Subject: summary of dendrogram software

From: Doree F Sitkoff <[email-masked]>
Date: Wed, 25 Apr 2001 19:45:46 -0400

All -

Thanks for your input and sorry for the delay in posting the
summary.

-Doree

Original question:
Does anyone know of software (PC or UNIX-based) that can take a
distance matrix as input, perform clustering and display back
results as a dendrogram - of high enough quality that it could be
used for poster or publication purposes?

I have investigated SAS/JMP however it appears that it cannot
take a distance matrix as input - it must calculate the matrix
within the program.

MINITAB does appear to be able to do this, however I am wondering
what other options we might have.

Thanks,
-Doree

> From Egon Willighagen ([email-masked]):
Have a look at R, an OpenSource version of S, a statistical
program. I use it to do just the thing you're asking for... You
can download the software from www.r-project.org and use the
hclust function.

> From Gerd Raether ([email-masked])
Xcluster can do a Mosaic and Map display in postscript format and
write out customized cluster-data. Information you will find at
http://www.schrodinger.com/MacroModel/completdes.html#xcluster
For more information please contact [email-masked]
(Europe) or [email-masked].
    (Note from Doree: The display is not so "pretty"...)

> From Peter Shenkin ([email-masked]):
Yes -- XCluster, (part of MacroModel). We print out something we
call the "clustering map" which contains the same info as the
dendrogram, but in a different format. (In geometric terms, I
believe it's the "dual".)  The "Dfile" method of XCluster takes
the distance matrix from a file, rather than computing it from an
ensemble of conformations. In this way, it can be used on
arbitrary preprocessed data.

> From Susan Atlas ([email-masked]):
We have used Matlab to do this but I would be interested in
hearing about any other options you find out about.

In addition, during informal discussions several people have
suggested investigating gene expression array software.