title: RDP3: a flexible and fast computer program for analyzing recombination.
abstract: RDP3 is a new version of the RDP program for characterizing recombination events in DNA-sequence alignments. 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 patterns of recombination within datasets and recombination-aware ancestral sequence reconstruction. Complementary to a high degree of analysis flow automation, RDP3 also has a highly interactive and detailed graphical user interface that enables more focused hands-on cross-checking of results with a wide variety of newly implemented phylogenetic tree construction and matrix-based recombination signal visualization methods. The new RDP3 can accommodate large datasets and is capable of analyzing alignments ranging in size from 1000 × 10 kilobase sequences to 20 × 2 megabase sequences within 48 h on a desktop PC.
  
  
  BACKGROUND
  RDP3 is available for free from its web site http://darwin.uvigo.es/rdp/rdp.html.
authors.affiliation: Computational Biology Group, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Centre for High Performance Computing, Rosebank, Cape Town, South Africa. darrenpatrickmartin@gmail.com
authors.forename: Darren P
authors.initials: DP
authors.lastname: Martin
authors.forename: Philippe
authors.initials: P
authors.lastname: Lemey
authors.forename: Martin
authors.initials: M
authors.lastname: Lott
authors.forename: Vincent
authors.initials: V
authors.lastname: Moulton
authors.forename: David
authors.initials: D
authors.lastname: Posada
authors.forename: Pierre
authors.initials: P
authors.lastname: Lefeuvre
mesh_terms: D000465:Algorithms; D030541:Databases, Genetic; D010802:Phylogeny; D011995:Recombination, Genetic / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods; D012984:Software; D014584:User-Computer Interface
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