UNIT 6.8 Using PEBBLE for the Evolutionary Analysis of Serially Sampled Molecular Sequences
Published Online: 1 MAY 2004
Copyright © 2003 by John Wiley and Sons, Inc.
Lab Protocol Title
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.
- Published Online: 1 MAY 2004
- 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.