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RDP3: a flexible and fast computer program for analyzing recombination

D. P. Martin, P. Lemey, M. Lott, V. Moulton, D. Posada, P. Lefeuvre
<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> </i> &nbsp;
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"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btq467">doi:10.1093/bioinformatics/btq467</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20798170">pmid:20798170</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2944210/">pmcid:PMC2944210</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/zlkbnqjtvjcitf7hb7ygt7au5m">fatcat:zlkbnqjtvjcitf7hb7ygt7au5m</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20131125031231/http://web.cbio.uct.ac.za:80/~darren/martina%202010.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/34/32/3432d67b351a7c615cee15451f3e646f45eb91c5.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btq467"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2944210" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

A novel exploratory method for visual recombination detection

Korbinian Strimmer, Kristoffer Forslund, Barbara Holland, Vincent Moulton
<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> </i> &nbsp;
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  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/12734013">pmid:12734013</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC156589/">pmcid:PMC156589</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/qpplzfnov5eddgcibregl2zpli">fatcat:qpplzfnov5eddgcibregl2zpli</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200319231632/http://ecite.utas.edu.au/X/A122423FE89175E1E053021911AC65C8" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/83/cc/83cc3c883442df335070b323e1da898c76f5087f.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC156589" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

HIV classification using the coalescent theory

Ingo Bulla, Anne-Kathrin Schultz, Fabian Schreiber, Ming Zhang, Thomas Leitner, Bette Korber, Burkhard Morgenstern, Mario Stanke
<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> </i> &nbsp;
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.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btq159">doi:10.1093/bioinformatics/btq159</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20400454">pmid:20400454</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2913666/">pmcid:PMC2913666</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/x6hjftx65jagzifabukynnd3um">fatcat:x6hjftx65jagzifabukynnd3um</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180727202412/https://watermark.silverchair.com/btq159.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAb8wggG7BgkqhkiG9w0BBwagggGsMIIBqAIBADCCAaEGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMLq8H0Wy8nyZFWDy5AgEQgIIBclvLKalh4PYdyRb8N6EVvvi_QIkpKXvRUkK72P2aKUF84Ieq-zmOXFT4k4xqm7MxevvYcc2mhJjs1LpzHXLNPksCTAOfkwTCCdiC7UJYqimGCb9ZxhzYABsduOgfuTYRlso5f5yAU37e_KtRr3Af35lm8KC8syCDMdSFuW19vQxOowbMdGjB6eJyzoXcuWCUzoWNVfqp45vGT3pdwS8OKHau_59VNDV-BdvBysKs0aNfCnTgHUxoiIGgxe6JS1YR8GPhDk0yt836XaU09uWp-8_awPqgen_u8lLExGeznzriyt9WCBcrQfj8Cg65sv01mrMWTm4Cz_Tun0ypZiKYv9U_RBVpOl3IZx7Mi7DsPMTn2ZaNRhCovIdqiJLW65fdXiHVkaNEFS95MEJfkKLr9UCCBvJmAPiG5kgAL_630xtSrhiRZgrxFvS6UM4Oe6xRTgD2VZH1CSuaqvobcWYP2Ae5tgurJs5oSDCI-bGyPfkHwU8" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/1a/09/1a09003e52aff8a262c551cd4fb974b9ad5bc5eb.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btq159"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2913666" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Identifying recombinants in human and primate immunodeficiency virus sequence alignments using quartet scanning

Philippe Lemey, Martin Lott, Darren P Martin, Vincent Moulton
<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> </i> &nbsp;
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.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-10-126">doi:10.1186/1471-2105-10-126</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/19397803">pmid:19397803</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2684544/">pmcid:PMC2684544</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/7wjemlkalvcfnmgvmtxbbyvddq">fatcat:7wjemlkalvcfnmgvmtxbbyvddq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20131125030838/http://web.cbio.uct.ac.za:80/~darren/Lemey%202009.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/a8/f5/a8f546aef6d1aeb2ed9b67f85fa097f0c7369c3a.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-10-126"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2684544" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Introgression browser: high-throughput whole-genome SNP visualization

