How do I estimate branch length of a maximum parsimony phylogeny in R?
@Nathan S. Watson-Haigh's answer does give branch lengths, but NOT parsimony branch lengths, which may be what the OP wanted.  nnls.phylo is giving distances calculated from a pairwise distance matrix. To get the parsimony branch lengths (i.e. number of changes mapped on to each branch), score the tree against the dataset using acctran:

treeRatchet &lt;- pratchet(primates)
treeRatchet.BL &lt;- acctran(treeRatchet,primates)
plot(treeRatchet.BL,main='Phylogeny (Parsimony branch lengths)')



Note that the branch lengths in the parsimony phylogram are 'chunkier' than those in the nnls.phylo phylogram -- that's because 


they are all integers, and 
they aren't corrected with reference to a model of substitution that considers multiple hits or base composition.