Who is Who in Phylogenetic Networks

Publications related to 'program t rex' : T-REX (tree and reticulogram reconstruction) is an application to reconstruct phylogenetic trees and reticulation networks from distance matrices. http://www.labunix.uqam.ca/~makarenv/trex.html, internet version here.   Order by:   Type | Year

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Associated keywords

abstract-network evaluation explicit-network exponential-algorithm FPT from-distances from-rooted-trees from-sequences from-species-tree from-triplets galled-tree hybridization lateral-gene-transfer level-k-phylogenetic-network likelihood median-network mu-distance NeighborNet netting parsimony phylogenetic-network phylogeny polynomial population-genetics Program-Arlequin Program-Level2 Program-Marlon Program-Network Program-Pyramids Program-Reticlad Program-Simplistic Program-Spectronet Program-SplitsTree Program-T-REX Program-TCS Program-WeakHierarchies pyramid reconstruction reticulogram software split split-decomposition split-network statistical-parsimony survey visualization weak-hierarchy

Article (Journal)

1 François-Joseph Lapointe. How to account for reticulation events in phylogenetic analysis: A review of distance-based methods. In Journal of Classification, Vol. 17:175-184, 2000. Keywords: abstract network, evaluation, from distances, phylogenetic network, Program Pyramids, Program SplitsTree, Program T REX, pyramid, reconstruction, reticulogram, split network, survey, weak hierarchy. Note: http://dx.doi.org/10.1007/s003570000016.         2 Vladimir Makarenkov. T-REX: reconstructing and visualizing phylogenetic trees and reticulation networks. In BIO, Vol. 17(7):664-668, 2001. Keywords: phylogenetic network, phylogeny, Program T REX, reconstruction, reticulogram, software, visualization. Note: http://www.labunix.uqam.ca/~makarenv/makarenv/Article_BIO.pdf.         3 Vladimir Makarenkov and Pierre Legendre. From a phylogenetic tree to a reticulated network. In JCB, Vol. 11(1):195-212, 2004. Keywords: abstract network, from distances, phylogenetic network, phylogeny, Program T REX, reticulogram. Note: http://www.labunix.uqam.ca/~makarenv/makarenv/article_JCB2004.pdf.         4 David A. Morrison. Networks in phylogenetic analysis: new tools for population biology. In IJP, Vol. 35:567-582, 2005. Keywords: median network, NeighborNet, phylogenetic network, phylogeny, population genetics, Program Network, Program Spectronet, Program SplitsTree, Program T REX, Program TCS, reconstruction, reticulogram, split decomposition, survey. Note: http://hem.fyristorg.com/acacia/papers/networks.pdf.         5 David Posada and Keith A. Crandall. Intraspecific gene genealogies: trees grafting into networks. In TEE, Vol. 16(1):37-45, 2001. Keywords: likelihood, median network, netting, parsimony, phylogenetic network, phylogeny, Program Arlequin, Program SplitsTree, Program T REX, Program TCS, pyramid, reticulogram, split decomposition, statistical parsimony, survey. Note: http://darwin.uvigo.es/download/papers/09.networks01.pdf.         6 Mohd Abdul Hai Zahid, Ankush Mittal and Ramesh C. Joshi. Use of Phylogenetic network and its reconstruction Algorithms. In Bioinformatics India, Vol. 2:47-58, 2004. Keywords: evaluation, from distances, NeighborNet, Program SplitsTree, Program T REX, split decomposition. Note: http://www.isical.ac.in/~zahid_t/publications/papers/1.pdf.         7 Galina Glazko, Vladimir Makarenkov, Jing Liu and Arcady Mushegian. Evolutionary history of bacteriophages with double-stranded DNA genomes. In Biology Direct, Vol. 2(36), 2007. Keywords: explicit network, from sequences, phylogenetic network, phylogeny, Program T REX. Note: http://dx.doi.org/10.1186/1745-6150-2-36.         Toggle abstract "Background: Reconstruction of evolutionary history of bacteriophages is a difficult problem because of fast sequence drift and lack of omnipresent genes in phage genomes. Moreover, losses and recombinational exchanges of genes are so pervasive in phages that the plausibility of phylogenetic inference in phage kingdom has been questioned. Results: We compiled the profiles of presence and absence of 803 orthologous genes in 158 completely sequenced phages with double-stranded DNA genomes and used these gene content vectors to infer the evolutionary history of phages. There were 18 well-supported clades, mostly corresponding to accepted genera, but in some cases appearing to define new taxonomic groups. Conflicts between this phylogeny and trees constructed from sequence alignments of phage proteins were exploited to infer 294 specific acts of intergenome gene transfer. Conclusion: A notoriously reticulate evolutionary history of fast-evolving phages can be reconstructed in considerable detail by quantitative comparative genomics. © 2007 Glazko et al; licensee BioMed Central Ltd." 8 Alix Boc and Vladimir Makarenkov. Towards an accurate identification of mosaic genes and partial horizontal gene transfers. In NAR, Vol. 39(21):e144, 2011. Keywords: explicit network, from sequences, lateral gene transfer, phylogenetic network, phylogeny, Program T REX, reconstruction. Note: http://dx.doi.org/10.1093/nar/gkr735.         Toggle abstract "Many bacteria and viruses adapt to varying environmental conditions through the acquisition of mosaic genes. A mosaic gene is composed of alternating sequence polymorphisms either belonging to the host original allele or derived from the integrated donor DNA. Often, the integrated sequence contains a selectable genetic marker (e.g. marker allowing for antibiotic resistance). An effective identification of mosaic genes and detection of corresponding partial horizontal gene transfers (HGTs) are among the most important challenges posed by evolutionary biology. We developed a method for detecting partial HGT events and related intragenic recombination giving rise to the formation of mosaic genes. A bootstrap procedure incorporated in our method is used to assess the support of each predicted partial gene transfer. The proposed method can be also applied to confirm or discard complete (i.e. traditional) horizontal gene transfers detected by any HGT inferring method. While working on a full-genome scale, the new method can be used to assess the level of mosaicism in the considered genomes as well as the rates of complete and partial HGT underlying their evolution. © 2011 The Author(s)." 9 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)." 10 Rinku Mathur and Neeru Adlakha. A graph theoretic model for prediction of reticulation events and phylogenetic networks for DNA sequences. In Egyptian Journal of Basic and Applied Sciences, Vol. 3(3):263-271, 2016. Keywords: from sequences, phylogenetic network, phylogeny, Program T REX. Note: http://dx.doi.org/10.1016/j.ejbas.2016.07.004.

