A Command-line version of the clustering programs:
There is a pair of free programs, calcdist and qclust, which together perform most of what my WWW cluster page does, but run from a command line prompt. This lets you batch many runs together, and simplifies getting large amounts of data in and out. There is also a simple program, rtdist, that generates random distance matrices from a random tree. They are available here:
Former 32-bit versions of these programs required the large file CYGWIN.DLL This is no longer needed, and should be erased from your directory. These programs are now built with the DJGPP C++ development system for DOS rather than the Cygnus port of Gnu tools to Windows '95. Both of these excellent development systems are free.
(go to index of programs)