Evidence map›Paper›PMID 40064777›Full record

ArticleMethods in molecular biology (Clifton, N.J.)2025

Recombination Analysis of Geminiviruses Using Recombination Detection Program (RDP).

Alvin Crespo-Bellido, Darren Patrick Martin, Siobain Duffy

Abstract read
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In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from 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.

2 · The registry

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.

3 · Its place in the literature

Who cites it

2 citing papers in PubMed.

  1. Article
  2. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

3 authors.

Alvin Crespo-BellidoDepartment of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA.
Darren Patrick MartinDivision of Computational Biology, Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa.
Siobain DuffyDepartment of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA. duffy@sebs.rutgers.edu.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Geminiviruses are recombination-prone, and characterizing this evolutionary process within their genomes is a frequent goal of researchers. RDP is a stand-alone Windows program combining many algorithms that detect and characterize recombination. It has been widely used by the geminivirus community (and beyond). Here we describe the use of RDP4 and RDP5 for analysis of geminiviral nucleotide sequences including: (i) obtaining a reasonable dataset for analysis, (ii) making a credible multiple sequence alignment and (iii) analyzing an alignment with RDP on that alignment. RDP to both characterize recombination events and to produce statistically recombination-free datasets for other molecular evolution analyses.

Indexed as

Computational BiologyGeminiviridaeRecombination, GeneticSoftwareAlgorithmsEvolution, MolecularGenome, ViralSequence AlignmentEvolutionHorizontal gene transferMultiple sequence alignmentPhylogeneticsRDP5RecombinationSub-alignment

Identifiers

PMID40064777

What OpenQuestion holds

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Registered trials

None linked

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.