BEAST 2 uses Markov chain Monte Carlo (MCMC) to average over tree space, so that each tree is weighted proportional to its posterior probability. BEAST 2 includes a graphical user-interface for …

MCMC chain. This is the main element that controls which posterior to calculate, how long to run the chain and all other properties, which operators to apply on the state space and where to log results. …

BEASTObject that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain.

Entry point for running a Beast task, for instance an MCMC or other probabilistic analysis, a simulation, etc.

Entry point for running a Beast task, for instance an MCMC or other probabilistic analysis, a simulation, etc.

Coupled MCMC. Two independent MCMC chains which will only stop after their clade posteriors have convergedNote that log file names should have $ (seed) in their name so that the first chain uses the …

Entry point for running a Beast task, for instance an MCMC or other probabilistic analysis, a simulation, etc.

Proposes a move in state space. A Metropolis-Hastings operator to update the log population sizes and precision parameter jointly under a Gaussian Markov random field prior

BEASTObject that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain.

BEASTObject that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. Distribution on a tree, typically a …