BIONJ: SOFTWARE AVAILABLE ON THE WEB
BIONJ is a new phylogenetic tree building algorithm. It follows the same
agglomerative scheme as NJ. Moreover, BIONJ uses a simple, first-order
model of the variances and covariances of evolutionary distance estimates.
This model is well adapted when these estimates are obtained from aligned
sequences. At each step it permits the selection, of the reduction which
minimizes the variance of the new distance matrix. In this way, we obtain
better estimates to choose the pair of taxa to be agglomerated during the
next steps. BIONJ retains the good properties of NJ - especially its low
run time. Computer simulations have been performed to determine BIONJ's
efficiency. When the substitution rates are low or when they are constant
among lineages, BIONJ is only slightly better than NJ. When the
substitution rates are higher and varying among lineages, BIONJ has a
clearly better topological accuracy. In the latter case, for the model
trees and the conditions of evolution tested, the topological error
reduction is on the average around 20%. With highly varying-rate trees and
with high substitution rates, the error reduction may even rise above 50 %,
while the probability of finding the correct tree may be augmented by as
much as 15%.
BIONJ is described in the July issue of MBE: 14(7), p. 685-695. The ps
files of this paper and related ones are available on my web page:
Moreover, a PHYLIP compatible version of BIONJ is available on this page.
It can be used with a PC or with SUN, and the source is given. Comments,
questions and suggestions are welcome.
GERAD, Montreal - Canada, olivierg at crt.umontreal.ca
LIRMM, Montpellier - France, gascuel at lirmm.fr