Merlin by Goncalo Abecasis is probably the most widely used linkage program. By using sparse tree approach it is extremely fast. I only wonder why its name is not Excalibur (the name of the famous sword that helped Artus to marry Guineva, to banish the Saxons and eventually becoming king of Brittania). Goncalo moved to the US – are you still working on that? Yea, yea.
