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Verbum et Ecclesia, 2008 And Zaccheus remained in the tree: Reconciliation and Justice and the Truth and Reconciliation CommissionSouth Africa s Truth and Reconciliation Commission (TRC) has been praised the world over for its work and its example is being followed by many ...
A Boesak
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EUCALYPT: efficient tree reconciliation enumerator. [PDF]
Algorithms Mol Biol, 2015 Phylogenetic tree reconciliation is the approach of choice for investigating the coevolution of sets of organisms such as hosts and parasites. It consists in a mapping between the parasite tree and the host tree using event-based maximum parsimony. Given a cost model for the events, many optimal reconciliations are however possible.
Donati B +4 more
europepmc +7 more sources
RECONCILIATION WITH NON-BINARY SPECIES TREES [PDF]
Computational Systems Bioinformatics, 2007 Reconciliation extracts information from the topological incongruence between gene and species trees to infer duplications and losses in the history of a gene family. The inferred duplication-loss histories provide valuable information for a broad range of biological applications, including ortholog identification, estimating gene duplication times ...
B, Vernot +3 more
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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
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Exploring and Visualizing Spaces of Tree Reconciliations [PDF]
Systematic Biology, 2018 Tree reconciliation is the mathematical tool that is used to investigate the coevolution of organisms, such as hosts and parasites. A common approach to tree reconciliation involves specifying a model that assigns costs to certain events, such as cospeciation, and then tries to find a mapping between two specified phylogenetic trees which minimizes the
Huber, Katharina +3 more
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Maximum parsimony reconciliation in the DTLOR model
BMC Bioinformatics, 2021 Background Analyses of microbial evolution often use reconciliation methods. However, the standard duplication-transfer-loss (DTL) model does not account for the fact that species trees are often not fully sampled and thus, from the perspective of ...
Jingyi Liu +5 more
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Reconciliation of Gene and Species Trees [PDF]
BioMed Research International, 2014 The first part of the paper briefly overviews the problem of gene and species trees reconciliation with the focus on defining and algorithmic construction of the evolutionary scenario. Basic ideas are discussed for the aspects of mapping definitions, costs of the mapping and evolutionary scenario, imposing time scales on a scenario, incorporating ...
Rusin, L. Y. +3 more
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ecceTERA: comprehensive gene tree-species tree reconciliation using parsimony [PDF]
Bioinformatics, 2016 Abstract Summary: A gene tree-species tree reconciliation explains the evolution of a gene tree within the species tree given a model of gene-family evolution. We describe ecceTERA, a program that implements a generic parsimony reconciliation algorithm, which accounts for gene duplication, loss and transfer (DTL) as well as speciation ...
Jacox, Edwin +4 more
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Best match graphs and reconciliation of gene trees with species trees [PDF]
Journal of Mathematical Biology, 2020 AbstractA wide variety of problems in computational biology, most notably the assessment of orthology, are solved with the help of reciprocal best matches. Using an evolutionary definition of best matches that captures the intuition behind the concept we clarify rigorously the relationships between reciprocal best matches, orthology, and evolutionary ...
Manuela Geiß +6 more
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Constructing an Evolutionary Tree and Path–Cycle Graph Evolution along It
Mathematics, 2023 The paper solves the problem of constructing an evolutionary tree and the evolution of structures along it. This problem has long been posed and extensively researched; it is formulated and discussed below.
Konstantin Gorbunov, Vassily Lyubetsky
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