Perfect Phylogeny vs Maximum parsimony I am searching various sources about phylogenetics. I saw some materials about perfect phylogeny and also phylogenies acquired from maximum parsimony constraint. They seem very similar to me. Are they the same?
No. A perfect phylogeny is one such that all characters evolve on the tree with no homoplasy, i.e. for a binary character, changes occur once from 0 -&gt; 1 but never from 1 -&gt; 0. A maximum parsimony phylogeny may produce a perfect phylogeny, but typically for real datasets some degree of homoplasy is required to explain character patterns.