BEAUti has a menu — View/Zoom In and View/Zoom out — which causes everything to scale up or down respectively. Once a particular zoom level is set in BEAUti, all other applications with a graphical user interface, like BEAST, TreeAnnotator, LogCombiner, etc. scale up to the same level. Also, by default scaling is such that they should look acceptable on high resolution screens.

Both BEAUti and BEAST have some improved error reporting.

One annoying bug was that BEAST closed its console window on XML parsing errors, making it impossible to read what was wrong with the XML file. This bug is solved now.

LogCombiner used to read in all log and tree files before writing them to the combined files. The new implementation processes input files line by line and directly write them to the combined log, so it requires much less memory than before.

Densitree updated to version 2.2.5, which supports export of DensiTree in SVG vector format.