ArticleVirus evolution2015
RDP4: Detection and analysis of recombination patterns in virus genomes.
Article in Virus evolution, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1,800 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
1,800 citing papers in PubMed, 1 synthesis or guideline pooled it, 3,388 citations in OpenAlex.
- Global epidemiology of tick-borneFrontiers in cellular and infection microbiology · 2026Pooled it
- Molecular characterization and pathogenicity of a novel Chinese porcine deltacoronavirus strain CH/HLJ/20 isolated from diarrheic piglets.Virulence · 2026Article
- Article
- Sand fly-associated phlebovirus with evidence of neutralizing antibodies in humans and dogs in Kosovo.Emerging microbes & infections · 2026Article
- Coronavirus surveillance in passerines reveals novel deltacoronaviruses in Eurasian tree sparrows with implications for One Health and livestock biosecurity.One health (Amsterdam, Netherlands) · 2026Article
- Article
- Phylogeographic epidemiology of Dabie bandavirus in East Asia: divergent transmission networks and genotype‑linked clinical severity.Infectious diseases of poverty · 2026Article
- Molecular characteristics, phylodynamics, and evolutionary changes of avian infectious bronchitis virus detected from chickens in Yunnan Province, 2021-2024.Poultry science · 2026Article
- Phylodynamic reconstruction of global evolution and geographic structure of maize chlorotic mottle virus.The Journal of general virology · 2026Article
- RNA Virus Diversity, Cross-Species Transmission, and Molecular Constraints in Two Closely Related Rat Species.Integrative zoology · 2026Article
- Molecular Epidemiology, Phylogeography, and Recombination Dynamics of PRRSV-2 Sublineage L1C in Mainland China.Viruses · 2026Article
- Emergence of canine parvovirus-2c in domestic cats and adaptive evolution of the NS1 gene: Molecular epidemiology of feline parvoviruses in Northern Vietnam (2022-2025).Veterinary world · 2026Article
- HIV superinfection reveals sequential reservoir reactivation and immune-driven rebound dynamics.Journal of virology · 2026Article
- Feline Kobuvirus in Domestic Cats in Northern Vietnam: Molecular Insights Reveal Adaptive Evolution in VP1 Protein.International journal of molecular sciences · 2026Article
- Comprehensive Analysis of Insertions in BVDV and Implications for Non-Homologous Recombination Mechanisms.Viruses · 2026Article
- Host specificity and horizontal gene transfer in the MIB-MIP immunoglobulin evasion system in Mycoplasma gallisepticum.Veterinary research · 2026Article
- The first complete genome sequence of iris yellow spot virus from South America and comparative analysis with isolates of different geographic origin.Archives of virology · 2026Article
- Genetic Adaptation Accompanying the Emergence of Inkoo Virus, the European Orthobunyavirus jamestownense.Annals of the New York Academy of Sciences · 2026Article
- Novel insights into tomato leaf curl New Delhi virus introduction and evolution in Southeastern France using an advanced long-read sequencing workflow.PLoS pathogens · 2026Article
- Article
1,740 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 3 institutions in 3 countries.
Funding
Abstract
RDP4 is the latest version of recombination detection program (RDP), a Windows computer program that implements an extensive array of methods for detecting and visualising recombination in, and stripping evidence of recombination from, virus genome sequence alignments. RDP4 is capable of analysing twice as many sequences (up to 2,500) that are up to three times longer (up to 10 Mb) than those that could be analysed by older versions of the program. RDP4 is therefore also applicable to the analysis of bacterial full-genome sequence datasets. Other novelties in RDP4 include (1) the capacity to differentiate between recombination and genome segment reassortment, (2) the estimation of recombination breakpoint confidence intervals, (3) a variety of 'recombination aware' phylogenetic tree construction and comparison tools, (4) new matrix-based visualisation tools for examining both individual recombination events and the overall phylogenetic impacts of multiple recombination events and (5) new tests to detect the influences of gene arrangements, encoded protein structure, nucleic acid secondary structure, nucleotide composition, and nucleotide diversity on recombination breakpoint patterns. The key feature of RDP4 that differentiates it from other recombination detection tools is its flexibility. It can be run either in fully automated mode from the command line interface or with a graphically rich user interface that enables detailed exploration of both individual recombination events and overall recombination patterns.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.