sample.poy

(* Note: This is just an example file.  Almost all these arguments are
   optional, and will default to what we think are reasonable values.  This is
   (will be) more fully documented in the documentation. *)

(* Clear POY's memory *)
wipe ()

(* Read a file and build 5 Wagner trees *)
read("whit.hen")
build(trees:5)

(* Perform an alternating SPR/TBR search on each stored tree, keeping one
   result *)
swap()

(* Keep up to 10,000 equally good trees in TBR neighborhood *)
swap(tbr, threshold:0, keep:10000)

(* Perform tree fusing *)
fuse(keep:5, iterations:10000, weighting:uniform, replace:better, swap(tbr))

(* Display trees and output to file *)
report(graph)
report("output.trees", trees)

(* Calculate Bremer support and display it *)
calculate_support(bremer, swap(spr))
report(supports)

(* Save the current POY state to a file (to resume later) *)
save("poy-session", "My sample POY session")

(* Quit *)
exit ()