When two nodes are linked, their common ancestral node is added to the tree and the terminal nodes with their respective branches are removed from the tree. In this method, the nucleotides of all DNA sequences at each nucleotide site are considered separately, and the log-likelihood of having these nucleotides are computed for a given topology by using a particular probability model. This procedure is repeated for all possible topologies, and topology that shows the highest likelihood is chosen as the final one. It is very similar to that of maximum likelihood method, but more evolutionary models can be incorporated. Instead of seeking the tree that maximizes the likelihood of observing the data, it seeks those trees with the greatest likelihood of given the data.
Bayesian analysis produces a set of trees of roughly equal likelihoods.
The Tree of Life - Phylogenetic trees on web. Expert Center for Taxonomic Identification - maintained in Netherlands. A Short training course for Molecular Systematics and Evolution at the site of The Natural History Museum, London and NUI Maynooth, Ireland. Training Course - Molecular Evolution workshop at Woods Hole. Using Parsimony and other Methods.