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RECOMP: A Parsimony-Based Method for Detecting Recombination., and . APBC, page 59-68. Imperial College Press, London, (2006)Arbor 3D: an interactive environment for examining phylogenetic and taxonomic trees in multiple dimensions., , and . Bioinform., 16 (11): 1003-1009 (2000)PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships., , and . BMC Bioinform., (2008)RIATA-HGT: A Fast and Accurate Heuristic for Reconstructing Horizontal Gene Transfer., , and . COCOON, volume 3595 of Lecture Notes in Computer Science, page 84-93. Springer, (2005)Identifiability Issues in Phylogeny-Based Detection of Horizontal Gene Transfer., , , and . Comparative Genomics, volume 4205 of Lecture Notes in Computer Science, page 215-229. Springer, (2006)GS2: an efficiently computable measure of GO-based similarity of gene sets., , and . Bioinform., 25 (9): 1178-1184 (2009)Techniques for Assessing Phylogenetic Branch Support: A Performance Study., and . APBC, page 187-196. Imperial College Press, London, (2006)The Signaling Petri Net-Based Simulator: A Non-Parametric Strategy for Characterizing the Dynamics of Cell-Specific Signaling Networks., , , , and . PLoS Comput. Biol., (2008)Confounding Factors in HGT Detection: Statistical Error, Coalescent Effects, and Multiple Solutions., , , and . J. Comput. Biol., 14 (4): 517-535 (2007)De Novo Signaling Pathway Predictions Based on Protein-Protein Interaction, Targeted Therapy and Protein Microarray Analysis., , , and . Systems Biology and Computational Proteomics, volume 4532 of Lecture Notes in Computer Science, page 108-118. Springer, (2006)