  Phylogenomics, even more so than traditional phylogenetics, needs to
represent the uncertainty in evolutionary trees due to systematic error. Here
we illustrate the analysis of genome-scale alignments of yeast, using robust
measures of the additivity of the fit of distances to tree when using flexi
Weighted Least Squares. A variety of DNA and protein distances are used. We
explore the nature of the residuals, standardize them, and then create
replicate data sets by resampling these residuals. Under the model, the results
are shown to be very similar to the conventional sequence bootstrap. With real
data they show up uncertainty in the tree that is either due to underestimating
the stochastic error (hence massively overestimating the effective sequence
length) and/or systematic error. The methods are extended to the very fast BME
criterion with similarly promising results.
