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PlantsModern breeding technologies and the development of quantitative trait locus (QTL) mapping have brought about a new era in peach breeding. This study examines the complex genetic structure that underlies the morphology of peach fruits, paying special ...
Umar Hayat +8 more
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Non-parametric correction of estimated gene trees using TRACTION
Algorithms for Molecular Biology, 2020 Motivation Estimated gene trees are often inaccurate, due to insufficient phylogenetic signal in the single gene alignment, among other causes. Gene tree correction aims to improve the accuracy of an estimated gene tree by using computational techniques ...
Sarah Christensen +4 more
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Detecting recombination from gene trees [PDF]
Molecular Biology and Evolution, 1998 In this article, a method is proposed for detecting recombination in the sequences of a gene from a set of closely related organisms. The method, the Homoplasy Test, is appropriate when the sequences are rather similar, differing by 1%-5% of nucleotides.
J, Maynard Smith, N H, Smith
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BMC Genomics, 2022 Background Drought stress is the most limiting factor for plant growth and crop production worldwide. As a major cereal crop, wheat is susceptible to drought. Thus, discovering and utilizing drought-tolerant gene resources from related species are highly
Fengkun Lu +6 more
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Coalescent histories for lodgepole species trees
, 2015 Coalescent histories are combinatorial structures that describe for a given gene tree and species tree the possible lists of branches of the species tree on which the gene tree coalescences take place. Properties of the number of coalescent histories for
Disanto, Filippo, Rosenberg, Noah A.
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Disk Covering Methods Improve Phylogenomic Analyses [PDF]
, 2014 Motivation: With the rapid growth rate of newly sequenced genomes, species tree inference from multiple genes has become a basic bioinformatics task in comparative and evolutionary biology.
Bayzid, Md Shamsuzzoha +2 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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BMC Bioinformatics, 2011 Introduction A gene tree for a gene family is often discordant with the containing species tree because of its complex evolutionary course during which gene duplication, gene loss and incomplete lineage sorting events might occur.
Zhang Louxin, Wu Taoyang
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Reconstruction of time-consistent species trees
Algorithms for Molecular Biology, 2020 Background The history of gene families—which are equivalent to event-labeled gene trees—can to some extent be reconstructed from empirically estimated evolutionary event-relations containing pairs of orthologous, paralogous or xenologous genes.
Manuel Lafond, Marc Hellmuth
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Partial Homology Relations - Satisfiability in terms of Di-Cographs [PDF]
, 2018 Directed cographs (di-cographs) play a crucial role in the reconstruction of evolutionary histories of genes based on homology relations which are binary relations between genes.
A Brandstädt +32 more
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