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RDP3: a flexible and fast computer program for analyzing recombination
<span title="2010-08-26">2010</span>
<i title="Oxford University Press (OUP)">
<a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wmo54ba2jnemdingjj4fl3736a" style="color: black;">Bioinformatics</a>
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Among other novelties, this version includes four new recombination analysis methods (3SEQ, VISRD, PHYLRO and LDHAT), new tests for recombination hot-spots, a range of matrix methods for visualizing over-all ...
signal visualization methods. ...
Among these are three new non-parametric recombination detection methods (3seq, visrd and phylpro; Boni et al., 2007; Lemey et al., 2009; Weiller, 1998) , a parametric recombination rate estimation method ...
<span class="external-identifiers">
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A novel exploratory method for visual recombination detection
<span title="2003-04-25">2003</span>
<i title="BMC">
<a target="_blank" rel="noopener" href="https://fatcat.wiki/container/6bzsiicmhvczjnsm7jbog7ysaa" style="color: black;">Genome Biology</a>
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A versatile visual approach for detecting recombination and identifying recombination breakpoints within a sequence alignment is presented. ...
Visual detection of recombination The basic strategy for visual detection of recombination is to first slide a window along the alignment in a stepwise, overlapping fashion, computing at each step a quartet ...
Computer program The highway and the occupancy plots, as well as trajectory filtering and animated quartet-mappings, are implemented in a user-friendly program called VisRD (Visual Recombination Detection ...
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HIV classification using the coalescent theory
<span title="2010-04-16">2010</span>
<i title="Oxford University Press (OUP)">
<a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4r72gbmtcrde5no3fwwogjs3cu" style="color: black;">Computer applications in the biosciences : CABIOS</a>
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model accounting for complex recombination patterns. ...
Results: We developed the program ARGUS that scores classifications of sequences into subtypes and recombinant forms. ...
VisRD finds no recombination at all. ...
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Identifying recombinants in human and primate immunodeficiency virus sequence alignments using quartet scanning
<span title="">2009</span>
<i title="Springer Nature">
<a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a>
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The new method is available in the VisRD v.3.0 package ...
Here, we extend a quartet-mapping based recombination detection method to enable identification of recombinant sequences without prior specifications of either query and reference sequences. ...
Acknowledgements We thank Liz Bailes for providing the SIV sequence data and David Posada for providing the simulated data sets and previous results for other recombination detection methods. ...
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<a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/19397803">pmid:19397803</a>
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Introgression browser: high-throughput whole-genome SNP visualization
<span title="2015-03-24">2015</span>
<i title="Wiley">
<a target="_blank" rel="noopener" href="https://fatcat.wiki/container/eyeekm765nepfjifdg2zcmtf2y" style="color: black;">The Plant Journal</a>
</i>
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<span title="2015-04-21">2015</span> <span class="release-stage" >pre-print</span> <span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1504.05612v1">arXiv:1504.05612v1</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/vlpyhyxqiba6lk33ycbdja2hz4">fatcat:vlpyhyxqiba6lk33ycbdja2hz4</a> </span>
Usually, the desired traits are monitored in consecutive crossing generations by marker-assisted selection, but their analyses fail in chromosome regions where crossover recombinants are rare or not viable ...
In a third example, we demonstrate the power of the IBROWSER in a panel of 600 Arabidopsis accessions, detecting the boundaries of a SNP-free region around a polymorphic 1.17 Mbp inverted segment on the ...
However, visRD and ReCombine only handle relatively small genomes, whereas SHOREmap, NGL and PHYLONET-HMM are targeting inbred lines. ...
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MinPD: distance-based phylogenetic analysis and recombination detection of serially-sampled HIV quasispecies
<span title="">2004</span>
<i >
<a target="_blank" rel="noopener" href="https://fatcat.wiki/container/3sztfdkxrbcorgsptnju63e33a" style="color: black;">Proceedings. IEEE Computational Systems Bioinformatics Conference</a>
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The proposed visualization of the phylogenetic tree\network further enhances the benefits of our methods. ...
Recombination may further complicate the analysis. Such relationships are not easily expressed by traditional phylogenetic methods. ...
An improvement on this method is VisRD, another visual detection method that does not require the reference strain to be identified in advance [20] . ...
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T-RECs: rapid and large-scale detection of recombination events among different evolutionary lineages of viral genomes
<span title="2017-01-05">2017</span>
<i title="Springer Nature">
<a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a>
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Many computational tools that detect recombination in viruses are not adapted for the ongoing genomic revolution. ...
different evolutionary lineages, (iv) manual inspection of detected recombination events by similarity plots and (v) annotation of genomic regions. ...
Potential recombination events are identified with the detected acceptor and donor sequences and visualized in a graphical window. ...
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Analysis of Next-generation Sequencing Data in Virology - Opportunities and Challenges
[chapter]
<span title="2016-01-14">2016</span>
<i title="InTech">
Next Generation Sequencing - Advances, Applications and Challenges
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(PHYLPRO) [105] and Visual Recombination Detection (VisRD) [106] . iii. ...
Recombination Detection Program version 4 (RDP4) package In order to detect recombination, various methods have been developed and are provided in RDP4 package [94] . ...
