Generalized Least Squares
The ordinary and weighted least squares methods described above assume independent distance estimates. If the distances are derived from genomic data their estimates covary, because evolutionary events on internal branches (of the true tree) can push several distances up or down at the same time. The resulting covariances can be taken into account using the method of generalized least squares, i.e. minimizing the following quantity
where are the entries of the inverse of the covariance matrix of the distance estimates.
Read more about this topic: Least Squares Inference In Phylogeny
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