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SylvX: a viewer for phylogenetic tree reconciliations

François Chevenet, Jean-Philippe Doyon, Celine Scornavacca, Edwin Jacox, Emmanuelle Jousselin, Vincent Berry
2015 Bioinformatics  
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  ...  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.  ...  Here we present SylvX, a reconciliation viewer which implements classical phylogenetic graphic operators (swapping, highlighting, etc.)  ... 
doi:10.1093/bioinformatics/btv625 pmid:26515823 fatcat:6jxjye3davel3llvczy3jign6u

A geography aware reconciliation method to investigate diversification patterns in host/parasite interactions [article]

Vincent Berry, Francois Chevenet, Jean-Philippe Doyon, Emmanuelle Jousselin
2017 bioRxiv   pre-print
In addition, we updated the reconciliation viewer SylvX in order to visualize ancestral character states on the phylogenetic trees and highlight zones that are geographically inconsistent in reconciliations  ...  With the development of robust methods in historical biogeography and the advent of next-generation sequencing that leads to better-resolved trees, a geography aware reconciliation method represents a  ...  SylvX takes a host tree in Newick format with node id numbers and a reconciliation (with symbiont 2 5 1 tree node id.).  ... 
doi:10.1101/166215 fatcat:glhft45f5nfordaauhfrh6f4ru

Visualizing Co-Phylogenetic Reconciliations [article]

Tiziana Calamoneri and Valentino Di Donato and Diego Mariottini and Maurizio Patrignani
2017 arXiv   pre-print
We introduce a hybrid metaphor for the visualization of the reconciliations of co-phylogenetic trees, that are mappings among the nodes of two trees.  ...  Our strategy combines a space-filling and a node-link approach.  ...  Acknowledgments We thank Riccardo Paparozzi for first experiments on the visualization of cophylogenetic trees.  ... 
arXiv:1708.09691v1 fatcat:g3ufkpjd7zho3pudscyceaal34

Visualizing Co-phylogenetic Reconciliations [chapter]

Tiziana Calamoneri, Valentino Di Donato, Diego Mariottini, Maurizio Patrignani
2018 Lecture Notes in Computer Science  
We introduce a hybrid metaphor for the visualization of the reconciliations of co-phylogenetic trees, that are mappings among the nodes of two trees.  ...  Our strategy combines a space-filling and a node-link approach.  ...  Acknowledgments We thank Riccardo Paparozzi for first experiments on the visualization of cophylogenetic trees.  ... 
doi:10.1007/978-3-319-73915-1_27 fatcat:fuorl5nysvev7fe3vnkbjzryla

Naturally Occurring Isoleucyl-tRNA Synthetase without tRNA-dependent Pre-transfer Editing

Nevena Cvetesic, Morana Dulic, Mirna Bilus, Nikolina Sostaric, Boris Lenhard, Ita Gruic-Sovulj
2016 Journal of Biological Chemistry  
Isoleucyl-tRNA synthetase (IleRS) is unusual among aminoacyl-tRNA synthetases in having a tRNA-dependent pre-transfer editing activity.  ...  Our phylogenetic analysis suggests that the ileS1 and ileS2 genes of contemporary bacteria are the descendants of genes that might have arisen by an ancient duplication event before the separation of bacteria  ...  Acknowledgments-We thank Jeff Errington (Newcastle University) for fruitful discussions about bacterial phylogeny and Alexander Esin (Imperial College London) for support and advice on IleRS tree construction  ... 
doi:10.1074/jbc.m115.698225 pmid:26921320 pmcid:PMC4861432 fatcat:ihshphmmb5cb7djr7wtx3h62j4