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

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.

Figure 1.

An example of a phylogenetic tree (hierarchical view) showing phylogenetic relationships for a group of nine vertebrate species.

Figure 2.

An example of a reticulogram (axial view) showing phylogenetic relationships for a group of nine vertebrate species.

Figure 3.

An example of a HGT network showing horizontal transfers of the gene rpl12e inferred for the group of 14 species originally considered by Matte-Taillez et al. [see Figure 1a in (58)]. Five gene transfers are indicated by dashed arrows. Numbers on transfers designate their order of inference. Bootstrap scores of the obtained transfers are indicated between parentheses.