Isometric gene tree reconciliation revisited [PDF]
Algorithms for Molecular Biology, 2017 Background Isometric gene tree reconciliation is a gene tree/species tree reconciliation problem where both the gene tree and the species tree include branch lengths, and these branch lengths must be respected by the reconciliation.
Broňa Brejová +4 more
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Pareto-optimal phylogenetic tree reconciliation. [PDF]
Bioinformatics, 2014 Motivation: Phylogenetic tree reconciliation is a widely used method for reconstructing the evolutionary histories of gene families and species, hosts and parasites and other dependent pairs of entities.
Libeskind-Hadas R +3 more
europepmc +8 more sources
Tree Reconciliation Methods for Host-Symbiont Cophylogenetic Analyses [PDF]
Life, 2022 Phylogenetic reconciliation is a fundamental method in the study of pairs of coevolving species. This paper provides an overview of the underlying theory of reconciliation in the context of host-symbiont cophylogenetics, identifying some of the major ...
Ran Libeskind-Hadas
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Potential allopolyploid origin of Ericales revealed with gene-tree reconciliation [PDF]
Frontiers in Plant Science, 2022 Few incidents of ancient allopolyploidization (polyploidization by hybridization or merging diverged genomes) were previously revealed, although there is significant evidence for the accumulation of whole genome duplications (WGD) in plants.
Shuai Nie +13 more
doaj +5 more sources
Horizontal gene transfer of Chlamydia: Novel insights from tree reconciliation. [PDF]
PLoS ONE, 2018 Recent comparative genomics studies have suggested that horizontal gene transfer (HGT) is one of the major processes in bacterial evolution. In this study, HGT events of 64 Chlamydia strains were investigated based on the pipeline employed in HGTree ...
Hyaekang Kim +4 more
doaj +5 more sources
Realistic Gene Transfer to Gene Duplication Ratios Identify Different Roots in the Bacterial Phylogeny Using a Tree Reconciliation Method [PDF]
Life, 2022 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 ...
Nico Bremer +3 more
doaj +2 more sources
On the complexity of non-binary tree reconciliation with endosymbiotic gene transfer [PDF]
Algorithms for Molecular Biology, 2023 Reconciling a non-binary gene tree with a binary species tree can be done efficiently in the absence of horizontal gene transfers, but becomes NP-hard in the presence of gene transfers.
Mathieu Gascon, Nadia El-Mabrouk
doaj +2 more sources
Support measures to estimate the reliability of evolutionary events predicted by reconciliation methods. [PDF]
PLoS ONE, 2013 The genome content of extant species is derived from that of ancestral genomes, distorted by evolutionary events such as gene duplications, transfers and losses.
Thi-Hau Nguyen +3 more
doaj +8 more sources
Tree reconciliation combined with subsampling improves large scale inference of orthologous group hierarchies [PDF]
BMC Bioinformatics, 2019 Background An orthologous group (OG) comprises a set of orthologous and paralogous genes that share a last common ancestor (LCA). OGs are defined with respect to a chosen taxonomic level, which delimits the position of the LCA in time to a specified ...
Davide Heller +2 more
doaj +2 more sources
Algorithms: simultaneous error-correction and rooting for gene tree reconciliation and the gene duplication problem [PDF]
BMC Bioinformatics, 2012 Background Evolutionary methods are increasingly challenged by the wealth of fast growing resources of genomic sequence information. Evolutionary events, like gene duplication, loss, and deep coalescence, account more then ever for incongruence between ...
Górecki Pawel, Eulenstein Oliver
doaj +2 more sources