BIONJ: an improved version of the NJ algorithm based
on a simple model of sequence data
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 97 issue of MBE: 14(7), p. 685-695. The ps
files of this paper and others related are available on my web page:
http://www.crt.umontreal.ca/~olivierg
Moreover, a free PHYLIP compatible version of BIONJ is available on this
page. It can be used with a PC or with a SUN UNIX, and the C source code
is given. Comments, questions and suggestions are welcome.
Olivier GASCUEL
LIRMM, 161 rue Ada,
34392 - Montpellier - FRANCE
gascuel at lirmm.fr
