Table 1.

Comparison between root inference methods.

		50 leaves Agreement
	Number Nodes	Maximal	Ortheus
Prune w/Pecan	30	0.880	0.579
	15	0.909	0.560
	7	0.912	0.555
Prune w/FSA	30	0.912	0.574
	15	0.893	0.523
	7	0.885	0.495
Prune w/MUSCLE	30	0.899	0.579
	15	0.896	0.555
	7	0.905	0.501

The average agreement score of Prune alignments when Maximal and Ortheus root inference methods are used. Fifty alignment problems with fifty leaf species and ~10 kilobases of sequence were used. Three underlying alignment algorithms and three different maximum sub-tree sizes were used in the comparison. The faster Maximal method performed better across all comparisons that Ortheus for this application.