Molecular Biology and Evolution, Vol 14, 685-695, Copyright © 1997 by Society for Molecular Biology and Evolution
O Gascuel
We propose an improved version of the neighbor-joining (NJ) algorithm of
Saitou and Nei. This new algorithm, BIONJ, follows the same agglomerative
scheme as NJ, which consists of iteratively picking a pair of taxa,
creating a new mode which represents the cluster of these taxa, and
reducing the distance matrix by replacing both taxa by this node. 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, from the class of admissible reductions, 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. Moreover, in comparison with NJ's estimates, these estimates
become better and better as the algorithm proceeds. BIONJ retains the good
properties of NJ--especially its low run time. Computer simulations have
been performed with 12-taxon model trees to determine BIONJ's efficiency.
When the substitution rates are low (maximum pairwise divergence
approximately 0.1 substitutions per site) or when they are constant among
lineages, BIONJ is only slightly better than NJ. When the substitution
rates are higher and vary among lineages,BIONJ clearly has 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 (maximum pairwise divergence approximately 1.0
substitutions per site), the error reduction may even rise above 50%, while
the probability of finding the correct tree may be augmented by as much as
15%.
ORIGINAL ARTICLE
BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data
GERAD, Ecole des HEC, Montreal, Quebec, Canada. gascuel@lirmm.fr
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|
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|
|
|
|
|
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|
|
|
|
|
|
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|
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|
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|
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|
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|
|
|
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|
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|
|
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|
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|
|
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|
|
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J. Friedrich, T. Dandekar, M. Wolf, and T. Muller ProfDist: a tool for the construction of large phylogenetic trees based on profile distances Bioinformatics, May 1, 2005; 21(9): 2108 - 2109. [Abstract] [Full Text] [PDF]
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 I. Rieu, M. Bots, C. Mariani, and K. A. P. Weterings Isolation and Expression Analysis of a Tobacco AINTEGUMENTA Ortholog (NtANTL) Plant Cell Physiol., May 1, 2005; 46(5): 803 - 805. [Abstract] [Full Text] [PDF]
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M. V. Coppi The hydrogenases of Geobacter sulfurreducens: a comparative genomic perspective Microbiology, April 1, 2005; 151(4): 1239 - 1254. [Abstract] [Full Text] [PDF]
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N. Salamin, T. R. Hodkinson, and V. Savolainen Towards Building the Tree of Life: A Simulation Study for All Angiosperm Genera Syst Biol, April 1, 2005; 54(2): 183 - 196. [Abstract] [Full Text] [PDF]
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L. M. Zahn, H. Kong, J. H. Leebens-Mack, S. Kim, P. S. Soltis, L. L. Landherr, D. E. Soltis, C. W. dePamphilis, and H. Ma The Evolution of the SEPALLATA Subfamily of MADS-Box Genes: A Preangiosperm Origin With Multiple Duplications Throughout Angiosperm History Genetics, April 1, 2005; 169(4): 2209 - 2223. [Abstract] [Full Text] [PDF]
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 J. C. Kim, Y. Y. Ou, J. L. Badano, M. A. Esmail, C. C. Leitch, E. Fiedrich, P. L. Beales, J. M. Archibald, N. Katsanis, J. B. Rattner, et al. MKKS/BBS6, a divergent chaperonin-like protein linked to the obesity disorder Bardet-Biedl syndrome, is a novel centrosomal component required for cytokinesis J. Cell Sci., March 1, 2005; 118(5): 1007 - 1020. [Abstract] [Full Text] [PDF]
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E. P. Ivanova, O. M. Onyshchenko, R. Christen, A. M. Lysenko, N. V. Zhukova, L. S. Shevchenko, and E. A. Kiprianova Marinomonas pontica sp. nov., isolated from the Black Sea Int J Syst Evol Microbiol, January 1, 2005; 55(1): 275 - 279. [Abstract] [Full Text] [PDF]
