Results 1 to 10 of about 14,320 (149)
Maximum parsimony reconciliation in the DTLOR model [PDF]
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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Hierarchical clustering of maximum parsimony reconciliations [PDF]
BMC Bioinformatics, 2019 Background Maximum parsimony reconciliation in the duplication-transfer-loss model is a widely-used method for analyzing the evolutionary histories of pairs of entities such as hosts and parasites, symbiont species, and species and genes. While efficient
Ross Mawhorter, Ran Libeskind-Hadas
doaj +4 more sources
On the computational complexity of the maximum parsimony reconciliation problem in the duplication-loss-coalescence model. [PDF]
Algorithms Mol Biol, 2017 Phylogenetic tree reconciliation is a widely-used method for inferring the evolutionary histories of genes and species. In the duplication-loss-coalescence (DLC) model, we seek a reconciliation that explains the incongruence between a gene and species tree using gene duplication, loss, and deep coalescence events.
Bork D +4 more
europepmc +5 more sources
The Most Parsimonious Reconciliation Problem in the Presence of Incomplete Lineage Sorting and Hybridization Is NP-Hard [PDF]
bioRxiv, 2021 The maximum parsimony phylogenetic reconciliation problem seeks to explain incongruity between a gene phylogeny and a species phylogeny with respect to a set of evolutionary events.
LeMay, Matthew +2 more
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Pareto-optimal phylogenetic tree reconciliation [PDF]
Bioinform., 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.
Bansal, Mukul S. +4 more
core +2 more sources
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2019 Phylogenetic tree reconciliation is widely used in the fields of molecular evolution, cophylogenetics, parasitology, and biogeography to study the evolutionary histories of pairs of entities. In these contexts, reconciliation is often performed using maximum parsimony under the Duplication-Transfer-Loss (DTL) event model.
Jordan Haack +4 more
openaire +4 more sources
BMC Bioinformatics, 2019 Background Maximum parsimony reconciliation in the duplication-transfer-loss model is widely used in studying the evolutionary histories of genes and species and in studying coevolution of parasites and their hosts and pairs of symbionts. While efficient
Santi Santichaivekin +2 more
doaj +2 more sources
BMC Bioinformatics, 2019 Background Reconciliation methods are widely used to explain incongruence between a gene tree and species tree. However, the common approach of inferring maximum parsimony reconciliations (MPRs) relies on user-defined costs for each type of event, which ...
Ross Mawhorter +3 more
doaj +2 more sources
Reconciliation Revisited: Handling Multiple Optima when Reconciling with Duplication, Transfer, and Loss [PDF]
Annual International Conference on Research in Computational Molecular Biology, 2013 Phylogenetic tree reconciliation is a powerful approach for inferring evolutionary events like gene duplication, horizontal gene transfer, and gene loss, which are fundamental to our understanding of molecular evolution.
A. Tofigh +23 more
core +3 more sources
Phylogenetic analysis of seven WRKY genes across the palm subtribe Attaleinae (Arecaceae) [corrected] identifies Syagrus as sister group of the coconut. [PDF]
PLoS ONE, 2009 BACKGROUND:The Cocoseae is one of 13 tribes of Arecaceae subfam. Arecoideae, and contains a number of palms with significant economic importance, including the monotypic and pantropical Cocos nucifera L., the coconut, the origins of which have been one ...
Alan W Meerow +9 more
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