Saulo Alves Aflitos, Gabino Sanchez-Perez, Dick de Ridder, Paul Fransz, Michael E. Schranz, Hans de Jong, Sander A. Peters
<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> &nbsp;
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.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1111/tpj.12800">doi:10.1111/tpj.12800</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25704554">pmid:25704554</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ucwmykkpsnd5rart2rzpuiunpy">fatcat:ucwmykkpsnd5rart2rzpuiunpy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200928181848/https://arxiv.org/ftp/arxiv/papers/1504/1504.05612.pdf" title="fulltext PDF download [not primary version]" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <span style="color: #f43e3e;">&#10033;</span> <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/4a/f6/4af66767b96b25e56b4fbb879e053ad7d2bd4b3c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1111/tpj.12800"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

MinPD: distance-based phylogenetic analysis and recombination detection of serially-sampled HIV quasispecies

Patricia Buendia, Giri Narasimhan
<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> </i> &nbsp;
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] .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/16448005">pmid:16448005</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3195421/">pmcid:PMC3195421</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/cgoioromonesboepgf3mnx6tmy">fatcat:cgoioromonesboepgf3mnx6tmy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20100620072914/http://users.cs.fiu.edu/~giri/bioinf/papers/CSB04.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/8d/ef/8def69e363e79cb3f8f888ceb5ef5935c55f198f.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3195421" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

T-RECs: rapid and large-scale detection of recombination events among different evolutionary lineages of viral genomes

Michail Tsimpidis, Georgios Bachoumis, Kalliopi Mimouli, Zaharoula Kyriakopoulou, David L. Robertson, Panayotis Markoulatos, Grigoris D. Amoutzias
<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> </i> &nbsp;
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.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12859-016-1420-z">doi:10.1186/s12859-016-1420-z</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28056784">pmid:28056784</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5216575/">pmcid:PMC5216575</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/zhh52btbjzek5ce76lcc7dgg24">fatcat:zhh52btbjzek5ce76lcc7dgg24</a> </span>
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Analysis of Next-generation Sequencing Data in Virology - Opportunities and Challenges [chapter]

Sunitha M. Kasibhatla, Vaishali P. Waman, Mohan M. Kale, Urmila Kulkarni-Kale
<span title="2016-01-14">2016</span> <i title="InTech"> Next Generation Sequencing - Advances, Applications and Challenges </i> &nbsp;
(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] .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5772/61610">doi:10.5772/61610</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/lqe7xufl4vf6ndeseyaicgswfi">fatcat:lqe7xufl4vf6ndeseyaicgswfi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190502180424/https://cdn.intechopen.com/pdfs/49336.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/5e/a1/5ea1226e16aefe9d7841348bf56be73064d18319.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5772/61610"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Phylodynamic Reconstruction Reveals Norovirus GII.4 Epidemic Expansions and their Molecular Determinants

J. Joukje Siebenga, Philippe Lemey, Sergei L. Kosakovsky Pond, Andrew Rambaut, Harry Vennema, Marion Koopmans, Colin Parrish
<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> </i> &nbsp;
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  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.ppat.1000884">doi:10.1371/journal.ppat.1000884</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20463813">pmid:20463813</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2865530/">pmcid:PMC2865530</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/vebyrnkvhrcsxndx6m45fwrmxu">fatcat:vebyrnkvhrcsxndx6m45fwrmxu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170811041748/http://origem.info/FIC/pdf/Siebenga_etal_Phylo_recon_norovirus_epi_exp_PLoSPath_May10.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/1c/00/1c0070f2cea560c814d58cefdfffc7550b599d86.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.ppat.1000884"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> plos.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2865530" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Interspecific Plastome Recombination Reflects Ancient Reticulate Evolution in Picea (Pinaceae)

Alexis R. Sullivan, Bastian Schiffthaler, Stacey Lee Thompson, Nathaniel R. Street, Xiao-Ru Wang
<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> </i> &nbsp;
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.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/molbev/msx111">doi:10.1093/molbev/msx111</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28383641">pmid:28383641</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5455968/">pmcid:PMC5455968</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/k5flvbyfarexjibvmqsnqphk5a">fatcat:k5flvbyfarexjibvmqsnqphk5a</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190227073207/http://pdfs.semanticscholar.org/7753/724038a5c9f3e2ddf6247665812bbff7ee21.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/77/53/7753724038a5c9f3e2ddf6247665812bbff7ee21.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/molbev/msx111"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5455968" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Interspecific plastome recombination reflects ancient reticulate evolution inPicea(Pinaceae) [article]

