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SylvX: a viewer for phylogenetic tree reconciliations

Abstract : Reconciliation methods aim at recovering the evolutionary processes that shaped the history of a given gene family including events such as duplications, transfers and losses by com- paring the discrepancies between the topologies of the associated gene and species trees. These methods are also used in the framework of host/parasite studies to recover co-diversification scen- arios including co-speciation events, host-switches and extinctions. These evolutionary processes can be graphically represented as nested trees. These interconnected graphs can be visually messy and hard to interpret, and despite the fact that reconciliations are increasingly used, there is a shortage of tools dedicated to their graphical management. Here we present SylvX, a reconciliation viewer which implements classical phylogenetic graphic operators (swapping, highlighting, etc.) and new methods to ease interpretation and comparison of reconciliations (multiple maps, mov- ing, shrinking sub-reconciliations)
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François Chevenet, Jean-Philippe Doyon, Celine Scornavacca, Edwin Jacox, Emmanuelle Jousselin, et al.. SylvX: a viewer for phylogenetic tree reconciliations. Bioinformatics, Oxford University Press (OUP), 2016, 32 (4), pp.608-610. ⟨10.1093/bioinformatics/btv625⟩. ⟨hal-01942605⟩

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