In bacteria and viruses, recombination and horizontal gene transfer (HGT) permit the direct exchange or acquisition of DNA into the genome from species other than the "parent". Two major challenges face attempts at reconstructing non-treelike evolution: (1) multiple sources of gene tree incongruence exist, making various reconciliation scenarios possible, and (2) reconstructing a given reconciliation scenario is computationally hard. In this thesis, we address the latter problem, describing new methods for reconstructing recombination and HGT events: RECOMP and RIATA-HGT. RECOMP is a recombination detection method, faster than all existing algorithms and as accurate as the best. RIATA-HGT is the first polynomial-time heuristic that reconstructs unrestricted HGT events based on gene tree incongruence. We also describe two studies characterizing the sources of statistical error in phylogenetic incongruence: ortholog inference and phylogeny estimation. These studies identify computational problems whose revision will improve the overall accuracy of phylogenetic incongruence-based, non-treelike evolution reconstruction tools.