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ICHEC Software

Information about software packages installed on the ICHEC systems.


Versions Installed

Fionn: 4.4e / 4.7a


PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. It is not good for tree making. It may be used to estimate parameters and test hypotheses to study the evolutionary process, when you have reconstructed trees using other programs such as PAUP*, PHYLIP, MOLPHY, PhyML, RaxML, etc.

The PAML package includes the following programs: baseml, basemlg, codeml, evolver, pamp, yn00, mcmctree, and chi2. Examples of analyses that can be performed using the package include:

  • Comparison and tests of phylogenetic trees (baseml and codeml).
  • Estimation of parameters in sophisticated substitution models, including models of variable rates among sites and models for combined analysis of multiple genes or site partitions (baseml and codeml).
  • Likelihood ratio tests of hypotheses through comparison of implemented models (baseml, codeml, chi2).
  • Estimation of divergence times under global and local clock models (baseml and codeml).
  • Likelihood (Empirical Bayes) reconstruction of ancestral sequences using nucleotide, amino acid and codon models (baseml and codeml).
  • Generation of datasets of nucleotide, codon, and amino acid sequence by Monte Carlo simulation (evolver).
  • Estimation of synonymous and nonsynonymous substitution rates and detection of positive selection in protein-coding DNA sequences (yn00 and codeml).
  • Bayesian estimation of species divergence times incorporating uncertainties in fossil calibrations (mcmctree).


PAML is maintained and distributed for academic use free of charge by Ziheng Yang.



Additional Notes

To use PAML load the relevant environment module:

module load bio paml/gcc/4.4e
module load bio paml/intel/4.7a

The PAML package consists of serial programs so they may be used in conjunction with the taskfarm utility for batch jobs. Further information can be obtained from http://abacus.gene.ucl.ac.uk/software/paml.html.

How to cite PAML:

Yang Z. (2007)
PAML 4: phylogenetic analysis by maximum likelihood.
Mol. Biol. Evol. 24(8): 1586-1591.

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