How can I limit the number of rearrangements PAUP* evaluates during a heuristic search?
There are several different ways to go about this. First, there is a “rearrlimit=n” option on the hsearch command, which limits the total number of rearrangements for each search to n. Second, there is a “timelimit=n” option, where n is the number of seconds that PAUP* will use to search for a tree. Note that if you use these options in conjuction with random-addition-sequence searches, the “limitperrep=y|n” determines whether to apply this limit on a per replicate or overall basis. You can also specify reconlimit=n, where n is the maximum “reconnection distance” for an SPR or TBR reconnection (1 is equivalent to NNI, infinity to TBR, and values in between restrict the size of the neighborhood of trees that are tested).
