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

Geneious itself is multi-threaded, so if you have access to multiple cores you can run several operations at once.  However most individual analyses within Geneious, such as alignment and tree-building functions, are not multi-threaded so will only use a single core.  There is no way to make these analyses run on multiple cores, as the ability to be parallelised has to be designed into the algorithm from the start.  The Geneious Assembler runs across multiple cores for part of its operation, but then draws the threads back to complete the analysis on a single core.

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