Who is Who in Phylogenetic Networks

Publications of Alpha B. Diallo     Order by:   Type | Year

Associated keywords

from-rooted-trees from-species-tree lateral-gene-transfer phylogenetic-network phylogeny Program-T-REX reconstruction reticulogram software

Article (Journal)

1 Alix Boc, Alpha B. Diallo and Vladimir Makarenkov. T-REX: a web server for inferring, validating and visualizing phylogenetic trees and networks. In NAR, Vol. 40(W1):W573-W579, 2012. Keywords: from rooted trees, from species tree, lateral gene transfer, phylogenetic network, phylogeny, Program T REX, reconstruction, reticulogram, software. Note: http://dx.doi.org/10.1093/nar/gks485.         Toggle 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. © 2012 The Author(s)."

InProceedings

2 Vladimir Makarenkov, Alix Boc, Charles Delwiche, Alpha B. Diallo and Hervé Philippe. New Efficient Algorithm for Modeling Partial and Complete Gene Transfer Scenarios. In IFCS06, Pages 341-349, springer, 2006. Note: http://www.labunix.uqam.ca/~makarenv/makarenv/IFCS_2006_M_et_al.pdf.