BEAST 2 Help Me Choose

# BEAST 2 Help Me Choose Kernel distribution

## Kernel distributions

Bactrian operators sample from a kernel distribution from which a proposal is created. The following kernel distributions are currently implemented, many of them propossed in Yang & Rodríguez (2013) and Thawornwattana et al (2018).

Name Distribution Bactrian?
uniform uniform distribution no
normal normal distribution no
laplace Laplace distribution no
t4 T-distribution with 4 degrees of freedom no
cauchy Cauchy distribution no
bactrian_normal normal distribution yes
bactrian_laplace Laplace distribution yes
bactrian_triangle triangle shaped distribution yes
bactrian_uniform uniform distribution yes
bactrian_t4 T-distribution with 4 degrees of freedom yes
bactrian_cauchy Cauchy distribution yes
bactrian_box box-shaped distribution yes
bactrian_airplane airplane distribution yes
bactrian_strawhat strawhat distribution yes

The default kernel distribution is the Bactrian normal distribution. This seems to perform well for a wide range of cases (see also BEAST 2 benchmark). So, there does not seem a compelling reason to switch – let me know if you know any.

## References

Yang Z, Rodríguez CE. Searching for efficient Markov chain Monte Carlo proposal kernels. Proceedings of the National Academy of Sciences. 2013 Nov 26;110(48):19307-12. doi: 10.1073/pnas.1311790110).

Thawornwattana Y, Dalquen D, Yang Z. Designing simple and efficient Markov chain Monte Carlo proposal kernels. Bayesian Analysis. 2018;13(4):1037-63. doi: 10.1214/17-BA1084,

## Bayesian evolutionary analysis by sampling trees

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