title: T-RECs: rapid and large-scale detection of recombination events among different evolutionary lineages of viral genomes.
abstract: BACKGROUND
  Many computational tools that detect recombination in viruses are not adapted for the ongoing genomic revolution. A computational tool is needed, that will rapidly scan hundreds/thousands of genomes or sequence fragments and detect candidate recombination events that may later be further analyzed with more sensitive and specialized methods.
  
  
  RESULTS
  T-RECs, a Windows based graphical tool, employs pairwise alignment of sliding windows and can perform (i) genotyping, (ii) clustering of new genomes, (iii) detect recent recombination events among different evolutionary lineages, (iv) manual inspection of detected recombination events by similarity plots and (v) annotation of genomic regions.
  
  
  CONCLUSIONS
  T-RECs is very effective, as demonstrated by an analysis of 555 Norovirus complete genomes and 2500 sequence fragments, where a recombination hotspot was identified at the ORF1-ORF2 junction.
authors.affiliation: Department of Biochemistry and Biotechnology, Bioinformatics Laboratory, University of Thessaly, Larisa, Greece.
authors.forename: Michail
authors.initials: M
authors.lastname: Tsimpidis
authors.affiliation: Department of Biochemistry and Biotechnology, Bioinformatics Laboratory, University of Thessaly, Larisa, Greece.
authors.forename: Georgios
authors.initials: G
authors.lastname: Bachoumis
authors.affiliation: Department of Biochemistry and Biotechnology, Bioinformatics Laboratory, University of Thessaly, Larisa, Greece.
authors.forename: Kalliopi
authors.initials: K
authors.lastname: Mimouli
authors.affiliation: Department of Biochemistry and Biotechnology, Molecular Virology Laboratory, University of Thessaly, Larisa, Greece.
authors.forename: Zaharoula
authors.initials: Z
authors.lastname: Kyriakopoulou
authors.affiliation: Faculty of Life Sciences, University of Manchester, Manchester, UK.
authors.forename: David L
authors.initials: DL
authors.lastname: Robertson
authors.affiliation: Department of Biochemistry and Biotechnology, Molecular Virology Laboratory, University of Thessaly, Larisa, Greece.
authors.forename: Panayotis
authors.initials: P
authors.lastname: Markoulatos
authors.affiliation: Department of Biochemistry and Biotechnology, Bioinformatics Laboratory, University of Thessaly, Larisa, Greece. amoutzias@bio.uth.gr.
authors.forename: Grigoris D
authors.identifier: http://orcid.org/0000-0001-5961-964X
authors.initials: GD
authors.lastname: Amoutzias
mesh_terms: D016000:Cluster Analysis; D053938:DNA Fragmentation; D004279:DNA, Viral / Q000235:genetics; D030541:Databases, Genetic; D019143:Evolution, Molecular; D016679:Genome, Viral; D060005:Genotyping Techniques; D029322:Norovirus / Q000235:genetics*; D011995:Recombination, Genetic; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D012984:Software
chemical_list: D004279:DNA, Viral
keywords: Graphical tool; Norovirus; Pairwise alignment; Recombination; Similarity plot; Virus