max rho higher than 100?

[Phylloxera]

Hello,

I have some less well characterized lentivirus genomes… so not HIV, but still anticipate (and see) high recombination. The question is ‘how high?’ Thus ldhat to estimate… simple, right? The only problem is my estimated recombination rates (via RDP) are >2 orders of magnitude higher than HIV and my rho is closer to 200. I want to try and validate this estimate by generating a complete lookup table and rerunning, but should I keep max rho at 100 for this? I’m way outside my theoretical and practical comfort zone on this so I’d like to know if you think it would ever be ok to make max rho higher than 100 in complete?

Thanks!

[mcvean]

There's no need - at least in my experience - to use a higher value in the lookup table. At rho=100, the two sites are essentially unlinked. Within the estimation algorithm, however, you may well want to change this - and the algorithm will continue to give sensible results as long as rho between adjacent sites (as opposed to the whole region) is <100. Let me know if you need more input.