Neigbour joining clustering (Saitou & Nei 1987) is an alternative method for hierarchical cluster analysis. The method was originally developed for phylogenetic analysis, but may be superior to UPGMA also for ecological data. In contrast with UPGMA, two branches from the same internal node do not need to have equal branch lengths. A phylogram (unrooted dendrogram with proportional branch lengths) is given.
Distance indices and bootstrapping are as for other cluster analysis. To run the bootstrap analysis, type in the number of required bootstratp replicates (e.g. 1000, 10000) in the “Boot N” box and press Enter to update the value.
Negative branch lengths are forced to zero, and transferred to the adjacent branch according to Kuhner & Felsenstein (1994).
The tree is by default rooted on the last branch added during tree construction (this is not midpoint rooting). Optionally, the tree can be rooted on any row in the data matrix, as selected in the Root menu.
Missing data supported by pairwise deletion.
References
Kuhner, M.K. & J. Felsenstein. 1994. A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Molecular Biology and Evolution 11:459-468.
Saitou, N. & M. Nei. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4:406-425