Question: For the past couple of days, I have been trying to understand what numbers on trees correspond to. If you could help me with that, it would be highly appreciated.
The trees are based on sequence similarity and are calculated from distance matrices determined from % identity or aggregate BLOSUM 62 score using either Average Distance (UPGMA) or Neighbour Joining algorithms (depending on your selection in the dialogue box).
The values in the trees are distances. For distance matrices such as a percentage identity tree the actual identity between a pair of sequences is 100 - sum(distances of branches between leaves).
The distance numbers in each branch can be added together to allow comparison.