Rosenberg lab at Stanford University


CLUMPP version 1.1.2 is available as of June 5, 2009

CLUMPP is a program that deals with label switching and multimodality problems in population-genetic cluster analyses. CLUMPP permutes the clusters output by independent runs of clustering programs such as structure, so that they match up as closely as possible. The user has the option of choosing one of three algorithms for aligning replicates, with a tradeoff of speed and similarity to the optimal alignment. A program note describing CLUMPP was published in Bioinformatics 23: 1801-1806 (2007). [Example]

[Download software package (includes the manual)] (you will be directed first to a registration page and we would very much appreciate if you register)
[Download manual]
[Download software note (Bioinformatics 23: 1801-1806)]

To use the UNIX versions, unzip and untar the files in an appropriate directory using

gunzip filename.tar.gz; tar xvf filename.tar
where "filename.tar.gz" is the downloaded file. Winzip will unzip the Windows version. Run the program by typing
in UNIX or
from a Dos prompt in Windows. It will permute the matrices in the input file to produce as close an alignment as possible.

Please send comments or problems with CLUMPP to Mattias Jakobsson.

October 15, 2014 — Users of CLUMPP may also find Distruct and CLUMPAK of interest.

Software history

June 18, 2010 - upload of version 1.1.2b software for windows
June 6, 2009 - upload of version 1.1.2 manual and software
October 10, 2007 - upload of version 1.1.1 manual and software
May 1, 2007 - upload of version 1.1 manual and software
December 22, 2006 - upload of version 1.0 manual and software