RDP3: a flexible and fast computer program for analyzing recombination

Bioinformatics. 2010 Oct 1;26(19):2462-3. doi: 10.1093/bioinformatics/btq467. Epub 2010 Aug 26.


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.

Availability: RDP3 is available for free from its web site http://darwin.uvigo.es/rdp/rdp.html.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Databases, Genetic
  • Phylogeny
  • Recombination, Genetic / genetics*
  • Sequence Analysis, DNA / methods
  • Software*
  • User-Computer Interface