Dirichlet Nucleotide Frequency Prior applet

The Dirichlet distribution is normally used to specify the prior distribution for equilibrium base frequencies in Bayesian phylogenetics. Unfortunately, 4 dimensions are required to plot the probability density, so I’ve resorted to showing you samples from the distribution instead plotted using a barycentric coordinate system.

Drag right-to-left (or left-to-right) with mouse to rotate view. Use controls below plot to change sampling distribution.

The proximity of a blue dot to vertex A is proportional to the relative frequency of A. Setting the A parameter to 100 and all others to 1 will result in all blue spheres clustered very close to the A vertex; this means that the frequency of A is very high relative to the frequencies of C, G, and T.

Acknowledgements

This applet makes use of d3js and Erik Bernhardsson’s very useful D3-3D code. Please see the GitHub site for details about licensing of other libraries that may have been used in the source code for this applet.

Licence

Creative Commons Attribution 4.0 International. License (CC BY 4.0). To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ or send a letter to Creative Commons, 559 Nathan Abbott Way, Stanford, California 94305, USA.