UNIT 6.8 Using PEBBLE for the Evolutionary Analysis of Serially Sampled Molecular Sequences

  1. Matthew Goode,
  2. Allen G. Rodrigo

Published Online: 1 MAY 2004

DOI: 10.1002/0471250953.bi0608s05

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Goode, M. and Rodrigo, A. G. 2004. Using PEBBLE for the Evolutionary Analysis of Serially Sampled Molecular Sequences. Current Protocols in Bioinformatics. 5:6.8:6.8.1–6.8.26.

Author Information

  1. Bioinformatics Institute and The Allan Wilson Centre for Molecular Ecology and Evolution, University of Auckland, Auckland, New Zealand

Publication History

  1. Published Online: 1 MAY 2004
  2. Published Print: MAR 2004


The PEBBLE (Phylogenetics, Evolutionary Biology, and Bioinformatics in a moduLar Environment) application is a relative newcomer to the field of phylogenetic applications. Although designed as a customizable generalist application, PEBBLE was initially developed to implement procedures for the analysis of sequences associated with different sampling times, e.g., rapidly evolving viral genes sampled over the course of infection, or ancient DNA sequences. The basic protocol describes the use of PEBBLE to infer a phylogenetic tree using the sUPGMA algorithm, and the inference of substitution rate parameters using maximum likelihood. The alternate and support protocols describe the simulation capabilities of PEBBLE, and general use of the PEBBLE application, respectively.