MSPKmerCounter is implemented in Java and thus can run on both Linux and Windows platforms.


MSPKmerCounter is a k-mer counter based on the minimum substring partitioning technique. It can count the appearances of k-mers in a fast and memory-efficient manner. MSPCounter is a command-line program that reads DNA sequences in FASTA format. It outputs the k-mer counts in binary format, which can be converted into the readable text format using the "Dump" command. Please refer to the manual below for more details.

Download MSPKmerCounter

Latest stable release (0.10.0): executable package source code
manual-MSPKmerCounter-0.10.0.pdf manual

Usage agreement

Downloading is for internal research purpose only. Redistribution and commercial usage are not permitted. For other interests, contact the authors.