Are you looking for existing software that does different kinds of 
hierarchical clustering? (different ways of deciding which pair of cases 
to combine.)
SPSS,  SAS, Visual Numerics, NTCLUST, PYTHON SCILIB, etc., etc.  already 
have a wide variety of approaches.
There are also many single algorithm programs.

Are you looking for algorithms that you can implement in new software?

go to www.spss.com/support
click <login to online tech support> (left pane)
click <login> (main pane)
login as "guest" password "guest"  click "ok"
click <statistics documentation> (left pane)
click <algorithms> (main pane)
click <proximities>  to see how a few dozen proximity/distance 
coefficients can be created.
click <cluster>  to see about several kinds of hierarchical clustering
click <TWOSTEP> to see about a nonhierarchical method
click <quick cluster> to see about  k-means clustering.  This is a much 
older method than TWOSTEP.

Hope this helps.  If it does not meet your needs, please give more 
detail about what you woud like to do.

Art Kendall
Social Research Consultants

Kejun (Kevin) Mei wrote:

>Can someone please tell me a clustering method that use
>a distance matrix as input? I tried implementing the Ward
>method, but found the final clusters are not so good in my
>application, when I trace how clusters are grouped and
>how cluster centers are updated. I am seeking an improved
>version of the Ward method, or any others.
>
>Thank you so much and have a great weekend.
>
>-Kevin
>
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