Results 11 to 20 of about 898,857 (281)
The inference of gene trees with species trees [PDF]
Systematic Biology, 2013 Molecular phylogeny has focused mainly on improving models for the reconstruction of gene trees based on sequence alignments. Yet, most phylogeneticists seek to reveal the history of species. Although the histories of genes and species are tightly linked,
Bastien Boussau +4 more
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Terraces in species tree inference from gene trees
BMC Ecology and Evolution, 2022 A terrace in a phylogenetic tree space is a region where all trees contain the same set of subtrees, due to certain patterns of missing data among the taxa sampled, resulting in an identical optimality score for a given data set.
Mursalin Habib +4 more
doaj +3 more sources
Gene tree and species tree reconciliation with endosymbiotic gene transfer. [PDF]
Bioinformatics, 2021 Abstract Motivation It is largely established that all extant mitochondria originated from a unique endosymbiotic event integrating an α−proteobacterial genome into an eukaryotic cell. Subsequently, eukaryote evolution has been marked by episodes of gene transfer, mainly from the mitochondria to the ...
Anselmetti Y +3 more
europepmc +4 more sources
Gene tree correction for reconciliation and species tree inference [PDF]
Algorithms for Molecular Biology, 2012 Background Reconciliation is the commonly used method for inferring the evolutionary scenario for a gene family. It consists in “embedding” inferred gene trees into a known species tree, revealing the evolution of the gene family by duplications and ...
Swenson Krister M +2 more
doaj +3 more sources
Gene tree species tree reconciliation with gene conversion [PDF]
Journal of Mathematical Biology, 2019 Gene tree/species tree reconciliation is a recent decisive progress in phylo-genetic methods, accounting for the possible differences between gene histories and species histories. Reconciliation consists in explaining these differences by gene-scale events such as duplication, loss, transfer, which translates mathematically into a mapping between gene ...
Hasic, Damir, Tannier, Eric
openaire +3 more sources
Gene tree parsimony for incomplete gene trees: addressing true biological loss. [PDF]
Algorithms Mol Biol, 2018 L'estimation des arbres d'espèces à partir d'arbres géniques peut être compliquée par la duplication et la perte de gènes, et la « parcimonie des arbres géniques » (GTP) est une approche pour estimer les arbres d'espèces à partir de plusieurs arbres géniques.
Bayzid MS, Warnow T.
europepmc +5 more sources
Maximum Gene-Support Tree [PDF]
Evolutionary Bioinformatics, 2008 Genomes and genes diversify during evolution; however, it is unclear to what extent genes still retain the relationship among species. Model species for molecular phylogenetic studies include yeasts and viruses whose genomes were sequenced as well as plants that have the fossil-supported true phylogenetic trees available.
Yunfeng Shan, Xiu-Qing Li
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Refining discordant gene trees [PDF]
BMC Bioinformatics, 2014 Evolutionary studies are complicated by discordance between gene trees and the species tree in which they evolved. Dealing with discordant trees often relies on comparison costs between gene and species trees, including the well-established Robinson-Foulds, gene duplication, and deep coalescence costs.
Górecki, Pawel, Eulenstein, Oliver
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Food Chemistry: X, 2022 Banana is one of most popular fruits globally due to health-promoting and disease-preventing effects, yet little is known about in situ metabolic changes across banana varieties.
Zhibin Yin +7 more
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Estimating Species Trees from Unrooted Gene Trees [PDF]
Systematic Biology, 2011 In this study, we develop a distance method for inferring unrooted species trees from a collection of unrooted gene trees. The species tree is estimated by the neighbor joining (NJ) tree built from a distance matrix in which the distance between two species is defined as the average number of internodes between two species across gene trees, that is ...
Liu, Liang, Yu, Lili
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