SPR Supertrees version history

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  • Faster SPR distance calculations
  • LGT analysis options
  • Outgroup rooting
  • Bipartition Clustering quickly ignores many SPR permutations
  • Option to break SPR distance ties with the RF distance


  • Bugfix release
  • Fixed a coding error that occasionally computed one more than the SPR distance between two trees


  • Trees can be multifurcating with -allow_multi option
  • Much faster SPR distance calculations
  • Many new options including collapsing unsupported bipartitions, fast consideration of unrooted trees with -simple_unrooted option, starting from a specified tree with -initial_tree option, limiting the radius of considered SPR permutations with -r option (-r 1 uses NNI permutations)


  • initial program version.
  • Computes rooted supertrees that minimize the rooted SPR distance using exact calculations or varying levels of approximation.
  • Optionally computes rooted supertrees that minimize the SPR distance to any rooting of a list of unrooted input trees.
  • Version used in "Subtree Prune-and-Regraft Supertrees."