Two tools here for estimation of recombination:
1. RDP
http://darwin.uvigo.es/rdp/rdp.html
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.
2. IRiS algorithm
it is not a program
http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001010
Recombination brings together DNA sequences that can be very distantly related, and, thus, quite different from each other. This is often cited as a main hurdle for using recombining regions (that is, most of the genome) to reconstruct sequence phylogeny. We have turned this argument around: chromosomes carrying a similar change in sequence pattern are likely to be descendants of the same recombination event, and thus, related. We have devised an algorithm that detects such changes in sequence patterns and identifies the descendants of a recombination event. After some fine-tuning, we have applied it to sequence data in several human populations and have found that recombination events recapitulate the history of these populations. This opens the possibility of adding recombination to the current allele-based analysis of population structure and history. Our method also provides a tool for the genomic analysis of recombination, both because it pinpoints recombination events rather than just estimating recombination rates, and because, being biased towards more recent events, it can offer a glimpse of the fast evolution of recombination.
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