UNIT 6.3 Getting a Tree Fast: Neighbor Joining and Distance-Based Methods

  1. Olivier Gascuel

Published Online: 1 NOV 2002

DOI: 10.1002/0471250953.bi0603s01

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Gascuel, O. 2002. Getting a Tree Fast: Neighbor Joining and Distance-Based Methods. Current Protocols in Bioinformatics. 6:6.3.

Author Information

  1. Equipe “Méthodes et Algorithmes pour la Bioinformatique”, LRMM-CNRS, Montpellier, France

Publication History

  1. Published Online: 1 NOV 2002
  2. Published Print: JAN 2003

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This unit provides instructions on how to construct a phylogenetic tree with several distance-based methods. Neighbor Joining (NJ) and other distance-based approaches (e.g., BIONJ, WEIGHBOR and FITCH) are fast methods for building phylogenetic trees. This makes them particularly effective for large-scale studies or for bootstrap applications, which require runs on multiple data sets. Like maximum-likelihood methods, distance methods are based on a sequence evolution model that is used to estimate the distance matrix. Computer simulations indicate that the topological accuracy of BIONJ, WEIGHBOR and FITCH is significantly better than that of NJ, and that the best distance-based methods are equivalent to parsimony in most cases.