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 assembly
Geneious 
Tadpole 
Velvet
Spades

Map to Reference
Geneious
Bowtie
Bowtie2 
TopHat
BBMAP
Minimap2 (Geneious Prime 2020 onwards)

Multiple alignment
MAFFT
Clustal Omega (Geneious Prime 2020 onwards)

Custom Blast (Blast+)

None of the 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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