RDP (Recombination detection program) is software that applies a number of recombination detection and analysis algorithms. 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, RDP 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. RDP 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.
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Martin DP, Lemey P, Lott M, Moulton V, Posada D, Lefeuvre P. (2010).
RDP3: a flexible and fast computer program for analyzing recombination.
Bioinformatics 26, 2462-2463