RT Journal Article SR Electronic T1 Exploring evolutionary relationships across the genome using topology weighting JF bioRxiv FD Cold Spring Harbor Laboratory SP 069112 DO 10.1101/069112 A1 Simon H. Martin A1 Steven M. Van Belleghem YR 2017 UL http://biorxiv.org/content/early/2017/01/18/069112.abstract AB We introduce the concept of topology weighting, a method for quantifying relationships between taxa that are not necessarily monophyletic, and visualising how these relationships change across the genome. A given set of taxa can be related in a limited number of ways, but if each taxon is represented by multiple sequences, the number of possible topologies becomes very large. Topology weighting reduces this complexity by quantifying the contribution of each ‘taxon topology’ to the full tree. We describe our method for topology weighting by iterative sampling of sub-trees (Twisst), and test it on both simulated and real genomic data. Overall, we show that this is an informative and versatile approach, suitable for exploring relationships in almost any genomic dataset.Scripts to implement the method described are available at github.com/simonhmartin/twisst.