I have a couple questions regarding LDhat:

1.) Just to confirm I am doing this correctly:

I am trying to calculate recombination/mutation rate in a bacterial dataset. I use the pairwise command with default settings and in the outfile.txt I get a ML estimate of 4Ner of 51 and a theta of 0.01358. A literature source (doi:10.1016/j.meegid.2007.07.007; authors acknowledge Gil McVean for help with LDhat so I assume they did it correctly) states that since 4Ner is the value for the entire region and theta per site, 4Ner needs to be divided by the length of my alignment (3062bp) to give rho. This ultimately gives me a recombination/mutation rate rho/theta of around 1.2, which seems reasonable to me.

2.) There seems to be considerable confusion in the literature whether LDHat allows the calculation of the ratio of rates at which recombination and mutation occur (termed rho/theta in programs such as ClonalFrame) or the ratio of probabilities that a site is altered through recombination or mutation (r/m in ClonalFrame terminology). As a consequence I am also confused. If I calculate rho/theta in LDhat, what am I getting?

Thank you for your help!