I'm trying to perform parameter resampling using Latin Hypercube sampling in HYPHY, and had a couple of questions:

1) Is it possible to perform LHS from the command line in HYPHY?

2) After resampling, it looks like some of my LHS samples have a likelihood value of -infinity.  I thought that the re-samples are chosen with probability somehow proportional to their likelihood, so that impossible parameter combinations would be excluded?  Any idea why some of the re-samples might have a likelihood value of -infinity?   (I chose M << N, so there should have been plenty of initial samples to choose from.

3)Is it correct to turn LHS samples into confidence bounds by taking the interval containing 95% of the resampled parameter estimates?

Thanks!!