Will Geneious Prime run multi-threaded? How do I make my analysis run across multiple cores?

Geneious Prime itself is multi-threaded, so if you have access to multiple cores you can run several operations at once.  However, only the following operations within Geneious are able to use multiple cores in a single analysis:  

De novo assemblers
Geneious 
Tadpole 
Velvet
Spades

Map to Reference
Bowtie
Bowtie2 
TopHat
Geneious
BBMAP

Custom Blast (Blast+)

None of the multiple/pairwise aligners or tree building algorithms will run on multiple CPUs.  These operations cannot be made to use multiple CPUs, as the ability to be parallelised has to be designed into the algorithm from the start.  

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