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Phylodynamic Reconstruction Reveals Norovirus GII.4 Epidemic Expansions and their Molecular Determinants
<span title="2010-05-06">2010</span>
<i title="Public Library of Science (PLoS)">
<a target="_blank" rel="noopener" href="https://fatcat.wiki/container/bcchuruegramvpr4vupdzp5jfm" style="color: black;">PLoS Pathogens</a>
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Therefore, we set out to study the population structure and changes thereof of GII.4 strains detected through systematic outbreak surveillance since the early 1990s. ...
While a number of the computationally determined adaptively evolving sites were on the surface of the capsid and possible subject to immune selection, we also detected sites that were subject to constrained ...
Using GARD (Genetic Algorithm for Recombination Detection), VisRD (Visual Recombination Detection) and RDP3 (Recombination detection program), significant phylogenetic variability was identified in this ...
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Interspecific Plastome Recombination Reflects Ancient Reticulate Evolution in Picea (Pinaceae)
<span title="2017-04-05">2017</span>
<i title="Oxford University Press (OUP)">
<a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4bimmtjdczetrfmnc3ijbmwpoy" style="color: black;">Molecular biology and evolution</a>
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While exceptions to these assumptions can profoundly influence evolutionary inference, detecting them can require extensive sampling, abundant sequence data, and detailed testing. ...
Support for interspecific recombination remained after controlling for sequence saturation, positive selection, and potential alignment artifacts. ...
As recombination can severely bias population and phylogenetic analyses (e.g. Schierup and Hein 2000) , new detection methods are warranted. ...
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Interspecific plastome recombination reflects ancient reticulate evolution inPicea(Pinaceae)
[article]
<span title="2016-12-30">2016</span>
<i title="Cold Spring Harbor Laboratory">
bioRxiv
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While exceptions to these assumptions can profoundly influence evolutionary inference, detecting them can require extensive sampling, abundant sequence data, and detailed testing. ...
Support for interspecific recombination remained after controlling for sequence saturation, positive selection, and potential alignment artifacts. ...
Then, RDP4 identifies the probable recombinant sequence using the PHYLPRO (Weiller 1998) , VISRD (Lemey et al. 2009 ), and EEEP (Beiko & Hamilton 2006) methods. ...
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Estimating the Intra-taxa Diversity, Population Genetic Structure, and Evolutionary Pathways of Cryptococcus neoformans and Cryptococcus gattii
<span title="2018-04-24">2018</span>
<i title="Frontiers Media SA">
<a target="_blank" rel="noopener" href="https://fatcat.wiki/container/r7trx2kj6je5jhtaoy3rztibgy" style="color: black;">Frontiers in Genetics</a>
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Additionally, analyzes in the Recombination Detection Program version 4 (RDP4) were developed (Martin et al., 2015) to detect and characterize recombination signals from the complete set of concatenated ...
In the case of C. gattii, although signals attributable to a process other than recombination were identified, only one possible recombinant was detected (ST-100-VGIII; Supplementary Table S5 ). ...
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Transmission of Single and Multiple Viral Variants in Primary HIV-1 Subtype C Infection
<span title="2011-02-09">2011</span>
<i title="Public Library of Science (PLoS)">
<a target="_blank" rel="noopener" href="https://fatcat.wiki/container/s3gm7274mfe6fcs7e3jterqlri" style="color: black;">PLoS ONE</a>
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Additional analysis involved distribution of individual viral distances, highlighter plots, recombination analysis, and estimation of tMRCA, and resolved 4 of the 5 remaining cases. ...
Specifically, phylogenetic reconstruction, inter-and intra-patient distribution of maximum and mean genetic distances, analysis of Poisson fitness, shape of highlighter plots, recombination analysis, and ...
RDP3 utilizes a range of non-parametric recombination detection methods including BOOTSCAN, MAXCHI, CHIMAERA, 3SEQ, GENECONV, SISCAN, PHYLPRO and VISRD [29] [30] [31] [32] [33] [34] . ...
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Strain-specific genome evolution in Trypanosoma cruzi, the agent of Chagas disease
<span title="2021-01-28">2021</span>
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isolates, but also provide evidence of the processes that generate and maintain that diversity, including extensive gene amplification, dispersion of copies throughout the genome and diversification via recombination ...
using the PHYLPRO, VISRD, and EEEP methods. ...
This pipeline uses the RDP4 package that employs a variety of methods to detect signals of recombination and then approximates breakpoints and the recombinant sequence [42] . ...
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A comparative analysis of SLA-DRB1 genetic diversity in Colombian (creoles and commercial line) and worldwide swine populations
<span title="2021-02-22">2021</span>
<i title="Springer Science and Business Media LLC">
<a target="_blank" rel="noopener" href="https://fatcat.wiki/container/tnqhc2x2aneavcd3gx5h7mswhm" style="color: black;">Scientific Reports</a>
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or mosaic), VisRD (for visual recombination detection in a sequence alignment) and BURT (for testing significance in factor analysis/analysis of variance) methods 64 . ...
The phylogenetic trees were visualised in the web tool Interactive Tree Of Life V3 (http://itol.embl.de) 63 ; the Recombination Detection Program (version 4) (RDP4) was also used. ...
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