BIONJ: an improved version of NJ

Olivier Gascuel gascuel at lirmm.fr
Wed Aug 27 07:27:28 EST 1997

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:


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.


LIRMM, 161 rue Ada,
34392 - Montpellier - FRANCE
gascuel at lirmm.fr

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