How do I obtain the clusterings associated with MCL iterands?
There are two options. If you are interested in clusterings containing overlap, you should go for the second. If not, use the first, but beware that the resulting clusterings may contain overlap. The first solution is to use -dump cls (probably in conjunction with either -L or -dumpi in order to limit the number of matrices written). This will cause mcl to write the clustering generically associated with each iterand to file. The -dumpstem option may be convenient as well. The second solution is to use the -dump ite option (-dumpi and -dumpstem may be of use again). This will cause mcl to write the intermediate iterands to file. After that, you can apply clmimac (interpret matrix as clustering) to those iterands. clmimac has a -tight parameter which affects the mapping of matrices to clusterings. It takes a value between 0 and 100 as argument. The default is 100 and corresponds with the strict mapping. Lowering the -tight value will generally result in clusterings containing more overl