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Sister-Scanning: a Monte Carlo procedure for assessing signals in recombinant sequences
TLDR
We have developed a method, that we call 'sister-scanning', for assessing phylogenetic and compositional signals in the various patterns of identity that occur between four nucleotide sequences. Expand
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PATRISTIC: a program for calculating patristic distances and graphically comparing the components of genetic change
BackgroundPhylogenies are commonly used to analyse the differences between genes, genomes and species. Patristic distances calculated from tree branch lengths describe the amount of genetic changeExpand
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Sugarcane yellow leaf virus: a novel member of the Luteoviridae that probably arose by inter-species recombination.
The 5895 nucleotide long single-stranded RNA genome of Sugarcane yellow leaf virus Florida isolate (SCYLV-F) includes six major ORFs. All but the first of these are homologous to genes of knownExpand
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The Prehistory of Potyviruses: Their Initial Radiation Was during the Dawn of Agriculture
Background Potyviruses are found world wide, are spread by probing aphids and cause considerable crop damage. Potyvirus is one of the two largest plant virus genera and contains about 15% of allExpand
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A novel pair of universal primers for the detection of potyviruses.
A novel pair of universal primers was developed to detect potyvirus species after conserved sites were identified using all full-length potyvirus sequences available by 2005. The breadth ofExpand
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The potyviruses of Australia
Many potyviruses have been found in Australia. We analyzed a selected region of the coat protein genes of 37 of them to determine their relationships, and found that they fall into two groups. HalfExpand
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Accumulating Variation at Conserved Sites in Potyvirus Genomes Is Driven by Species Discovery and Affects Degenerate Primer Design
Unknown and foreign viruses can be detected using degenerate primers targeted at conserved sites in the known viral gene sequences. Conserved sites are found by comparing sequences and so theExpand
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Time--the emerging dimension of plant virus studies.
Recent research has revealed that some plant viruses, like many animal viruses, have measurably evolving populations. Most of these viruses have single-stranded positive-sense RNA genomes, but a fewExpand
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Evidence that a plant virus switched hosts to infect a vertebrate and then recombined with a vertebrate-infecting virus.
  • M. Gibbs, G. Weiller
  • Biology, Medicine
  • Proceedings of the National Academy of Sciences…
  • 6 July 1999
There are several similarities between the small, circular, single-stranded-DNA genomes of circoviruses that infect vertebrates and the nanoviruses that infect plants. We analyzed circovirus andExpand
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A reevaluation of the higher taxonomy of viruses based on RNA polymerases.
In order to assess the validity of classifications of RNA viruses, published alignments and phylogenies of RNA-dependent RNA and DNA polymerase sequences were reevaluated by a Monte CarloExpand
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