It is now possible to run Cluster 3.0 as a command line program. This may be useful if you want to run Cluster 3.0 on a remote server, and also allows automatic processing a large number of data files by running a batch script. Note, however, that the Python and Perl interfaces to the C Clustering Library are much better suited for this task and more powerful than the command line program (see the manual for the C Clustering Library at http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/cluster.pdf).
The installation process of the command line version of Cluster 3.0 is straightforward; it compiled out of the box on Cygwin, Mac OS X, Linux, and Unix. To install, download the source code from http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster, and run
configure --without-x
make
make install
The executable is called cluster
. To run this program, execute
cluster [options]
in which the options consist of the following command line parameters:
-f
filename-l
-cg a|m
a
: Subtract the mean of each row m
: Subtract the median of each row -ng
-ca a|m
a
: Subtract the mean of each column m
: Subtract the median of each column -na
-u
jobname-g [0..9]
-e [0..9]
-m [msca]
m
: Pairwise complete- (maximum-) linkage (default) s
: Pairwise single-linkage c
: Pairwise centroid-linkage a
: Pairwise average-linkage
-k
number-s
-x
number-y
number-v, --version
-h, --help
For the command line options -g, -e, the following integers can be used to specify the distance measure:
0
1
2
3
4
5
6
7
8