Greetings,
I used GARD a while back on the UCSD cluster and now I am trying to find where in the data the 95% CI are listed, although I am not sure that is included in the output. Do you have a suggestion for how I could calculate the 95% CI? Thanks!

-Crystal 

Thanks Sergei. I just got reviewer comments back on a manuscript and one part of my analysis that I was dinged on was that I only used GARD to infer breakpoints. So I am reanalyzing the data also with RDP, and by eye it looks like the RDP recombinant regions cluster near GARD breakpoints, but I would like to be able to state whether or not they fall within the 95% CI. If you are interested, this is specifically what was stated:

1. Detection of recombination breakpoints using SBP and GARD can be
misleading. These methods are quite robust, but their performance can be
affected by several factors that can produce false positives, such as
recombination rate, exponential population growth (star-like topologies)
and patterns of substitution rate correlation. To ensure robustness, the
authors should have compared several recombination detection methods
based on different sets of underlying assumptions (e.g. the programs
implemented in RDP, the split decomposition based test implemented in
SplitsTrees).

-Crystal