Penalized and Weighted K-means Software Download Page

Cite the main reference paper if results obtained from this software are used in manuscripts:

George C. Tseng. (2007). Penalized and weighted K-means for clustering with scattered objects and prior information in high-throughput biological data. Bioinformatics. 23:2247-2255.

download ; This version contains C++ and C code and may not compile well in some Linux environment.

A more convenient variation in R package (penalized partition around medoids; PPAM) is available. Unlike the requirement of K-means to have data in Euclidean space, PPAM is more flexible to take any distance matrix.

Questions, bug reports and suggestions can be sent to Chi Song (

Some clustering routines in the C library are modified from a public clustering software by Michiel de Hoon.
M. J. L. de Hoon, S. Imoto, J. Nolan, and S. Miyano: Open Source Clustering Software. Bioinformatics, 20 (9): 1453--1454 (2004).