Recombination Detection Program (RDP) view and edit fasta files, apply a number of recombination detection and analysis algorithms. A single highly automated analysis tool that can simultaneously analyse large sequence alignments with a range of different recombination detection methods. Although I have tried to make the program accessible to casual users (i.e. people uncomfortable with the use of UNIX/DOS command lines who would like a quick and simple answer to some recombination related question), the program both provides access to a wide range of analysis options and enables a high degree of interactivity in the analysis of recombination.

The main strength of RDP3 is that it simultaneously uses a range of different recombination detection methods to both detect and characterise the recombination events that are evident within a sequence alignment without any prior user indication of a non-recombinant set of reference sequences.

A number of different alignment file formats are recognized by RDP3 including PHYLIP, MFA, XMFA, GDE, FASTA, CLUSTAL, GCG, NEXUS, MEGA and DNAMAN. To open a file press the "Open" button in the command button panel) and select the file to be opened. The directory from which the file is selected is "remembered" by RDP3 when it is shut down. Once loaded the aligned sequences and their names are displayed in the "sequence display panel". Also displayed are the degrees of nucleotide identity in different regions of the aligned sequences in an "identity display panel".

Besides alignment files, RDP3 project files (with a ".rdp" extension) may also be loaded. In addition to aligned sequences these files also contain information on possible recombination events detected in previous analysis sessions.

RDP3 can also read ORF positions and names from GenBank files. The program requires (1) that a GenBank file be opened after an alignment file and (2) that one of the sequences within the multiple alignment is the same as the sequence in the GenBank file. RDP3 will automatically scan the sequences in the alignment to check whether any match the sequence in the GenBank file. If ORF information is supplied to RDP3 and breakpoint distribution analyses are performed it will test for variations in recombination breakpoint distributions relative to ORF boundaries as described in Lefuvre et al. (2009). If you are unable to load a particular GenBank file successfully, send me the file together with your alignment and I'll fix the problem for you.

RDP3 can also read protein structure information from protein data bank files (i.e. those files with a .pdb extension). If the genome regions being analysed encode proteins with associated structures any number of different .pdb files can be loaded.

The license of this software is Freeware, you can free download and free use this calculator software.