Getting a tree fast: Neighbor Joining, FastME, and distance-based methods

Richard Desper 1 Olivier Gascuel 2
2 MAB - Méthodes et Algorithmes pour la Bioinformatique
LIRMM - Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier
Abstract : Neighbor Joining (NJ), FastME, and other distance-based programs including BIONJ, WEIGHBOR, and (to some extent) FITCH, are fast methods to build phylogenetic trees. This makes them particularly effective for large-scale studies or for bootstrap analysis, 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 matrix of pairwise evolutionary distances. Computer simulations indicate that the topological accuracy of FastME is best, followed by FITCH, WEIGHBOR, and BIONJ, while NJ is worse. Moreover, FastME is even faster than NJ with large data sets. Best-distance methods are equivalent to parsimony in most cases, but become more accurate when the molecular clock is strongly violated or in the presence of long (e.g., outgroup) branches. This unit describes how to use distance-based methods, focusing on NJ (the most popular) and FastME (the most efficient today). It also describes how to estimate evolutionary distances from DNA and proteins, how to perform bootstrap analysis, and how to use CLUSTAL to compute both a sequence alignment and a phylogenetic tree.
Type de document :
Chapitre d'ouvrage
Andreas D. Baxevanis. Current Protocols in Bioinformatics, 6, Wiley, pp.Unit 6.3, 2006, 1934-3396. 〈10.1002/0471250953.bi0603s15〉. 〈www.lirmm.fr/mab〉
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https://hal-lirmm.ccsd.cnrs.fr/lirmm-00324116
Contributeur : Olivier Gascuel <>
Soumis le : mercredi 24 septembre 2008 - 10:15:43
Dernière modification le : jeudi 24 mai 2018 - 15:59:22

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Richard Desper, Olivier Gascuel. Getting a tree fast: Neighbor Joining, FastME, and distance-based methods. Andreas D. Baxevanis. Current Protocols in Bioinformatics, 6, Wiley, pp.Unit 6.3, 2006, 1934-3396. 〈10.1002/0471250953.bi0603s15〉. 〈www.lirmm.fr/mab〉. 〈lirmm-00324116〉

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