BEAUti

BEAUti now allows imports of calibrations from NEXUS files, so you can specify tip dates, distributions on tip dates, monophyletic constraints and clade calibrations in a NEXUS file. This is especially handy when there are a large number of calibrations or when a large number of clades need to be defined.

BEAUti now has a “File/Launch Apps” menu to start applications provided by packages, such as the GUI for doing a Path Sampling analysis (as the AppStore does).

In Windows and Linux, the *BEAST template went missing at the second time BEAUti was started due to a bug in the way packages are handled. This is fixed now.

Streamlined upgrades of BEAST so when you can upgrade BEAST as simple as upgrading any package. When upgrading BEAST, BEAUti exits and when restarting it downloads the latest version — which may take a little time.

BEAST

On OSX, a common problem was that a CUDA driver was installed to support BEAGLE, but that there is no hardware that is CUDA enabled. The result was a crash of BEAST without an error message, which made it hard to find out what went wrong. In this version a test is done for this condition, and if it exists, instructions are provided on how to uninstall CUDA drivers, which should fix the problem.

The CLI script for BEAST should have less trouble loading the BEAGLE library in Linux and OSX.

Two operators have improved operator tuning resulting in slightly better performance (higher ESSs) in most cases.

There are some improvements in reporting error conditions, which should help diagnose problems.

LogAnalyser

A bug crept into v2.4.0 causing LogAnalyser not to show progress on loading and processing the log file when started from CLI, which is fixed now.