InProceedings

11 Sergey Bereg and Kathryn Bean. Constructing Phylogenetic Networks from Trees. In BIBE05, Pages 299-305, 2005. Keywords: evaluation, from distances, phylogenetic network, phylogeny, Program SplitsTree, Program T REX, reconstruction, split, split network. Note: http://dx.doi.org/10.1109/BIBE.2005.19.         Toggle abstract We present a new method of constructing a phylogenetic network from a given phylogenetic tree. It is based on a procedure that locally improves the tree. The procedure is quite general and can be applied to phylogenetic networks. By repeating local improvements user can introduce a given number of recombination cycles. A sequence of networks with decreasing distance deviation can be generated. The algorithm is efficient and shows a good performance on an example with plants. This is due to the fact that the update in every step is local and optimal. © 2005 IEEE.

InBook

12 Vladimir Makarenkov, Dmytro Kevorkov and Pierre Legendre. Phylogenetic Network Construction Approaches. In Applied Mycology and Biotechnology, Vol. 6:61-97, 2006. Keywords: from distances, hybridization, lateral gene transfer, median network, NeighborNet, netting, Program Arlequin, Program Network, Program Pyramids, Program Reticlad, Program SplitsTree, Program T REX, Program TCS, Program WeakHierarchies, pyramid, reticulogram, split, split decomposition, split network, survey, weak hierarchy. Note: http://www.labunix.uqam.ca/~makarenv/makarenv/MKL_article.pdf.

PhdThesis

13 Leo van Iersel. Algorithms, Haplotypes and Phylogenetic Networks. PhD thesis, Eindhoven University of Technology, The Netherlands, 2009. Keywords: evaluation, explicit network, exponential algorithm, FPT, from triplets, galled tree, level k phylogenetic network, mu distance, phylogenetic network, phylogeny, polynomial, Program Level2, Program Marlon, Program Simplistic, Program T REX, reconstruction. Note: http://www.win.tue.nl/~liersel/thesis_vaniersel_viewing.pdf.         14 Alix Boc. Détection des transferts horizontaux de gènes : modèles et algorithmes appliqués à l'évolution des espèces et des langues. PhD thesis, Université du Québec à Montréal, Canada, 2012. Keywords: explicit network, from rooted trees, from species tree, phylogenetic network, phylogeny, Program T REX, reconstruction. Note: http://www.collectionscanada.gc.ca/obj/thesescanada/vol2/QMUQ/TC-QMUQ-4658.pdf.