In Geneious R6.1 and later, Custom BLAST in Geneious can use BLAST+. (This feature is not available in Geneious R6.0 and earlier).
If you initially set up custom BLAST using Geneious R6.1 or later, Geneious will automatically set up and use BLAST+.
If you set up custom BLAST using Geneious 6.0 or earlier, Geneious will use BLAST. If you have upgraded since then to 6.1 or later, you can upgrade Custom Blast to use Blast+ (Geneious will not upgrade to use BLAST+ automatically).
To upgrade to Blast+, follow these instructions:
1. Download the BLAST+ file for your operating system from ftp://ftp.ncbi.nih.gov/blast/executables/blast+/LATEST
2. Check your current Custom BLAST location by going to Tools→Add/Remove Database→Set Up Search Services and selecting Custom BLAST in the drop-down.
3. Unpack the file you downloaded and copy the contents to the same folder as your current Custom BLAST (don't replace it)
4. Go into your current Custom BLAST folder and copy the "data" folder in to the new BLAST+ folder
5. Change the "Database Location" for Custom BLAST in Geneious to the BLAST+ folder.