Phylogeny | Construct/Test Maximum Likelihood Tree (ML)
A phylogenetic tree is constructed for the data by the Maximum Likelihood method. In this method, an initial tree is first built using a fast but suboptimal method such as Neighbor-Joining, and its branch lengths are adjusted to maximize the likelihood of the data set for that tree topology under the desired model of evolution. Then variants of the topology are created using the NNI (nearest neighbor Interchange) method to search for topologies that fit the data better. Maximum-Likelihood branch lengths are computed for these variant tree topologies and the greatest likelihood retained as the best choice so far. This search continues until no greater likelihoods are found. This method can be used for both nucleotide and protein data. Users may supply their own initial tree instead of having MEGA create a Neighbor-Joining tree. Users may also select other options besides NNI for searching.