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!  :-?

Hi Crystal,

Your Linux box seems to be missing SVN (which is a package used to manage source code); but I wouldn't recommend running GARD on large alignments on a single PC -- that would take too long. You can send me your alignment by e-mail and I can run it through GARD on our cluster; this is probably the easiest solution for a one-off analysis. There are many programs for detecting recombination - you can always try Dave Robertson's page at Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login (although it may be a bit out of date).

Sergei

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