Results 31 to 40 of about 101,371 (270)

A Linear-Time Algorithm for the Isometric Reconciliation of Unrooted Trees

Algorithms, 2020
In the reconciliation problem, we are given two phylogenetic trees. A species tree represents the evolutionary history of a group of species, and a gene tree represents the history of a family of related genes within these species.
Broňa Brejová, Rastislav Královič
doaj   +1 more source

Gene-tree reconciliation with MUL-trees to resolve polyploidy events [PDF]

Systematic Biology, 2016
AbstractPolyploidy can have a huge impact on the evolution of species, and it is a common occurrence, especially in plants. The two types of polyploids - autopolyploids and allopolyploids - differ in the level of divergence between the genes that are brought together in the new polyploid lineage. Because allopolyploids are formed via hybridization, the
Thomas, Gregg W.C., Hussain Ather, S., Hahn, Matthew W.   +2 more
openaire   +2 more sources

On the impact of uncertain gene tree rooting on duplication-transfer-loss reconciliation

BMC Bioinformatics, 2018
Background Duplication-Transfer-Loss (DTL) reconciliation is a powerful and increasingly popular technique for studying the evolution of microbial gene families.
Soumya Kundu, Mukul S. Bansal
doaj   +1 more source

Evolution through segmental duplications and losses: a Super-Reconciliation approach

Algorithms for Molecular Biology, 2020
The classical gene and species tree reconciliation, used to infer the history of gene gain and loss explaining the evolution of gene families, assumes an independent evolution for each family.
Mattéo Delabre, Nadia El-Mabrouk, Katharina T. Huber, Manuel Lafond, Vincent Moulton, Emmanuel Noutahi, Miguel Sautie Castellanos   +6 more
doaj   +1 more source

Efficient Exploration of the Space of Reconciled Gene Trees [PDF]

, 2013
Gene trees record the combination of gene level events, such as duplication, transfer and loss, and species level events, such as speciation and extinction.
Boussau, Bastien, Daubin, Vincent, Rosikiewicz, Wojciech, Szöllősi, Gergely J., Tannier, Eric   +4 more
core   +6 more sources

Structural properties of the reconciliation space and their applications in enumerating nearly-optimal reconciliations between a gene tree and a species tree

BMC Bioinformatics, 2011
Introduction A gene tree for a gene family is often discordant with the containing species tree because of its complex evolutionary course during which gene duplication, gene loss and incomplete lineage sorting events might occur.
Zhang Louxin, Wu Taoyang
doaj   +1 more source

xenoGI 3: using the DTLOR model to reconstruct the evolution of gene families in clades of microbes

BMC Bioinformatics, 2023
To understand genome evolution in a group of microbes, we need to know the timing of events such as duplications, deletions and horizontal transfers. A common approach is to perform a gene-tree / species-tree reconciliation.
Nuo Liu, Tonatiuh A. Gonzalez, Jacob Fischer, Chan Hong, Michelle Johnson, Ross Mawhorter, Fabrizia Mugnatto, Rachael Soh, Shifa Somji, Joseph S. Wirth, Ran Libeskind-Hadas, Eliot C. Bush   +11 more
doaj   +1 more source

Bacterial microevolution and the Pangenome [PDF]

, 2020
The comparison of multiple genome sequences sampled from a bacterial population reveals considerable diversity in both the core and the accessory parts of the pangenome.
A Bankevich, AE Darling, AE Darling, AJ Page, AO Kislyuk, B Charlesworth, C Buckee, C Collins, C Wiuf, CM Thomas, CS Pepperell, DJ Wilson, DR Zerbino, E Jacox, F Lassalle, GE Sims, GJ Szollosi, GJ Szollosi, GJ Szollosi, H Ochman, IJ Wilson, J Hedge, J Lawrence, JB Joy, JFC Kingman, KAA Jolley, KE Dingle, KT Konstantinidis, L Li, L Petersen, M Csurös, M Nordborg, M Pagel, M Steinegger, M Touchon, M Vos, M Vos, M Vos, MJ Ward, MTG Holden, NA Rosenberg, NJ Croucher, P Donnelly, PAP Moran, R Griffiths, RC Griffiths, RG Everitt, RK Aziz, S Castillo-Ramírez, S Kurtz, S Wright, SF Altschul, SK Sheppard, SK Sheppard, SS Abby, SV Angiuoli, T Ohta, T Seemann, TG Vaughan, WP Maddison, X Didelot, X Didelot, X Didelot, X Didelot, X Didelot, X Didelot, X Didelot, Z Yang, Z Zhou   +68 more
core   +1 more source

SylvX: a viewer for phylogenetic tree reconciliations [PDF]

Bioinformatics, 2015
Abstract Motivation: Reconciliation methods aim at recovering the evolutionary processes that shaped the history of a given gene family including events such as duplications, transfers and losses by comparing the discrepancies between the topologies of the associated gene and species trees. These methods are also used in the framework of
Chevenet, François, Doyon, Jean-Philippe, Scornavacca, Celine, Jacox, Edwin, Jousselin, Emmanuelle, Berry, Vincent   +5 more
openaire   +5 more sources

BUCKy: Gene tree/species tree reconciliation with Bayesian concordance analysis [PDF]

Bioinformatics, 2010
Abstract Motivation: BUCKy is a C++ program that implements Bayesian concordance analysis. The method uses a non-parametric clustering of genes with compatible trees, and reconstructs the primary concordance tree from clades supported by the largest proportions of genes.
Bret R, Larget, Satish K, Kotha, Colin N, Dewey, Cécile, Ané   +3 more
openaire   +2 more sources