GeLL is a General Likelihood Library for use in phylogenetics. It is intended to provide classes that facilitate investigating new models and techniques. It is not intended for everyday use in phylogenetic studies as it is optimised for easy use of new models rather than speed.

GeLL achieves this versatility by allowing models to be defined using an array of Strings where each string represents an equation. This allows new models to be defined quickly and easily. The driver executable included allows many different models to be run simply by changing the text file defining the model.

Packages Show Hide
A quick start guide, including instalation instructions, is avaliable. Click here to get it. It is also included in every download package. (quickstart.pdf).
Capabilities Show Hide
GeLL has the following capabilities:
Packages Show Hide

GeLL comes in three different packages:

Documentation Show Hide

GeLL comes with full javadoc documentation in the javadoc directory here.

GeLL includes a driver that should be capable of doing most basic computations. This is documented in the driver documentation here.

The GeLL packages also include an example program. As well as the source code file an annotated version of the source is here. If you are thinking of writing your own program using the GeLL library it is recommended you take a look at this example.

The core capability of GeLL is the ability to define and use new models. As such how models are defined in covered in more details here. Also included is a more in-depth discussion of how parameters are defined and constrained.

A description of the test cases is included here in the test package.

Tips & Tricks Show Hide
Citation Show Hide
Money, D. and Whelan, S. (2012) GeLL: Generalized Likelihood Library (
Known Issues Show Hide
Release Notes Show Hide
1.0 2 February 2012 1.1 4 April 2012 1.2 23 April 2012 1.3 14 August 2012 2.0 14 April 2014
License Show Hide

GeLL is avaliable under GPL v3.

The EigenvalueDecomposition and LUDecomposition classes are from JAMA and as such are in the public domain.

The test package contains both executables and example datasets from PAML. This example dataset is also used for the example execution using The applicable license for these components is as follows:

© Copyright 1993-2008 by Ziheng Yang
The software package is provided "as is" without warranty of any kind. In no event shall the author or his employer be held responsible for any damage resulting from the use of this software, including but not limited to the frustration that you may experience in using the package. The program package, including source codes, example data sets, executables, and this documentation, is distributed free of charge for academic use only. Permission is granted to copy and use programs in the package provided no fee is charged for it and provided that this copyright notice is not removed.
Contact Show Hide

The latest stable release of the library is available at, while the latest developmental version is available at

The author is contactable at

References Show Hide
  1. Felsenstein, J. 1981. Evolutionary trees from DNA sequences: A maximum likelihood approach. Journal of Molecular Evolution, 17:368–376.
  2. Felsenstein, J. 1992. Phylogenies from restriction sites: A Maximum-Likelihood approach. Evolution, 46:159–173.
  3. Felsenstein, J. 2003. Inferring phylogenies. Sinauer Associates Sunderland, Mass., USA.
  4. Yang, Z., S. Kumar, and M. Nei. 1995. A new method of inference of ancestral nucleotide and amino acid sequences. Genetics, 141:1641–1650.
  5. Pupko, T., I. Pe, R. Shamir, and D. Graur. 2000. A fast algorithm for joint reconstruction of ancestral amino acid sequences. Molecular Biology and Evolution, 17:890–896.
  6. Pupko, T., I. Pe’er, M. Hasegawa, D. Graur, and N. Friedman. 2002. A branchand- bound algorithm for the inference of ancestral amino-acid sequences when the replacement rate varies among sites: Application to the evolution of five gene families. Bioinformatics, 18:1116–1123.
  7. Yang, Z. 2006. Computational molecular evolution. Oxford University Press, USA.
  8. Boussau, B. and Gouy, M. 2006 Efficient Likelihood Computations with Nonreversible Models of Evolution. Systematic Biology, 55:756-768.