RDP3: a flexible and fast computer program for analyzing recombination

TLDR

RDP3 is a new version of the RDP program for detecting recombination events in DNA sequence alignments. RDP3 adds four new recombination detection methods, hotspot tests, matrix visualization, and recombination‑aware ancestral reconstruction, and provides an interactive GUI and automated workflow that can analyze 1,000–20,000 sequences up to 2 Mb in size within 48 h on a desktop PC. RDP3 is freely available at http://darwin.uvigo.es/rdp/rdp.html; contact [e-mail]; see the manual for detailed method descriptions and usage instructions.

Abstract

Abstract Summary: 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 Contact: [e-mail] Supplementary information: The RDP3 program manual contains detailed descriptions of the various methods it implements and a step-by-step guide describing how best to use these.