François Chevenet1, Jean-Philippe Doyon2, Celine Scornavacca3, Edwin Jacox3, Emmanuelle Jousselin4, Vincent Berry5. 1. MIVEGEC, CNRS 5290, IRD 224, Université de Montpellier, France, Institut de Biologie Computationnelle, LIRMM, UMR 5506 CNRS, Université de Montpellier, France. 2. Institut de Biologie Computationnelle, LIRMM, UMR 5506 CNRS, Université de Montpellier, France. 3. ISEM-UMR 5554 CNRS IRD, Université de Montpellier, France and. 4. INRA-UMR 1062 CBGP, Centre de Biologie pour la Gestion de Populations, Montferrier-sur-Lez, France. 5. MIVEGEC, CNRS 5290, IRD 224, Université de Montpellier, France.
Abstract
MOTIVATION: 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). AVAILABILITY AND IMPLEMENTATION: SylvX is an open source, cross-platform, standalone editor available for Windows and Unix-like systems including OSX. It is publicly available at www.sylvx.org.
MOTIVATION: 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). AVAILABILITY AND IMPLEMENTATION: SylvX is an open source, cross-platform, standalone editor available for Windows and Unix-like systems including OSX. It is publicly available at www.sylvx.org.
Authors: Alejandro Palomo; Anders G Pedersen; S Jane Fowler; Arnaud Dechesne; Thomas Sicheritz-Pontén; Barth F Smets Journal: ISME J Date: 2018-03-07 Impact factor: 10.302
Authors: Steffen Buessecker; Marike Palmer; Dengxun Lai; Joshua Dimapilis; Xavier Mayali; Damon Mosier; Jian-Yu Jiao; Daniel R Colman; Lisa M Keller; Emily St John; Michelle Miranda; Cristina Gonzalez; Lizett Gonzalez; Christian Sam; Christopher Villa; Madeline Zhuo; Nicholas Bodman; Fernando Robles; Eric S Boyd; Alysia D Cox; Brian St Clair; Zheng-Shuang Hua; Wen-Jun Li; Anna-Louise Reysenbach; Matthew B Stott; Peter K Weber; Jennifer Pett-Ridge; Anne E Dekas; Brian P Hedlund; Jeremy A Dodsworth Journal: Nat Commun Date: 2022-06-30 Impact factor: 17.694
Authors: Wandrille Duchemin; Guillaume Gence; Anne-Muriel Arigon Chifolleau; Lars Arvestad; Mukul S Bansal; Vincent Berry; Bastien Boussau; François Chevenet; Nicolas Comte; Adrián A Davín; Christophe Dessimoz; David Dylus; Damir Hasic; Diego Mallo; Rémi Planel; David Posada; Celine Scornavacca; Gergely Szöllosi; Louxin Zhang; Éric Tannier; Vincent Daubin Journal: Bioinformatics Date: 2018-11-01 Impact factor: 6.937