beast2
beast2 copied to clipboard
CompEvol
Bayesian Evolutionary Analysis by Sampling Trees
When node numbers get out of order (e.g. after resuming an MCMC run), it is possible that the `printTranslate` method misses a comma for the last node number but adds...
The RPNCalculator has an argnames input that is ignored when `RPNCalculator.updateValues` is called, resulting in unexpected values when RPNCalculator is used in a prior.
Allow as optional inputs for TreeLikelihood and GenericTreeLikelihood: * RootDistribution for specifying root frequencies or a root sequence (for usage with rootfreqs package https://github.com/rbouckaert/rootfreqs) * TipDistribution for specifying error models...
This method can show up in the profiler when using large starbeast3 analyses as the most computationally expensive method, so some optimisation would be helpful for these kind of analyses....
Hello, I successfully ran a stochastic model but its deterministic equivalent does not work. The deterministic version throws the error - **validate and intialize error: incrementLineages: conditionOnInclusion is true, but...
This is more a question about existing features than a new feature request; if these features are not already native to BEAST, then I imagine they'll have to be implemented...
https://github.com/CompEvol/beast2/blob/master/release/Linux/jrebin/beast relies on `uname -m` returning "x86_64", and then defines "$LD_LIBRARY_PATH" required to launch BEAST. But in M1 chip, it returns "arm64", so the user has to set "$LD_LIBRARY_PATH" in...
Hi all, I'm using the beast2 package on a windows machine (windows 10), and after testing all beauti versions v.2.7.x, including under compatibility mode, none of them actually saves the...
Having the Java error bellow when trying to Run Beast2 Using Nexus File produced by converting a VCF file to a genlight in R and then converting the genlight to...
