beast-mcmc
beast-mcmc copied to clipboard
beast-dev
Bayesian Evolutionary Analysis Sampling Trees
I'm trying to run beast with the flag mc3_chains but it doesn't produce any results. The screan shown several warnings `WARNING: Likelihood component, null, created but not used in the...
Hello, I'm Trying to run BEAST v1.10.4 but it terminates with an error and I get this error message : "Fatal exception: Cannot invoke "dr.evomodel.tree.TreeModel$Node.getHeight()" because "< local2 >.rightChild" is...
This PR is modified from a [previous PR](https://github.com/beast-dev/beast-mcmc/pull/1129) following @msuchard's suggestion. One of the commits (commit `859f33f`) contained in this pull request has been fully revised to remove the unnecessary...
If one runs [this](https://github.com/beast-dev/beast-mcmc/files/2421933/test_skygrid_stuck.txt) XML with `-seed 1` (or any other seed for that matter) the `logPopSizes` will get stuck pretty much instantly. Have tried with more gridpoints, makes no...
I came across this problem when running the TreeAnnotator. I have changed the -Xmx of TreeAnnotator to 10GB but it did not work. Here are some information that may be...
During development I often jump between branches and jar files. This pull request aims to make that process more robust by automatically storing the last tag (including version), current commit,...
Hi, I am trying to estimate the diverging times of samples from different sources using the WGS SNPs. All the samples are the same species. I am wondering if the...
**Please do not merge yet** ## The idea Place a proper prior on the (constant) population size `Ne` and then integrate it out of the coalescent likelihood. (i) Employing an...
``` Using BEAGLE library v3.1.0 for accelerated, parallel likelihood evaluation 2009-, BEAGLE Working Group - https://beagle-dev.github.io/ Citation: Ayres et al (2012) Systematic Biology 61: 170-173 | doi:10.1093/sysbio/syr100 Random number seed:...
The operator currently keeps a list of NodeRef object to propose moves for a set of taxa. This causes a bug with the store/restore methods of the treeModel. The list...
