ArticlePLoS computational biology2009
Accurate detection of recombinant breakpoints in whole-genome alignments.
Article in PLoS computational biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Recombination and phylogenetic inference.Evolutionary journal of the Linnean Society · 2025Article
- Distributed genotyping and clustering of Neisseria strains reveal continual emergence of epidemic meningococcus over a century.Nature communications · 2023Article
- SPLATCHE3: simulation of serial genetic data under spatially explicit evolutionary scenarios including long-distance dispersal.Bioinformatics (Oxford, England) · 2019Article
- Flavivirus and Filovirus EvoPrinters: New alignment tools for the comparative analysis of viral evolution.PLoS neglected tropical diseases · 2017Article
- A scalability study of phylogenetic network inference methods using empirical datasets and simulations involving a single reticulation.BMC bioinformatics · 2016Article
- Spatial and temporal simulation of human evolution. Methods, frameworks and applications.Current genomics · 2014Article
- A unifying model of genome evolution under parsimony.BMC bioinformatics · 2014Article
- An HMM-based comparative genomic framework for detecting introgression in eukaryotes.PLoS computational biology · 2014Article
- Molecular evolution of Zika virus during its emergence in the 20(th) century.PLoS neglected tropical diseases · 2014Article
- Computer programs and methodologies for the simulation of DNA sequence data with recombination.Frontiers in genetics · 2013Article
- Article
- The impact of mutation and gene conversion on the local diversification of antigen genes in African trypanosomes.Molecular biology and evolution · 2012Article
- Simulation of molecular data under diverse evolutionary scenarios.PLoS computational biology · 2012Article
- A novel computational method identifies intra- and inter-species recombination events in Staphylococcus aureus and Streptococcus pneumoniae.PLoS computational biology · 2012Article
- Article
- Conversion events in gene clusters.BMC evolutionary biology · 2011Article
- More accurate recombination prediction in HIV-1 using a robust decoding algorithm for HMMs.BMC bioinformatics · 2011Article
- Evaluation of methods for detecting conversion events in gene clusters.BMC bioinformatics · 2011Article
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Authors and funding
2 authors.
Funding
Abstract
We propose a novel method for detecting sites of molecular recombination in multiple alignments. Our approach is a compromise between previous extremes of computationally prohibitive but mathematically rigorous methods and imprecise heuristic methods. Using a combined algorithm for estimating tree structure and hidden Markov model parameters, our program detects changes in phylogenetic tree topology over a multiple sequence alignment. We evaluate our method on benchmark datasets from previous studies on two recombinant pathogens, Neisseria and HIV-1, as well as simulated data. We show that we are not only able to detect recombinant regions of vastly different sizes but also the location of breakpoints with great accuracy. We show that our method does well inferring recombination breakpoints while at the same time maintaining practicality for larger datasets. In all cases, we confirm the breakpoint predictions of previous studies, and in many cases we offer novel predictions.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.