Using PEBBLE for the evolutionary analysis of serially sampled molecular sequences

Current Protocols in Bioinformatics
Matthew Goode, A G Rodrigo

Abstract

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.

References

Feb 22, 1990·Journal of Theoretical Biology·F RodríguezJ R Medina
Jan 1, 1981·Journal of Molecular Evolution·J Felsenstein
Apr 29, 1998·Molecular Biology and Evolution·A Rambaut, L Bromham
Mar 3, 1999·Proceedings of the National Academy of Sciences of the United States of America·A G RodrigoJ I Mullins
Sep 15, 1999·Proceedings of the National Academy of Sciences of the United States of America·T Leitner, J Albert
Mar 4, 2000·Proceedings of the National Academy of Sciences of the United States of America·J A LeonardA Cooper
Mar 22, 2001·Mathematical Biosciences·M Steel, A McKenzie
Jun 23, 2001·Molecular Biology and Evolution·A DrummondA G Rodrigo
Mar 23, 2002·Science·D M LambertC Baroni

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