingUsage(0,1)] [outputFile] [draw(0,1)]

For example:
Java -jar incrementalMitosis.jar 2.25 2.6 t7.10k.dat 10000 euclidean 1 t7.10k-outputFile.txt 1
Java -jar incrementalMitosis.jar 2.15 2.5 t8.8k.dat 8000 euclidean 1 t8.8k-outputFile.txt 1

Where inputFilename contains the patterns to cluster. Each line represents a pattern and the pattern's features are separated by white spaces. The outputFile contains the output where each line represents a pattern and at the end of the line is the cluster id that this pattern belongs to. Also, if you choose to draw the results, you can see the visualization of the clusters.
Please check the sample run in the Release folder.