Neighbor-joining and UPGMA trees for progressive alignment. Here we show the same set of four sequences and the order in which they will be aligned according to a neighbor-joining tree (above) and a UPGMA tree (below). Notice that t and u are the most closely related pair, but (s, t) and (u, v) are evolutionary neighbors. With neighbor joining, t and u are not aligned to each other until the root, in contrast to UPGMA, which aligns s and t as the first pair.
Edgar BMC Bioinformatics 2004 5:113 doi:10.1186/1471-2105-5-113