I have been searching for recombination analysis tools. (for mammalian genome data, not virus or bacteria)
I think "ReCombine"(https://doi.org/10.1371/journal.pone.0025509) is the tool that is not that outdated, but there is no tutorial for the tool and it is very difficult to understand as a beginner.
I have also looked at RAT, T-RECs... and other possible tools that can be searched on google. But none of them were appropriate for my research.
If you could recommend to me the tools for recombination analysis or tutorials for "ReCombine", it would be grateful.