A critical step before phylogenetic analysis and molecular selection analysis is to detect recombination and either remove recombinant sequences or partition the alignment into different spans that a recombination-free. The problem is that there are so many different recombination detection programs available. These have been nicely review by Posada (2002) and some of the programs have been benchmarked by Kosakovsky Pond and Frost (2005).
I decided to compile all the programs that are available but there are so many that I am sure I have missed some. If you know of any others, please leave a comment below.
I have split the programs into the same four different categories as Posada (2002) but some programs implement multiple methods so it gets a bit tricky. The size of the font relates to the number of citations each program/publication has received in Google Scholar. As you can see, there are some clear favourites.
You can click on the names of the programs and this should either take you to the publication abstract on Pubmed or to the website for the software.