entries of the inverse of the covariance matrix of the distance estimates. Computational Complexity Finding the tree and branch lengths minimizing the least squares residual is an NP-complete problem. However, for a given tree, the optimal branch lengths can be determined in time for ordinary least squares, time for weighted least squares, and time for generalised least squares (given the inverse of the covariance matrix). External links PHYLIP, a freely distributed phylogenetic analysis package containing an implementation of the weighted least squares method PAUP, a similar package available for purchase Darwin, a programming environment with a library of functions for statistics, numerics, sequence and phylogenetic analysis References Computational phylogenetics