Hi all,
I am learning to use BEAST2 and have made some Maximum Clade Credibility phylogenetic trees from a handful of virus isolates I have sequenced. I am trying to learn how to interpret my trees. My posterior probabilities all look good and normal (most are values between 0.7 - 1, many are close to 1). But my branch lengths are all fairly large values, like on the order of 30,000+. I'm a little confused as to why this is, since to my understanding the branch lengths represent the nucleotide substitutions per site. Based on this understanding, and from comparing my trees to those shown in the BEAST tutorials online, I was expecting to see branch length values between 0 and 1 (ie, percentages).
Any ideas what's going wrong here, if anything? Links or troubleshooting suggestions welcome as well.
