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Bioinformatics Institute


Pebble (Phylogenetics, Evolutionary Biology, and Bioinformatics in a moduLar Environment) is a powerful application for Phylogenetic analysis. The primary purpose of Pebble is to provide tools for analysis and simulation of serially sampled sequence data (through maximum likelihood, and least-squares methods). Implemented forms of simulation include: trees, via a coalescent model, and sequence alignments, given an input tree and substitution model. Extra functionality includes data manipulation tools for sequence alignments and phylogenetic trees, as well as useful inbuilt alignment construction and editing facilities.

OS Support

Pebble is written using the Java programming language. As such it is relatively cross-platform independent. Versions are provided for Windows, Linux and MacOS.


Pebble is provided as is, with no warranty. The developers, the Bioinformatics Institute, The University of Auckland, and any other associated parties, provide no warranty for the use of Pebble. While every effort is taken to provide a reliable and trustworthy application, the authors, and associated parties, accept no liability for any damages, loss, or inconvenience caused by the use of Pebble.

Install Pebble

Windows and Mac OS X

Click on the appropriate link below to run the installer.


Right-click on the appropriate link, select "Save Link As..." and save the installer in a convenient place. After downloading open a commandline shell and go to the directory where you saved the installer.
To run the installer, at the prompt type: sh ./Pebble-unix-v1-0.bin

Windows Download (6.0 Mb)
Mac OS X Download (5.6 Mb)
Linux/Unix Download (5.8 Mb)
Sample data file ( Download (24 kb)