1. Save your work and shut down Jalview
2. Open a Terminal window (use spotlight or the Launcher and type 'Terminal' to locate the Terminal App), and type:
defaults write -g CGFontRenderingFontSmoothingDisabled -bool NO
3. Start Jalview again and load an alignment to check that the fonts are now legible.
Thanks to Marcin for reporting this issue and testing the workaround via issues.jalview.org/browse/JAL-3134