Gene tree correction for reconciliation and species tree inference: Complexity and algorithms
نویسندگان
چکیده
منابع مشابه
Computational approaches to species phylogeny inference and gene tree reconciliation.
An intricate relation exists between gene trees and species phylogenies, due to evolutionary processes that act on the genes within and across the branches of the species phylogeny. From an analytical perspective, gene trees serve as character states for inferring accurate species phylogenies, and species phylogenies serve as a backdrop against which gene trees are contrasted for elucidating ev...
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Gene tree/species tree reconciliation is a recent decisive progress in phylogenetic 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 tree nodes and species tree nodes or branche...
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MOTIVATION BUCKy is a C++ program that implements Bayesian concordance analysis. The method uses a non-parametric clustering of genes with compatible trees, and reconstructs the primary concordance tree from clades supported by the largest proportions of genes. A population tree with branch lengths in coalescent units is estimated from quartet concordance factors. AVAILABILITY BUCKy is open s...
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UNLABELLED : 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, involving sampled and unsampled lineages, within undated, fully ...
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The supertree problem asking for a tree displaying a set of consistent input trees has been largely considered for the reconstruction of species trees. Here, we explore this framework for the sake of reconstructing a gene tree from a set of input gene trees on partial data. The phylogenetic tree for the species containing the genes of interest can be used to choose among the many possible compa...
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ژورنال
عنوان ژورنال: Journal of Discrete Algorithms
سال: 2014
ISSN: 1570-8667
DOI: 10.1016/j.jda.2013.06.001