Prunier is a greedy algorithm to reconcile a gene tree and a species tree under an Subtree Pruning algorithm, which is considered a good model for lateral gene transfer (LGT). Its philosophy is to try to remove one after the other those parts of the tree (subtrees) that are responsible for the highest conflict. Sometimes however, in complex LGT scenarii, it is necessary to remove several independent parts of the tree to eliminate a single conflicting branch. In such cases, the first implementation of Prunier could fail at finding a good LGT scenario, and typically inferred very high numbers of LGT, most of them explaining only statistically unsupported conflict
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Abby S.S., Tannier E., Gouy M. and Daubin V.
Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests.
BMC Bioinformatics 2010, 11:324