Category Archives: Lessons

Jukes Cantor Model of DNA substitution

We have had a series of posts introducing several foundational tools in phylogenetic inference including Bayesian reasoning, Markov Chain Monte Carlo, and the gamma distribution’s many uses in phylogenetics. Today, we’ll continue with this theme in a crosspost from my UH colleague Floyd Reed‘s laboratory blog. Here, Floyd gives a simple derivation of the Jukes Cantor model of DNA substitution. Here it is in lightly edited form:

In previous posts I talked about irreversible and reversible mutations between two states or alleles.  However, there are four nucleotides, A, C, G, and T.  How can we model mutations among these four states at a single nucleotide site?  It turns out that this is important to consider for things like making gene trees to represent species relationships.  If we just use the raw number of differences between two species’ DNA sequences we can get misleading results.  It is actually better to estimate and correct for the total number of changes that have occurred, some fraction of which may not be visible to us.  The simplest way to do this is the Jukes-Cantor (1969) model.

Imagine a nucleotide can mutate with the same probability to any other nucleotide, so that the mutation rates in all directions are equal and symbolized by \mu.


So from the point of view of the “A” state you can mutate away with a probability of 3\mu (lower left above).  However, another state will only mutate to an “A” with a probability of \mu (lower right above); the “T” could have just as easily mutated to a “G” or “C” instead of an “A”.
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List of a General Advice For Aspiring Phylogeneticists

For the past few years, we’ve maintained a growing list of general advice for folks interested in doing applied phylogenetics. We’ve now transferred this page to the new site. The first piece of advice on this page is to use a simple text editor rather than a complicated word processor when working with input and output files from phylogenetic software; the figures below show how much of a difference this can make.

Fig 1: This is what a text file should look like when opened in a text editor (in this case, the text editor is TextWrangler).

Fig 1: This is what a text file should look like when opened in a text editor (in this case, the text editor is TextWrangler).


Fig. 2: This is what the same text above looks like if we save it as a Microsoft .doc formatted file.

Drop us a line if you can think of other basic advice you’d like to see added to our list!