In Geneious R8 and later the EMBOSS tools (which were available under the Annotate and Predict menu in previous Geneious versions) are now external plugins and must be installed under the plugins menu. The EMBOSS protein analysis plugin 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 here.