Bayesian Evolutionary Analysis by Sampling Trees
Java Other
Latest commit 7b94c45 Sep 6, 2017 @tgvaughan tgvaughan Fixed hidden input field prob reveaeled by input validation #732.
The "frequencies" input to the BinaryCovarion model is a required
input inhereted from the parent substitution model class.  This
input was apparently being set to "optional" at runtime via the
BinaryCovarion constructor.  However, because another input
"vfrequencies" specific to the BC class was assigned to the field
frequencies, hiding the field of the "frequencies" input, this
adjustment was in fact never made.

This issue didn't show up in unit testing because the unit test
used initByName() to initialize the BC instance, which until #732
did not check whether the input values satisfied the validation rules.

README.md

BEAST 2

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.