Hello.  I am working with a two datasets that are roughly 3000nt in length with 126 and 75 sequences, which is why I am not able to use the online version of GARD for recombination detection.  Even when I remove 26 sequences of the first dataset I am only able to identify a single breakpoint because not all breakpoints are examined.  Using HyPHY standalone is easy enough, but I am not able to run GARD without the MPI environment, which I do not even begin to understand.  Is there an alternative?  I do believe MPI is installed on a Linux machine that is available to me (because when I enter $mpicc, I do not get an error), but when I try to download HyPHY to that machine using the commands you provide, I get an error!

-bash: svn: command not found

Is there an alternative to using GARD in the MPI environment?  I saw on another post that you do have a serial version of GARD...are you making that available, and can it be used on a PC?  If not, are there any other recombination detection methods available, that you would recommend, that can ID multiple breakpoints that may affect a topology?  Thank you! 

Thank you so much !  I will send it to you right now!