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

It includes class that allow computation of the following:
The {@code 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.