The EMBOSS tools which were available under the Annotate and Predict menu in previous Geneious versions are now available as separate plugins. EMBOSS protein analysis includes antigenic to predict antigenic regions, sigcleave to predict signal cleavage sites, and garnier to predict secondary structures. The EMBOSS Nucleotide Analysis plugin includes tfscan to search for transcription factors, and tcode which provides a protein coding prediction graph.
When these plugins are installed, the protein coding prediction graph will be available under the Graphs tab, and the other options will show up under the Annotate and Predict menu. Further information on these applications is available at http://emboss.open-bio.org/