Neighbor Joining (Construct Phylogeny)

Phylogeny | Construct/Test Neighbor-Joining Tree…

This command is used to construct (or Test) a neighbor-joining (NJ) tree (Saitou & Nei 1987). The NJ method is a simplified version of the minimum evolution (ME) method, which uses distance measures to correct for multiple hits at the same sites, and chooses a topology showing the smallest value of the sum of all branches as an estimate of the correct tree. However, the construction of an ME tree is time-consuming because, in principle, the S values for all topologies have to be evaluated and the number of possible topologies (unrooted trees) rapidly increases with the number of taxa.

With the NJ method, the S value is not computed for all or many topologies. The examination of different topologies is imbedded in the algorithm, so that only one final tree is produced. This method does not require the assumption of a constant rate of evolution so it produces an unrooted tree. However, for ease of inspection, MEGA displays NJ trees in a manner similar to rooted trees. The algorithm of the NJ method is somewhat complicated and is explained in detail in Nei and Kumar (2000).

For constructing the NJ tree, MEGA may request that you specify the distance estimation method, subset of sites to include, and whether to conduct a test of the inferred tree through an Analysis Preferences dialog box.