This library provides classes to perform likelihood calculations on phylogenetic trees.

See: Description

Packages 
Package Description
Alignments
Provides class for dealing with "alignments" and the sites in an alignment.
Ancestors
Provides classed to calculate ancestral reconstruction.
Exceptions
Provides exceptions that are common across the package.
Executable
Provides a general driver executable
Likelihood
Provides classes for calculating the likelihood of a tree given a model and an alignment.
Maths
Provides maths classes.
Models
Provides classes for defining a phylogenetic model.
ModelTest  
Optimizers
Provides classes for optimising a likelihood.
Parameters
Provides classes for defining parameters used in the various calculations.
Simulations
Provides a class to create simulated data.
Trees
Provides classes to define a tree.
Utils
Provides various utility classes.
This library provides classes to perform likelihood calculations on phylogenetic trees.

It includes class that allow computation of the following:
  • Likelihood - Using the method of Felsenstein 1981[1]. Unobserved data can also be accounted for, per Felsenstein 1992[2]. Confidence intervals for a parameter can also be calculated as discussed in Felsenstein 2003[3].
  • Ancestral Reconstruction
    • Marginal Reconstruction - Using the basic method of Yang, Kurma and Nei 1995[4].
    • Joint Reconstruction - Using the methods of Pupko et al 2000[5] and Pupko et al 2002[6].
  • Simulated data - Using the standard methods as described, for example, in Yang 2006[7].

The Executable package contains two executable - a general purpose driver and some example code that shows how to do some simple computation.

References
  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.