Phylogenetic Tree Distance Corrector
If you have a distance-backed phylogenetic tree displayed, you can activate a graphical window that permits you to manipulate interactively the nature of score corrections. Read here a description of what a score correction means and why it is important.
The calculation of the distance correction is according to the formula:
Dc = Dr + k DrN / (1 - DrM)
where Dc is the corrected distance, Dr is the raw distance, and k, N, and M are arbitrary constants used to curve-fit. I have no idea whether this is a good curve-fitting function but it seems to work relatively well as a first attempt. The current Bonsai defaults for these are k = 0.6, N = 2.0, and M = 1.0. It is unclear to me whether M is necessary.
The distance corrector window displays the shape of the correction function and permits the user to dynamically change k, N, and M. As k tends toward zero, the correction term tends to zero and k = 0 is equivalent to no correction. Increasing N or M makes the curve more inflected. In addition to the function display, the correction is also dynamically linked to the tree so that you can see the tree change as the correction changes.
Limited experimentation to date suggests that there is no one best curve to correct NJ tree distances. Using the evolution simulator one can construct phylogenies with known truths. When a tree is constructed from divergent sequences with different patterns of conservation clustering (but otherwise identically modeled), the correction function required to approximate the real history is slightly different. On a positive note, it should in principle be possible to derive an estimate of the clustering pattern from a real alignment and use an appropriately matched correcting function.
James H. Thomas, Department of Genome Sciences, University of Washington