Hi Jack,
To answer your questions (if you are looking for more documentation, look at Multimedia File Viewing and Clickable Links are available for Registered Members only!! You need to
and Multimedia File Viewing and Clickable Links are available for Registered Members only!! You need to
1. Generally speaking you should be OK, so long as you use a partitioning analysis. When writing the GARD paper we found that this correction works well even for close to 'free recombination' scenarios.
2. "85 potential breakpoints" refers to how many positions in the alignment could have been tested for a presence of recombination breakpoint. This statistic tells you how many variable sites you have in your alignment (essentially), and how many combinations of 1 and 2 out of 85 there are (3655). This is more of a diagnostic of how complex the problem is, not of what the solutions are.
3. See the first above. Reliable is a relative term . Posterior probabilities of as low as 0.5 have been used to detect selection in other applications, but 0.9 or 0.95 is more customary. Datamonkey defaults are 20 for Bayes factors and 0.9 for posterior probabilities.
Sergei