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The “tree of life” describes the evolution of life and the evolutionary relationships between organisms. The root of the tree is the common ancestor to all life on Earth. All other species radiate from this point, much like the branches of a tree. The numerous tips of these branches on the tree of life represent every living, or extant, species. Extinct species, which are species that no longer exist, can be found towards the center of the tree. Currently, these organisms, both...
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SylvX: a viewer for phylogenetic tree reconciliations.

François Chevenet1, Jean-Philippe Doyon2, Celine Scornavacca3

  • 1MIVEGEC, CNRS 5290, IRD 224, Université de Montpellier, France, Institut de Biologie Computationnelle, LIRMM, UMR 5506 CNRS, Université de Montpellier, France.

Bioinformatics (Oxford, England)
|October 31, 2015
PubMed
Summary

SylvX is a new software tool that helps visualize and manage complex evolutionary histories of gene families. It simplifies the interpretation of gene duplications, transfers, and losses, aiding evolutionary studies.

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Area of Science:

  • Evolutionary biology
  • Bioinformatics
  • Phylogenetics

Background:

  • Reconciliation methods reconstruct evolutionary processes like gene duplications, transfers, and losses by comparing gene and species trees.
  • These methods are crucial for host/parasite studies, aiding in the recovery of co-diversification scenarios.
  • Visualizing these evolutionary processes as nested trees can be complex and challenging to interpret.

Purpose of the Study:

  • To introduce SylvX, a novel reconciliation viewer designed for graphical management of evolutionary histories.
  • To provide tools that enhance the interpretation and comparison of phylogenetic reconciliations.
  • To address the shortage of dedicated tools for managing complex evolutionary graphs.

Main Methods:

  • SylvX implements standard phylogenetic graphic operators such as swapping and highlighting.
  • It introduces new functionalities for easier interpretation, including multiple maps and manipulation of sub-reconciliations (moving, shrinking).
  • The software is an open-source, cross-platform, standalone editor.

Main Results:

  • SylvX offers enhanced visualization capabilities for gene family evolution.
  • The tool facilitates the interpretation of complex phylogenetic relationships and evolutionary events.
  • It provides a user-friendly interface for managing and comparing reconciliation scenarios.

Conclusions:

  • SylvX effectively addresses the need for better graphical management tools in phylogenetic reconciliation.
  • The software aids researchers in understanding complex evolutionary histories and co-diversification patterns.
  • SylvX is a valuable, accessible resource for the bioinformatics and evolutionary biology communities.