Phylogenetic tree problems can be categorized into the following classes:
1) Given genes/genomes, how to construct a phylogenetic tree, there are majorly three kinds of methods to use:
i distance based method, such as NJ, UPGMA
ii maximum parsimonious method.
iii maximum likelihood method.
2) Given a phylogenetic tree, reconstruct the ancient genes/gene orders of intermediate node in the phy-tree.
3) Given a Phylogenetic tree, evaluate the quality of the tree.
Now, there are 11 papers collected in this part.