Under maximum parsimony , branch lengths measure the inferred number of substitutions that have occurred on a particular branch. Under maximum parsimony, this value will always be a whole number. Character weighting is based on the assumption that some sites in a sequence are evolving rapidly enough that they introduce noise into an analysis that has the potential to overwhelm the evolutionary signal. A genetic distance is an estimate of the amount of genetic change that has occurred between two sequences since they diverged from a common ancestor. There isn t one.
Some methods work well for some data sets and poorly for others.
There is an emerging consensus in the field regarding what methods tend to be better than others and we now have a reasonable idea as to the weak points of different methods. When there are 4 species, there are 16 possible ways of arranging those species into a phylogenetic tree.