Cargando…

Realistic Gene Transfer to Gene Duplication Ratios Identify Different Roots in the Bacterial Phylogeny Using a Tree Reconciliation Method

The rooting of phylogenetic trees permits important inferences about ancestral states and the polarity of evolutionary events. Recently, methods that reconcile discordance between gene-trees and species-trees—tree reconciliation methods—are becoming increasingly popular for rooting species trees. Ro...

Descripción completa

Detalles Bibliográficos
Autores principales:	Bremer, Nico, Knopp, Michael, Martin, William F., Tria, Fernando D. K.
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	MDPI 2022
Materias:	Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9322720/ https://www.ncbi.nlm.nih.gov/pubmed/35888084 http://dx.doi.org/10.3390/life12070995

Ejemplares similares

On the impact of uncertain gene tree rooting on duplication-transfer-loss reconciliation
por: Kundu, Soumya, et al.
Publicado: (2018)

Algorithms: simultaneous error-correction and rooting for gene tree reconciliation and the gene duplication problem
por: Górecki, Pawel, et al.
Publicado: (2012)

Gene tree and species tree reconciliation with endosymbiotic gene transfer
por: Anselmetti, Yoann, et al.
Publicado: (2021)

Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer and loss
por: Bansal, Mukul S., et al.
Publicado: (2012)

Efficient error correction algorithms for gene tree reconciliation based on duplication, duplication and loss, and deep coalescence
por: Chaudhary, Ruchi, et al.
Publicado: (2012)

HGTree: database of horizontally transferred genes determined by tree reconciliation
por: Jeong, Hyeonsoo, et al.
Publicado: (2016)

On the complexity of non-binary tree reconciliation with endosymbiotic gene transfer
por: Gascon, Mathieu, et al.
Publicado: (2023)

Reconciliation of Gene and Species Trees
por: Rusin, L. Y., et al.
Publicado: (2014)

Horizontal gene transfer of Chlamydia: Novel insights from tree reconciliation
por: Kim, Hyaekang, et al.
Publicado: (2018)

Isometric gene tree reconciliation revisited
por: Brejová, Broňa, et al.
Publicado: (2017)

Gene tree correction for reconciliation and species tree inference
por: Swenson, Krister M, et al.
Publicado: (2012)

Most parsimonious reconciliation in the presence of gene duplication, loss, and deep coalescence using labeled coalescent trees
por: Wu, Yi-Chieh, et al.
Publicado: (2014)

Gene Duplications Are At Least 50 Times Less Frequent than Gene Transfers in Prokaryotic Genomes
por: Tria, Fernando D K, et al.
Publicado: (2021)

Best match graphs and reconciliation of gene trees with species trees
por: Geiß, Manuela, et al.
Publicado: (2020)

Lateral gene transfer, rearrangement, reconciliation
por: Patterson, Murray, et al.
Publicado: (2013)

A Preliminary List of Horizontally Transferred Genes in Prokaryotes Determined by Tree Reconstruction and Reconciliation
por: Jeong, Hyeonsoo, et al.
Publicado: (2017)

Reconstructing a SuperGeneTree minimizing reconciliation
por: Lafond, Manuel, et al.
Publicado: (2015)

Structural properties of the reconciliation space and their applications in enumerating nearly-optimal reconciliations between a gene tree and a species tree
por: Wu, Taoyang, et al.
Publicado: (2011)

Reconciliation and local gene tree rearrangement can be of mutual profit
por: Nguyen, Thi Hau, et al.
Publicado: (2013)

Biologically feasible gene trees, reconciliation maps and informative triples
por: Hellmuth, Marc
Publicado: (2017)

Potential allopolyploid origin of Ericales revealed with gene-tree reconciliation
por: Nie, Shuai, et al.
Publicado: (2022)

Reconciliation feasibility in the presence of gene duplication, loss, and coalescence with multiple individuals per species
por: Rogers, Jennifer, et al.
Publicado: (2017)

STRIDE: Species Tree Root Inference from Gene Duplication Events
por: Emms, David M, et al.
Publicado: (2017)

Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests
por: Abby, Sophie S, et al.
Publicado: (2010)

Pareto-optimal phylogenetic tree reconciliation
por: Libeskind-Hadas, Ran, et al.
Publicado: (2014)

EUCALYPT: efficient tree reconciliation enumerator
por: Donati, Beatrice, et al.
Publicado: (2015)

Gene Duplications Trace Mitochondria to the Onset of Eukaryote Complexity
por: Tria, Fernando D K, et al.
Publicado: (2021)

An efficient exact algorithm for computing all pairwise distances between reconciliations in the duplication-transfer-loss model
por: Santichaivekin, Santi, et al.
Publicado: (2019)

HGTree v2.0: a comprehensive database update for horizontal gene transfer (HGT) events detected by the tree-reconciliation method
por: Choi, Youngseok, et al.
Publicado: (2022)

Horizontal gene transfer in human-associated microorganisms inferred by phylogenetic reconstruction and reconciliation
por: Jeong, Hyeonsoo, et al.
Publicado: (2019)

SPRIT: Identifying horizontal gene transfer in rooted phylogenetic trees
por: Hill, Tobias, et al.
Publicado: (2010)

Phylogeny analysis from gene-order data with massive duplications
por: Zhou, Lingxi, et al.
Publicado: (2017)

GeneRax: A Tool for Species-Tree-Aware Maximum Likelihood-Based Gene Family Tree Inference under Gene Duplication, Transfer, and Loss
por: Morel, Benoit, et al.
Publicado: (2020)

Exact median-tree inference for unrooted reconciliation costs
por: Górecki, Paweł, et al.
Publicado: (2020)

Tree Reconciliation Methods for Host-Symbiont Cophylogenetic Analyses
por: Libeskind-Hadas, Ran
Publicado: (2022)

Evolution through segmental duplications and losses: a Super-Reconciliation approach
por: Delabre, Mattéo, et al.
Publicado: (2020)

Genomic duplication problems for unrooted gene trees
por: Paszek, Jarosław, et al.
Publicado: (2016)

Selection on Horizontally Transferred and Duplicated Genes in Sinorhizobium (Ensifer), the Root-Nodule Symbionts of Medicago
por: Epstein, Brendan, et al.
Publicado: (2014)

Selection on Horizontally Transferred and Duplicated Genes in Sinorhizobium (Ensifer), the Root-Nodule Symbionts of Medicago
por: Epstein, Brendan, et al.
Publicado: (2015)

Inferring angiosperm phylogeny from EST data with widespread gene duplication
por: Sanderson, Michael J, et al.
Publicado: (2007)

Cannot write session to /tmp/vufind_sessions/sess_hiqa890btr7aqkomq7p6264oiq