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PAML 4: phylogenetic analysis by maximum likelihood.

Ziheng Yang1

  • 1Department of Biology, Galton Laboratory, University College London, London, UK. z.yang@ucl.ac.uk

Molecular Biology and Evolution
|May 8, 2007
PubMed
Summary
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PAML (Phylogenetic Analysis by Maximum Likelihood) is a software package for analyzing DNA and protein sequences. It offers advanced evolutionary models for hypothesis testing and estimating evolutionary parameters.

Area of Science:

  • Computational Biology
  • Evolutionary Biology
  • Bioinformatics

Background:

  • Phylogenetic analysis is crucial for understanding evolutionary relationships.
  • Existing tools may lack comprehensive evolutionary models for complex biological hypotheses.

Purpose of the Study:

  • To introduce PAML (Phylogenetic Analysis by Maximum Likelihood), version 4, a software package for phylogenetic analyses.
  • To highlight the capabilities of PAML in evolutionary model implementation and hypothesis testing.

Main Methods:

  • Utilizes maximum likelihood (ML) methods for phylogenetic tree analysis.
  • Implements a wide range of evolutionary models for sequence evolution.
  • Provides tools for parameter estimation and hypothesis testing.

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Main Results:

  • PAML facilitates estimation of synonymous (dN) and nonsynonymous (dS) substitution rates.
  • Enables inference of positive Darwinian selection using phylogenetic comparisons.
  • Supports ancestral sequence reconstruction and analysis of heterogeneous data sets.
  • Allows estimation of species divergence times with fossil calibration uncertainties.

Conclusions:

  • PAML (Phylogenetic Analysis by Maximum Likelihood) is a versatile tool for diverse evolutionary studies.
  • Its extensive model repertoire aids in testing biological hypotheses and understanding molecular evolution.
  • The package is accessible across multiple operating systems and includes example datasets.