A Request For The Recombination Detection Software Of Rechmm

Question

[Ontheway]

Hi, I have a set of orthologous genes and i want to detect the probable recombination events in these genes. Though there are some softwares or algorithms for recombination detection, some of them are only used in windows platform and some can not be used for Installation Failure in linux. I want to run the recombination detection in a batch mode or in command, so the softwares or algorithm launched in linux are what i want. recHMM and RB-finder are the two algorithms for me. Do you have the copies of both algorithms? If you do, please send me the copies, and i will appreciate your help. Thank you!

Answer 1

[Giovanni M Dall'Olio]

These all seems to be very old and no-longer-maintained software.

• Why don't you try something more recent?
• Which installation errors did you get when installing the other software?
• Have you tried to contact the authors?

Some more recent software to detect recombination hotspots are LDhat and Phase, although these usually detect recombination events from intra-population variation data. Alternatively, you may download the Recombination tracks from the UCSC browser, which will probably give you more accurate results and without having to compute them. Note that in general, you have a great variation of recombination hotspots within the same species, so this may complicate your analysis a bit.

[Ontheway]

Thank you for your reply. And there is another question: I want to detect the recombination breakpoint in a set of prokaryotic genes. aRE the softwares, like LDhat and Phase, which is based on population genetics, appropriate for recombination detection in Prokaryote?