Geneious Prime is able to find differentially expressed genes between two or more sample conditions. This can be done through one of two methods: the built-in Geneious method, or the DESeq2 method. The Geneious method should be used when there are two samples only. For more than two samples, the DESeq2 method should be used and requires at least two replicates per condition.
To compare expression levels, you must first assemble the reads for each sample, to the same reference sequence(s), then run Calculate Expression Levels from the Annotate & Predict menu on each contig assembly. This will save an Expression Level track for each contig on the reference sequence(s). To compare these tracks, select the reference sequence document(s) and go to Annotate & Predict → Compare Expression Levels.
If your samples map to multiple reference sequences, you should run both Calculate Expression Levels and Compare Expression Levels on all contigs from a single sample at once to produce correct results in all cases. However, when using the Geneious method, Compare Expression Levels can optionally be run on just one reference sequence at a time when using a normalization system other than Median of Gene Expression Ratios.