T-REX: a web server for inferring, validating and visualizing phylogenetic trees and networks. 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.
Keywords for this software
References in zbMATH (referenced in 9 articles )
Showing results 1 to 9 of 9.
- Elsayed, Wesam M.; Elmogy, Mohammed; El-Desouky, B. S.: DNA sequence reconstruction based on innovated hybridization technique of probabilistic cellular automata and particle swarm optimization (2021)
- Bouvel, Mathilde; Gambette, Philippe; Mansouri, Marefatollah: Counting phylogenetic networks of level 1 and 2 (2020)
- van Iersel, Leo; Moulton, Vincent; Murakami, Yukihiro: Reconstructibility of unrooted level-(k) phylogenetic networks from distances (2020)
- Francis, A.; Huber, K. T.; Moulton, V.: Tree-based unrooted phylogenetic networks (2018)
- Francis, Andrew; Huber, Katharina T.; Moulton, Vincent; Wu, Taoyang: Bounds for phylogenetic network space metrics (2018)
- Barahona, Pedro; Bel-Enguix, Gemma; Dahl, Veronica; Jiménez-López, M.; Krippahl, Ludwig: Generation of classification trees from variable weighted features (2014) ioport
- Makarenkov, Vladimir; Boc, Alix; Legendre, Pierre: A new algorithm for inferring hybridization events based on the detection of horizontal gene transfers (2014)
- Kanj, Iyad A.; Nakhleh, Luay; Than, Cuong; Xia, Ge: Seeing the trees and their branches in the network is hard (2008)
- Zahid, M. A. H.; Mittal, Ankush; Joshi, R. C.: A pattern recognition-based approach for phylogenetic network construction with constrained recombination (2006)