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Background  Phylogenetic trees based on sequences from a set of taxa can be incongruent due to horizontal gene transfer (HGT). By identifying the HGT events, we can reconcile the gene trees and derive a taxon tree that adequately represents the species' evolutionary history. One HGT can be represented by a rooted Subtree Prune and Regraft ( R SPR) operation and the number of  R SPRs separating two trees corresponds to the minimum number of HGT events. Identifying the minimum number of  R SPRs separating two trees is NP-hard, but the problem can be reduced to fixed parameter tractable. A number of heuristic and two exact approaches to identifying the minimum number of  R SPRs have been proposed. This is the first implementation delivering an exact solution as well as the intermediate trees connecting the input trees.    Results  We present the SPR Identification Tool (SPRIT), a novel algorithm that solves the fixed parameter tractable minimum  R SPR problem and its GPL licensed Java implementation. The algorithm can be used in two ways, exhaustive search that guarantees the minimum  R SPR distance and a heuristic approach that guarantees finding a solution, but not necessarily the minimum one. We benchmarked SPRIT against other software in two different settings, small to medium sized trees i.e. five to one hundred taxa and large trees i.e. thousands of taxa. In the small to medium tree size setting with random artificial incongruence, SPRIT's heuristic mode outperforms the other software by always delivering a solution with a low overestimation of the  R SPR distance. In the large tree setting SPRIT compares well to the alternatives when benchmarked on finding a minimum solution within a reasonable time. SPRIT presents both the minimum  R SPR distance and the intermediate trees.    Conclusions  When used in exhaustive search mode, SPRIT identifies the minimum number of  R SPRs needed to reconcile two incongruent rooted trees. SPRIT also performs quick approximations of the minimum  R SPR distance, which are comparable to, and often better than, purely heuristic solutions. Put together, SPRIT is an excellent tool for identification of HGT events and pinpointing which taxa have been involved in HGT.

SPRIT: Identifying horizontal gene transfer in rooted phylogenetic trees