Java Other
alexeid Confusing behaviour for MRCAPriors when using tip *dates*, rather tha…
…n tip *ages*. The MRCAPrior is a prior on a *date* not an *age* but everything else in the output is ages leading to a confusing inconsistency for the user. Users frequently set MRCAPrior as an *age* when it is interpreted in the case of a tip *date* analysis as a *date*. This small change is to at least give a hint of this in the name of the statistic in the output. But more thought is needed.
Latest commit f6f325e Jun 21, 2018

README.md

BEAST 2

Build Status

BEAST is a cross-platform program for Bayesian inference using MCMC of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. We include a simple to use user-interface program for setting up standard analyses and a suit of programs for analysing the results.

NOTE: This directory contains the BEAST 2 source code, and is therefore of interest primarily to BEAST 2 developers. For binary releases, user tutorials and other information you should visit the project website at www.beast2.org.

Development Rules and Philosophy

Aspects relating to BEAST 2 development such as coding style, version numbering and design philosophy are discussed on the BEAST 2 web page at http://beast2.org/core-development-rules/.

License

BEAST 2 is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version.

This software is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License contained in the file COPYING for more details.