ArticleEvolutionary bioinformatics online2009
A mixture model and a hidden markov model to simultaneously detect recombination breakpoints and reconstruct phylogenies.
Article in Evolutionary bioinformatics online, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Drift, selection and recombination bias drive the evolution of a non-ribosomal peptide.Nature ecology & evolution · 2026Article
- Biosynthetic origin of anticancer dolastatin 15 reveals a noncanonical NRPS architecture enabling 2-keto acid activation.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Selecting a Window Size for Phylogenomic Analyses of Whole Genome Alignments Using AIC.Systematic biology · 2026Article
- Recombination and phylogenetic inference.Evolutionary journal of the Linnean Society · 2025Article
- MAST: Phylogenetic Inference with Mixtures Across Sites and Trees.Systematic biology · 2024Article
- Genetic Variability of Bovine Leukemia Virus: Evidence of Dual Infection, Recombination and Quasi-Species.Pathogens (Basel, Switzerland) · 2024Article
- Repeated gain and loss of a single gene modulates the evolution of vascular plant pathogen lifestyles.Science advances · 2020Article
- Split Scores: A Tool to Quantify Phylogenetic Signal in Genome-Scale Data.Systematic biology · 2017Article
- Inferring Local Genealogies on Closely Related Genomes.Comparative genomics : RECOMB ... International Workshop, RCG ... : revised selected papers. RECOMB-CG (Conference) · 2017Article
- The inference of gene trees with species trees.Systematic biology · 2015Review
- Probabilistic graphical model representation in phylogenetics.Systematic biology · 2014Article
- An evaluation of the hybrid speciation hypothesis for Xiphophorus clemenciae based on whole genome sequences.Evolution; international journal of organic evolution · 2013Article
- Replicon-dependent bacterial genome evolution: the case of Sinorhizobium meliloti.Genome biology and evolution · 2013Article
- The Physalis peruviana leaf transcriptome: assembly, annotation and gene model prediction.BMC genomics · 2012Article
- Detecting phylogenetic breakpoints and discordance from genome-wide alignments for species tree reconstruction.Genome biology and evolution · 2011Article
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3 authors.
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Abstract
Homologous recombination is a pervasive biological process that affects sequences in all living organisms and viruses. In the presence of recombination, the evolutionary history of an alignment of homologous sequences cannot be properly depicted by a single bifurcating tree: some sites have evolved along a specific phylogenetic tree, others have followed another path. Methods available to analyse recombination in sequences usually involve an analysis of the alignment through sliding-windows, or are particularly demanding in computational resources, and are often limited to nucleotide sequences. In this article, we propose and implement a Mixture Model on trees and a phylogenetic Hidden Markov Model to reveal recombination breakpoints while searching for the various evolutionary histories that are present in an alignment known to have undergone homologous recombination. These models are sufficiently efficient to be applied to dozens of sequences on a single desktop computer, and can handle equivalently nucleotide or protein sequences. We estimate their accuracy on simulated sequences and test them on real data.
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