ArticleBMC bioinformatics2015
Evolution of genes neighborhood within reconciled phylogenies: an ensemble approach.
Article in BMC bioinformatics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Reconciling multiple genes trees via segmental duplications and losses.Algorithms for molecular biology : AMB · 2019Article
- Phylogenetic signal from rearrangements in 18 Anopheles species by joint scaffolding extant and ancestral genomes.BMC genomics · 2018Article
- Ancestral Genome Reconstruction on Whole Genome Level.Current genomics · 2017Review
- DeCoSTAR: Reconstructing the Ancestral Organization of Genes or Genomes Using Reconciled Phylogenies.Genome biology and evolution · 2017Article
- Fast ancestral gene order reconstruction of genomes with unequal gene content.BMC bioinformatics · 2016Article
- Ancestral gene synteny reconstruction improves extant species scaffolding.BMC genomics · 2015Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
contextThe reconstruction of evolutionary scenarios for whole genomes in terms of genome rearrangements is a fundamental problem in evolutionary and comparative genomics. The DeCo algorithm, recently introduced by Bérard et al., computes parsimonious evolutionary scenarios for gene adjacencies, from pairs of reconciled gene trees. However, as for many combinatorial optimization algorithms, there can exist many co-optimal, or slightly sub-optimal, evolutionary scenarios that deserve to be considered. CONTRIBUTION: We extend the DeCo algorithm to sample evolutionary scenarios from the whole solution space under the Boltzmann distribution, and also to compute Boltzmann probabilities for specific ancestral adjacencies.
resultsWe apply our algorithms to a dataset of mammalian gene trees and adjacencies, and observe a significant reduction of the number of syntenic conflicts observed in the resulting ancestral gene adjacencies.
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