Alexis R. Sullivan, Bastian Schiffthaler, Stacey Lee Thompson, Nathaniel R. Street, Xiao-Ru Wang
<span title="2016-12-30">2016</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
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.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/097519">doi:10.1101/097519</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/zbkbyyabpreppookfw6yderz7m">fatcat:zbkbyyabpreppookfw6yderz7m</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190501012724/https://www.biorxiv.org/content/biorxiv/early/2017/03/13/097519.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/d3/62/d362ec2910ac3477e4e8e13dd698d406ac4d87a0.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/097519"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Estimating the Intra-taxa Diversity, Population Genetic Structure, and Evolutionary Pathways of Cryptococcus neoformans and Cryptococcus gattii

Marina Muñoz, Milena Camargo, Juan D. Ramírez
<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> </i> &nbsp;
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 ).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fgene.2018.00148">doi:10.3389/fgene.2018.00148</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29740480">pmid:29740480</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5928140/">pmcid:PMC5928140</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/pvnhupu6vzaujltvnm7daptucy">fatcat:pvnhupu6vzaujltvnm7daptucy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190304031113/http://pdfs.semanticscholar.org/bfc1/7ef316b9aecf2390059cc5a64b581464a842.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/bf/c1/bfc17ef316b9aecf2390059cc5a64b581464a842.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fgene.2018.00148"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> frontiersin.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5928140" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Transmission of Single and Multiple Viral Variants in Primary HIV-1 Subtype C Infection

Vladimir Novitsky, Rui Wang, Lauren Margolin, Jeannie Baca, Raabya Rossenkhan, Sikhulile Moyo, Erik van Widenfelt, M. Essex, Jean-Pierre Vartanian
<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> </i> &nbsp;
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] .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0016714">doi:10.1371/journal.pone.0016714</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21415914">pmid:21415914</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3048432/">pmcid:PMC3048432</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/3elyaep2zbcy7isbsyeflnk53a">fatcat:3elyaep2zbcy7isbsyeflnk53a</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170927183718/http://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0016714&amp;type=printable" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/95/94/95949b675eca523fb98b3197fd70fbae58dcd6e7.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0016714"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> plos.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3048432" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Strain-specific genome evolution in Trypanosoma cruzi, the agent of Chagas disease

Wei Wang, Duo Peng, Rodrigo P. Baptista, Yiran Li, Jessica C. Kissinger, Rick L. Tarleton, Nicolai Siegel
<span title="2021-01-28">2021</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> </i> &nbsp;
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] .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.ppat.1009254">doi:10.1371/journal.ppat.1009254</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/33508020">pmid:33508020</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ec2htafezvhovgqka6bwligi5a">fatcat:ec2htafezvhovgqka6bwligi5a</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210226122947/https://storage.googleapis.com/plos-corpus-prod/10.1371/journal.ppat.1009254/2/ppat.1009254.pdf?X-Goog-Algorithm=GOOG4-RSA-SHA256&amp;X-Goog-Credential=wombat-sa%40plos-prod.iam.gserviceaccount.com%2F20210226%2Fauto%2Fstorage%2Fgoog4_request&amp;X-Goog-Date=20210226T122947Z&amp;X-Goog-Expires=3600&amp;X-Goog-SignedHeaders=host&amp;X-Goog-Signature=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" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/3a/80/3a806349365e299e141d4e06f37b3b5e972433a6.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.ppat.1009254"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> plos.org </button> </a>

A comparative analysis of SLA-DRB1 genetic diversity in Colombian (creoles and commercial line) and worldwide swine populations

Carmen Teresa Celis-Giraldo, Michel David Bohórquez, Milena Camargo, Carlos Fernando Suárez, Anny Camargo, Kewin Rodríguez-Obediente, Alejandra Martínez, Carlos Edmundo Lucero, Byron Hernández, Raúl Manzano-Román, Manuel Alfonso Patarroyo
<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> </i> &nbsp;
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.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41598-021-83637-8">doi:10.1038/s41598-021-83637-8</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/33619347">pmid:33619347</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7900169/">pmcid:PMC7900169</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/j32dz4c6u5a63chegfxp33dbdi">fatcat:j32dz4c6u5a63chegfxp33dbdi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210718101133/https://www.nature.com/articles/s41598-021-83637-8.pdf?error=cookies_not_supported&amp;code=508861bc-f2de-45f7-a8ee-93eb20d6c9b4" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/5a/4f/5a4f6dcc89744b1d2c6aa2c3aafbac41f4613d98.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41598-021-83637-8"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7900169" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>
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