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RDP4: Detection and analysis of recombination patterns in virus genomes

published in: Virus Evolution

date of publication: 2015-05-26

main subject: virus

Cites articles 48

Date

Title

Authors

2014-09-26

SDT: a virus classification tool based on pairwise sequence alignment and identity calculation
2014-06-17

Patterns of recombination in HIV-1M are influenced by selection disfavouring the survival of recombinants with disrupted genomic RNA and protein structures
2014-02-22

Constraints from protein structure and intra-molecular coevolution influence the fitness of HIV-1 recombinants.

Simon C Lovell
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2014-05-01

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2013-03-30

Systematic phylogenetic analysis of influenza A virus reveals many novel mosaic genome segments

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2012

Genetic variability among complete human respiratory syncytial virus subgroup A genomes: bridging molecular evolutionary dynamics and epidemiology

Philippe Lemey, Emmanuel J H J Wiertz, Nicolaas J G Jansen
2012-05

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

Marc A. Suchard, Aaron Earl Darling, Fredrik Ronquist, Maxim Teslenko, Paul J. van der Mark, Daniel L. Ayres, Sebastian Höhna, Bret Larget, John Huelsenbeck, Liang Liu
2011-08-01

Homologous recombination in negative sense RNA viruses

Guan-Zhu Han, Michael Worobey
2011-06-29

Reconstructing the history of maize streak virus strain a dispersal to reveal diversification hot spots and its origin in southern Africa

Philippe Lemey, Michelo Simuyandi, Gordon William Harkins, Rob W Briddon, Edward Rybicki
2011-05-19

Analysing recombination in nucleotide sequences

David Posada
2010

The spread of tomato yellow leaf curl virus from the Middle East to the world

Philippe Lemey
2010-09-29

RNA structures facilitate recombination-mediated gene swapping in HIV-1

Etienne Simon-Loriere, Matteo Negroni
2010-09-10

The population genomics of begomoviruses: global scale population structure and gene flow
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FastTree 2--approximately maximum-likelihood trees for large alignments

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2010-04

The effect of recombination on the reconstruction of ancestral sequences

Miguel Arenas, David Posada
2010-07-17

Correlation between recombination junctions and RNA secondary structure elements in poliovirus Sabin strains.
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Molecular mechanisms of recombination restriction in the envelope gene of the human immunodeficiency virus

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

Philippe Lemey
2008-12-30

Widely conserved recombination patterns among single-stranded DNA viruses

Pierre Lefeuvre
2008-03-19

Homologous recombination is very rare or absent in human influenza A virus

Edward C. Holmes
2007-11-01

Avoidance of protein fold disruption in natural virus recombinants

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2007-04-03

An exact nonparametric method for inferring mosaic structure in sequence triplets

David Posada, Maciej Boni
2007-02-21

Extensive intrasubtype recombination in South African human immunodeficiency virus type 1 subtype C infections

Bette Korber, Christian Brander, Tanmoy Bhattacharya, Bruce D. Walker, Photini Kiepiela, David Heckerman, Philip J. R. Goulder, Senica Chetty, James Mullins, Gerald H Learn, David C. Nickle
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Recombination patterns in aphthoviruses mirror those found in other picornaviruses
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Konrad Scheffler
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Nicholas Hamilton
2006-01-01

Frequency and dynamics of recombination within different species of human enteroviruses.
2005-09-21

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Article - wd:Q30394442

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