These are chat archives for dereneaton/ipyrad

18th
Nov 2017
tommydevitt
@tommydevitt
Nov 18 2017 02:57
@dereneaton Thanks, Deren. It's nice to have those options in the analysis tools, as in the bpp tool. I agree that it makes sense to include invariant loci in coalescent-based methods. Just wanted to be sure I wasn't missing something.
siriusb
@siriusb-nox
Nov 18 2017 11:16
@dereneaton thanks a lot for your prompt reply, and for the hint on RADami. I will contact then Andrew and perhaps I can get RADami running on my ipyard loci data. As for the ML tree that makes topologically sense (but poorly supported) that I obtained from the super matrix concatenated loci, do you know perhaps why is this happening? Again, I will be extremely grateful for any advice or piece of information you could provide on how to improve the support on my ML phylogeny (e.g. some parameters in ipyrad that could let to more optimal results). Thanks very much!