SylvX: a viewer for phylogenetic tree reconciliations

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 comparing 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 scenarios 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, moving, shrinking sub-reconciliations). SylvX is an open source, cross-platform, standalone editor available for Windows and Unix-like systems including OS X. It is publicly available at Contact:

Example of a SylvX output

Coming soon ! SylvX compatible with RecPhyloXML - a format for reconciled gene trees
Jul 2017 SylvX v.36 Annotation of Host tree and Reconcilaition screenshot
October 2015 SylvX: a viewer for phylogenetic tree reconciliations Bioinformatics
March 2015 SylvX: first release

F. Chevenet(*), J.P. Doyon, C. Scornavacca, E. Jacox, E. Jousselin, V. Berry
SylvX: a viewer for phylogenetic tree reconciliations
Bioinformatics (2016) 32 (4): 608-610

(*) corresponding author

  • 1) Download & Install ActiveTcl
  • 2) Download SylvX package (v.42) (multi-platforms)
  • 3) under the Linux or OSX OS : from a terminal, goto to downloaded SylvX package, then command "wish", then from the wish prompt, command "source sylvx.tcl". Under the Windows OS: double click the sylvx.tcl file (sylvx package).