Dear friends I reformulate the question. I think I did not formulate it properly. I have some data on some sites. I can define a dissimilarity between each pair of sites. Using this dissimilarity, I have clustered the sites using the hclust algorithm, with method ward. I then obtain 48 clusters, by cutting the tree using cutree with k=48. I would now like to estimate the distance between each pair of the 48 resulting clusters. I have read the documentation, but I cannot find a solution. Any clue on how I can do that? This is a snippet of the code: distPredTurn<-as.dist(dissimilarityMatrix) hctr<-hclust(distPredTurn,"ward") cutree(hctr,k=48) Regards -- Corrado Topi Global Climate Change & Biodiversity Indicators Area 18,Department of Biology University of York, York, YO10 5YW, UK Phone: + 44 (0) 1904 328645, E-mail: ct529 at york.ac.uk