2012
DOI: 10.1186/1471-2105-13-s19-s6
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From event-labeled gene trees to species trees

Abstract: BackgroundTree reconciliation problems have long been studied in phylogenetics. A particular variant of the reconciliation problem for a gene tree T and a species tree S assumes that for each interior vertex x of T it is known whether x represents a speciation or a duplication. This problem appears in the context of analyzing orthology data.ResultsWe show that S is a species tree for T if and only if S displays all rooted triples of T that have three distinct species as their leaves and are rooted in a speciat… Show more

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Cited by 46 publications
(98 citation statements)
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References 49 publications
(56 reference statements)
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“…Methods of this type include notably LOFT (Van der Heijden et al, 2007) and COCO-CL (Jothi et al, 2006). Recently, a number of methods exploit a fundamental property of orthology graphs, in which vertices are genes and edges depict orthology: a graph G is a valid orthology graph if and only if it is P 4free (Hernandez-Rosales et al, 2012;Hellmuth et al, 2013;Lafond and El-Mabrouk, 2014;Hellmuth et al, 2015;Dondi et al, 2017a;Lafond et al, 2016;Jones et al, 2016;Dondi et al, 2017b), i.e. G has no path on 4 vertices without a shortcut.…”
Section: Introductionmentioning
confidence: 99%
“…Methods of this type include notably LOFT (Van der Heijden et al, 2007) and COCO-CL (Jothi et al, 2006). Recently, a number of methods exploit a fundamental property of orthology graphs, in which vertices are genes and edges depict orthology: a graph G is a valid orthology graph if and only if it is P 4free (Hernandez-Rosales et al, 2012;Hellmuth et al, 2013;Lafond and El-Mabrouk, 2014;Hellmuth et al, 2015;Dondi et al, 2017a;Lafond et al, 2016;Jones et al, 2016;Dondi et al, 2017b), i.e. G has no path on 4 vertices without a shortcut.…”
Section: Introductionmentioning
confidence: 99%
“…Genes that share a common origin (homologs) can be classified into orthologs, paralogs, and xenologs depending whether they originated by a speciation, duplication or horizontal gene transfer (HGT) event [16,22]. Recent advances in mathematical phylogenetics [19,24] have shown that the knowledge of these event-relations (orthologs, paralogs and xenologs) suffices to construct event-labeled gene trees and, in some case, also a species tree [18,25,20].…”
Section: Introductionmentioning
confidence: 99%
“…In the last years, the decision problems associated with these questions have been extensively studied, both when is full , i.e., involves a constraint for each pair of genes in V [7, 8], and when it is not [9]. …”
Section: Introductionmentioning
confidence: 99%
“…Hernandez-Rosales et al [7] showed that ( T , s ) is consistent with a species tree S if and only S displays all triplets in t r ( T , s ). In light of this result, Hellmuth et al [10] gave a framework for finding the DS-tree and species tree for which the maximum number of triplets are displayed, using Integer Linear Programming.…”
Section: Introductionmentioning
confidence: 99%
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