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Motivation: Phylogenetic reconstruction of tumor evolution has emerged as a crucial tool for making sense of the complexity of emerging cancer genomic datasets. Despite the growing use of phylogenetics in cancer studies, though, the field has only slowly adapted to many ways that tumor evolution differs from classic species evolution. One crucial question in that regard is how to handle inference of structural variations (SVs), which are a major mechanism of evolution in cancers but have beendoi:10.1093/bioinformatics/bty270 pmid:29950001 pmcid:PMC6022719 fatcat:bzknk2ermnbunokatq5mszaole