Recombination Breakpoint Detection

Question

[Ontheway]

Hi, I am looking for a software to detect the recombination breakpoint in a set of genes. Because I have a large set of genes, I hope to run the detection in a batch mode. then a software implemented in Linux is what I want. Unfortunately, few were found. DualBrother or Cbrother is one which can be implemented in linux, but there were errors when they were installing. it was devastating for me. So I am here to ask for help. Does anyone recommend a favorite and available method for detecting recombination breakpoints in linux?

Answer 1

[tim]

You might want to try http://www.maths.bris.ac.uk/~madjl/finestructure/chromopainter_info.html

[guitarfx]

Should gene model be taken into account for the fasta passed to GARD? I could see arguments for keeping them in ( to retain the data) or taking them out (given exons will likely be under a different selective pressure)

Answer 2

[GR]

GARD from Hyphy. You can also run it on their server or on your own server if the families are large.