Using PEBBLE for the evolutionary analysis of serially sampled molecular sequences.


Journal Article

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.

Full Text

Cited Authors

  • Goode, M; Rodrigo, AG

Published Date

  • May 2004

Published In

Volume / Issue

  • Chapter 6 /

Start / End Page

  • Unit - 6.8

PubMed ID

  • 18428729

Pubmed Central ID

  • 18428729

Electronic International Standard Serial Number (EISSN)

  • 1934-340X

International Standard Serial Number (ISSN)

  • 1934-3396

Digital Object Identifier (DOI)

  • 10.1002/0471250953.bi0608s05


  • eng