Phylogenetic Tree

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.