T-REX: a web server for inferring, validating and visualizing phylogenetic trees and networks

TLDR

T‑REX is a web server for reconstructing phylogenetic trees, reticulation networks, and detecting horizontal gene transfer events. It integrates tools such as MUSCLE, MAFFT, Neighbor Joining, NINJA, BioNJ, PhyML, RAxML, a random tree generator, and distance‑to‑sequence models, and offers fast methods for tree inference from complete or incomplete distance matrices, reticulogram and HGT network reconstruction, validation, and interactive visualization. The server is accessible at www.trex.uqam.ca.

Abstract

T-REX (Tree and reticulogram REConstruction) is a web server dedicated to the reconstruction of phylogenetic trees, reticulation networks and to the inference of horizontal gene transfer (HGT) events. T-REX includes several popular bioinformatics applications such as MUSCLE, MAFFT, Neighbor Joining, NINJA, BioNJ, PhyML, RAxML, random phylogenetic tree generator and some well-known sequence-to-distance transformation models. It also comprises fast and effective methods for inferring phylogenetic trees from complete and incomplete distance matrices as well as for reconstructing reticulograms and HGT networks, including the detection and validation of complete and partial gene transfers, inference of consensus HGT scenarios and interactive HGT identification, developed by the authors. The included methods allows for validating and visualizing phylogenetic trees and networks which can be built from distance or sequence data. The web server is available at: www.trex.uqam.ca.