BEAST 2 Help Me Choose

BEAST 2 Help Me Choose GTR rate AC

GTR rate AC

Substitution rate between A and C (default 1) in the GTR (Tavaré, 1986) nucleotide substitution model.


Since the transversion rates (A <=> C, A <=> T, C <=> G and G <=> T) tend to be smaller than transition rates (A <=> G and C <=> T), one expects a value smaller than 1 for rate AC. The default of 1 makes a good starting value if estimated. If not estimated, a value based on prior information can be used, but this would reduce the uncertainty in the analysis.


Rate AC can vary per dataset, so it is usually estimated. Note that at least one of the GTR rates needs to be fixed (i.e. not estimated), because estimating them all leads to unidentifiability due to BEAST normalising rates so that the average rate is 1. Fixing a transition rate (rate AG or rate CT) usually provides more numerical stability than fixing a transversion rate), so setting estimate for rate AC to true is recommended.


Since rate AC is a rate parameter, it should always be positive and have a lower bound of at least 0. This is only relevant if estimate is true and ignored otherwise.


An upper value for the rate AC parameter is usually not set, though rate AC is usually in the range of 0 to 1. This is only relevant if estimate is true and ignored otherwise.


Tavaré S. Some probabilistic and statistical problems in the analysis of DNA sequences. Lectures on mathematics in the life sciences. 1986 Dec 31;17(2):57-86.

See also substitution models.

Bayesian evolutionary analysis by sampling trees

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