I am using the Bioinformatics Toolbox 2.0 (R14SP1+). The Release Notes for this toolbox mention :
In Bioinformatics Toolbox 2.0 the functions seqlogo, seqshowwords, seqshoworfs, and showalignment use Java based figures. Currently on the Macintosh, Java figures are not enabled by default. If you use these functions on a Macintosh, you should start MATLAB with the -UseJavaFigures flag.
However when I start MATLAB as follows:
matlab -UseJavaFigures
MATLAB seems to ignore the flag.
Best Answer