Homoplasy Test: Noel Smith and John Maynard Smith
PIST: Andrew Rambaut and Michael Worobey
Methods that use phylogenetic trees to detect the presence of recombination:
Methods that use phylogenetic trees and require the presence of obviously mosaic sequences:
4SIS: Jun Fan and David Robertson
BARCE: Grainne McGuire and Dirk Husmeier [also implemented in TOPALi]
DualBrothers: Recombination Detection Software: Vladimir Minin, Karin Dorman, Fang Fang and Marc Suchard
JAMBE: Dirk Husmeier [also implemented in TOPALi]
LARD: Andrew Rambaut [also implemented in RDP2]
SimPlot: Stuart Ray [implements bootscanning] [also implemented in RDP2]
PLATO: Nick Grassly, Andrew Rambaut and Edward Holmes
RecPars: Kim Fisker and Jotun Hein
REGA HIV-1 subtyping tool: Tulio de Oliveirea
SERAD: Dirk Husmeier [also implemented in TOPALi]
TOPAL: Grainne McGuire and Frank Wright [versions 1 and 2; also implemented in TOPALi and RDP2]
VisRD: Korbinian Strimmer, Kristoffer Forslund and Vincent MoultonMethods that analyze patterns of sites:
Partimatrix: Ingrid Jakobsen, Susan Wilson and Simon Easteal
Reticulate: Ingrid Jakobsen and Simon Easteal [also implemented in RDP2]
RDP & RDP2: Darren Martin, Edward Rybicki, C. Williamson and David Posada
SiScan: Mark Gibbs, John Armstrong and Adrian Gibbs [also implemented in RDP2]
STEPHENS: Fredrick Prat and Guy Drouin
Phi test: Trevor Bruen[also implemented in SplitTree]
Stepwise: Jinko Graham, Brad McNeney and Francoise Seillier-Moiseiwistch
FRAG-DIST: Jun Fan and David Robertson
Recco: Jochen Maydt
CODOUBLE: Fredrick Prat and Guy Drouin
GENECONV: Stanley Sawyer [replaces VTDIST] [also implemented in RDP2]
Maynard Smith's Maximum Chi-Squared Method: Nick Ross and Brian Spratt [also implemented in RDP2] PhylPro: Georg Weiller RAT: Graham Etherington, Jo Dicks and Ian Roberts RIP: Adam Siepel and Bette Korber [online tool] RIP3.0: Adam Siepel, Chuck Calef and Bette Korber [online tool]
Sawyer's Runs Tests: Nick Ross and Brian Spratt [see also GENECONV]
SAWYER: Fredrick Prat and Guy Drouin [see also GENECONV] SimPlot: Stuart Ray [implements similarity/diversity plotting]
SNEATHST (Sherman Test): Peter Sneath Swaap and Swaap PH: David PrideMethods that do not require a multiple alignment:
BLAST Genotyping Tool: Uwe Plikat and Colombe Chappey [online tool] JPHMM: Anne-Kathrin Schultz, Ming Zhang, Thomas Leitner et al. [online tool]Population genetics based methods:
DnaSP: Julio Rozas and Ricardo Rozas
sequenceLD and fins: Paul Fearnhead and Peter Donnelly
LDhat package: Gil McVean, Philip Awadalla and Paul Fearnhead
RECOMBINE: Mary Kuhner, Jon Yamato and Joe Felsenstein
SITES: Jody Hey
Bootscanning Package: Wayne Cobb and Mika Salminen [mirrored at KTL, Finland] [also implemented in RDP2]
LIKEWIND: John Archibald and Andrew Roger