Description
With a batch of virus or species sequences you want to know when the lineages split and how fast they spread, but ordinary tree building software hands you a single tree with no timing or uncertainty. BEAST X does Bayesian evolutionary analysis, using MCMC sampling to estimate the phylogenetic tree, divergence times and evolutionary rates together, each with a credible interval.
The latest 10.5.0 zip is about 89 MB, so the link goes to the project's Releases page and nothing is mirrored here. It is Java based and cross platform, and the bundled BEAUti is the companion GUI for importing sequences, choosing models and setting parameters, producing the analysis file BEAST runs without hand written XML.
Bayesian evolutionary analysis: MCMC sampling estimates the tree, divergence times and rates with credible intervals
BEAUti GUI: import sequences, pick the substitution model and clock, set priors, and generate the analysis file in a few clicks with no XML editing
Molecular clock models: assume one rate for all branches or let it vary between branches to fit real data better
Cross platform: runs on Windows, macOS and Linux through Java, and big analyses can move to a server
Open source and free: the code and release packages are public on GitHub
The latest 10.5.0 zip is about 89 MB, so the link goes to the project's Releases page and nothing is mirrored here. It is Java based and cross platform, and the bundled BEAUti is the companion GUI for importing sequences, choosing models and setting parameters, producing the analysis file BEAST runs without hand written XML.
Features
Bayesian evolutionary analysis: MCMC sampling estimates the tree, divergence times and rates with credible intervals
BEAUti GUI: import sequences, pick the substitution model and clock, set priors, and generate the analysis file in a few clicks with no XML editing
Molecular clock models: assume one rate for all branches or let it vary between branches to fit real data better
Cross platform: runs on Windows, macOS and Linux through Java, and big analyses can move to a server
Open source and free: the code and release packages are public on GitHub
