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

See:
          Description

Packages
Alignments Provides class for dealing with "alignments" and the sites in an alignment.
Ancestors Provides classed to calculate ancestral reconstruction.
Constraints Provides classes to constrain the state of internal nodes.
Exceptions Provides exceptions that are common across the package.
Executable Provides a general driver executable and an example 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 defing a phylogenetic model.
Optimizers Provides classes for optimising a likelihood.
Parameters Provides classes for defining parameters used in the various calculations.
Simulations Provides a class to create simulate data.
Trees Provides classes to define a tree and any constraints on that 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:


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.