| What: | tclcluspack: tcl extension to compute a clustering given a set of protein sequences or a set of points in a n dimensional space. |
| Where: | http://www.lbgi.fr/~moumou/TclTk/ |
| Description: | Tcl binding to the ClusPack program developped by N. Wicker. Several clustering methods are implemented (kmeans, mixture model, hierarchic) and several methods to determine the number of groups (secator, DPC, AIC, BIC). |
| Updated: | 11/2014 |
| Contact: | luc.moulinier at unistra.fr |
This extension creates a new clustering out of the data returning a list of clusters, each cluster being a list containing the index of the elements constituting the cluster in sorted order.
The data may be of two types: a list of protein sequences, or a list of points in an n-dimensional space (for example :
set dataList {{x00 x01 x02 x03 x04} {x10 x11 x12 x13 x14} ... {xn0 xn1 xn2 xn3 xn4}}Be aware that data should be the first parameter after the tclcluspack command.
The minimal form of the tclcluspack command is :
tclcluspack dataList -dt datatype -cm clustering_method' -nbc cluster_detection ?options?
Several options can control the clustering and the output, see documentation.
Documentation is available here : http://www.lbgi.fr/~moumou/TclTk/tclcluspack.html and the source code (and some binaries) either as a zip file (http://www.lbgi.fr/~moumou/TclTk/Downloads/tclcluspack0.1.zip ) or a tar-gzipped (http://www.lbgi.fr/~moumou/TclTk/Downloads/tclcluspack0.1.tar.gz )
Density of points clustering, application to transcriptomic data analysis. Wicker N, Dembele D, Raffelsberger W, Poch O. Nucleic Acids Res. 2002 Sep 15;30(18):3992-4000
Secator: a program for inferring protein subfamilies from phylogenetic trees. Wicker N, Perrin GR, Thierry JC, Poch O. Mol Biol Evol. 2001 Aug;18(8):1435-41.