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M. Xu, J. Guo, Y. Cen, X. Zhong, W. Cao, and G. Sun Shewanella decolorationis sp. nov., a dye-decolorizing bacterium isolated from activated sludge of a waste-water treatment plant Int J Syst Evol Microbiol, January 1, 2005; 55(1): 363 - 368. [Abstract] [Full Text] [PDF]
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A. Das, S. Mohanty, and W. Stephan Inferring the Population Structure and Demography of Drosophila ananassae From Multilocus Data Genetics, December 1, 2004; 168(4): 1975 - 1985. [Abstract] [Full Text] [PDF]
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E. P. Ivanova, R. Christen, Y. V. Alexeeva, N. V. Zhukova, N. M. Gorshkova, A. M. Lysenko, V. V. Mikhailov, and D. V. Nicolau Brevibacterium celere sp. nov., isolated from degraded thallus of a brown alga Int J Syst Evol Microbiol, November 1, 2004; 54(6): 2107 - 2111. [Abstract] [Full Text] [PDF]
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N. Faury, D. Saulnier, F. L. Thompson, M. Gay, J. Swings, and F. L. Roux Vibrio crassostreae sp. nov., isolated from the haemolymph of oysters (Crassostrea gigas) Int J Syst Evol Microbiol, November 1, 2004; 54(6): 2137 - 2140. [Abstract] [Full Text] [PDF]
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I. Brettar, R. Christen, and M. G. Hofle Aquiflexum balticum gen. nov., sp. nov., a novel marine bacterium of the Cytophaga-Flavobacterium-Bacteroides group isolated from surface water of the central Baltic Sea Int J Syst Evol Microbiol, November 1, 2004; 54(6): 2335 - 2341. [Abstract] [Full Text] [PDF]
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 A. P. de Koning and P. J. Keeling Nucleus-Encoded Genes for Plastid-Targeted Proteins in Helicosporidium: Functional Diversity of a Cryptic Plastid in a Parasitic Alga Eukaryot. Cell, October 1, 2004; 3(5): 1198 - 1205. [Abstract] [Full Text] [PDF]
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 M. Taniguchi, T. Kanehisa, T. Sawabe, R. Christen, and T. Ikeda Molecular phylogeny of Neocalanus copepods in the subarctic Pacific Ocean, with notes on non-geographical genetic variations for Neocalanus cristatus J. Plankton Res., October 1, 2004; 26(10): 1249 - 1255. [Abstract] [Full Text] [PDF]
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E. P. Ivanova, N. M. Gorshkova, N. V. Zhukova, A. M. Lysenko, E. A. Zelepuga, N. G. Prokof'eva, V. V. Mikhailov, D. V. Nicolau, and R. Christen Characterization of Pseudoalteromonas distincta-like sea-water isolates and description of Pseudoalteromonas aliena sp. nov. Int J Syst Evol Microbiol, September 1, 2004; 54(5): 1431 - 1437. [Abstract] [Full Text] [PDF]
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E. P. Ivanova, S. Flavier, and R. Christen Phylogenetic relationships among marine Alteromonas-like proteobacteria: emended description of the family Alteromonadaceae and proposal of Pseudoalteromonadaceae fam. nov., Colwelliaceae fam. nov., Shewanellaceae fam. nov., Moritellaceae fam. nov., Ferrimonadaceae fam. nov., Idiomarinaceae fam. nov. and Psychromonadaceae fam. nov. Int J Syst Evol Microbiol, September 1, 2004; 54(5): 1773 - 1788. [Abstract] [Full Text] [PDF]
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L. S. Vinh and A. von Haeseler IQPNNI: Moving Fast Through Tree Space and Stopping in Time Mol. Biol. Evol., August 1, 2004; 21(8): 1565 - 1571. [Abstract] [Full Text] [PDF]
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D. M. Martin, J. Faldt, and J. Bohlmann Functional Characterization of Nine Norway Spruce TPS Genes and Evolution of Gymnosperm Terpene Synthases of the TPS-d Subfamily Plant Physiology, August 1, 2004; 135(4): 1908 - 1927. [Abstract] [Full Text] [PDF]
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D. Houzelstein, I. R. Goncalves, A. J. Fadden, S. S. Sidhu, D. N. W. Cooper, K. Drickamer, H. Leffler, and F. Poirier Phylogenetic Analysis of the Vertebrate Galectin Family Mol. Biol. Evol., July 1, 2004; 21(7): 1177 - 1187. [Abstract] [Full Text] [PDF]
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S. I. Nikolaev, C. Berney, J. F. Fahrni, I. Bolivar, S. Polet, A. P. Mylnikov, V. V. Aleshin, N. B. Petrov, and J. Pawlowski From the Cover: The twilight of Heliozoa and rise of Rhizaria, an emerging supergroup of amoeboid eukaryotes PNAS, May 25, 2004; 101(21): 8066 - 8071. [Abstract] [Full Text] [PDF]
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