BEAST 2

[1] Using MCMC, it estimates rooted, timed phylogenies using a range of substitution and clock models, and a variety of tree priors.

BEAUti also allows users to specify the parameters for the MCMC analysis, such as the chain length and the sampling frequency.

This makes it a user-friendly way to run BEAST 2, as it eliminates the need for users to manually edit XML input files.

This makes it easier to add new functionality to the analysis without needing to manually download and install the packages.

[6] LPhy is a probabilistic programming language for defining phylogenetic analyses with a syntax similar to OpenBUGS.