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

By Alix Boc, Alpha Boubacar Diallo, Vladimir Makarenkov. Nucleic Acids Res., 2012

494 citations recorded by the source corpus.

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.

Subfields: Ecology, Evolution, Behavior and Systematics, Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/39c807f59957ec1badc29cb593b19a1225dd1921

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Citations in the corpus

Evolview v2: an online visualization and management tool for customized and annotated phylogenetic trees (2016, methodology): “A wide variety of tree visualization software and online tools have thus been developed, such as the ETE toolkit (5), TreeView (6), TreeVec-tor (7), Dendroscope (8), iTol (9), jsPhyloSVG (10), Phy-loWidget (11), T-REX (12), Treelink (13), TreeGraph 2 (14) and many others (see https://en.wikipedia.or”
The phylogenomic forest of bird trees contains a hard polytomy at the root of Neoaves (2016, methodology): “This was complemented with networks based on simulated nine-taxon gene trees from a random tree generator (Boc et al. 2012) and simulated nine-taxon retroposon presence/absence patterns (i.e. all 512 possible strings of nine binary digits).”
Biogeography of Amazonian fishes: deconstructing river basins as biogeographic units (2017, background): “…reticulations can certainly be incorporated in branching diagrams, by means of reticulograms (Grande, 1985; Rosen, 1985; Makarenkov, Legendre, 2004; Alix et al., 2012), as unresolved cladograms (Grande, 1985), as different area cladograms for each historical period (Rosen, 1985) or as reticulated…”
NGPhylogeny.fr: new generation phylogenetic services for non-specialists (2019, methodology): “fr (1) is widely used and cited, and CIPRES (6), TRex (7) and Phylemon (8) also belong to this category.”
W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis (2016, unknown): “Thus, many web applications with intuitive user-interface were developed (e.g. (10,11)).”
GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes (2020, background): “19 and 20).”